Tue Oct 8 12:29:19 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/recon-all -3T -parallel -s PIB23-310_VYr0_Bay3prisma -i /data/jsp/human2/SortedMRI/PIB/PIB23-310_VYr0_Bay3prisma/study7/PIB23-310.MR.HEAD_PERLMUTTER.0007.0100.2024.01.11.10.35.56.39318.14517493.IMA -all subjid PIB23-310_VYr0_Bay3prisma setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Actual FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 build-stamp.txt: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 1029556 maxlocks unlimited maxsignal 1029556 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 251Gi 186Gi 14Gi 23Mi 50Gi 63Gi Swap: 111Gi 138Mi 111Gi ######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275) 7.3.2 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:19-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:19-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:19-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:20-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:21-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:22-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:22-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:22-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:22-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:22-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:22-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/08-17:29:22-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma mri_convert /data/jsp/human2/SortedMRI/PIB/PIB23-310_VYr0_Bay3prisma/study7/PIB23-310.MR.HEAD_PERLMUTTER.0007.0100.2024.01.11.10.35.56.39318.14517493.IMA /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig/001.mgz mri_convert /data/jsp/human2/SortedMRI/PIB/PIB23-310_VYr0_Bay3prisma/study7/PIB23-310.MR.HEAD_PERLMUTTER.0007.0100.2024.01.11.10.35.56.39318.14517493.IMA /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig/001.mgz reading from /data/jsp/human2/SortedMRI/PIB/PIB23-310_VYr0_Bay3prisma/study7/PIB23-310.MR.HEAD_PERLMUTTER.0007.0100.2024.01.11.10.35.56.39318.14517493.IMA... Starting siemensRead() INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Starting sdcmLoadVolume() Getting Series No INFO: Found 210 files in /data/jsp/human2/SortedMRI/PIB/PIB23-310_VYr0_Bay3prisma/study7 INFO: Scanning for Series Number 7 Scanning Directory INFO: found 208 files in series INFO: loading series header info. RunNo = 6 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 INFO: (256 256 208), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 INFO: rescale not needed datatype = 4, short=4, float=3 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /data/jsp/human2/SortedMRI/PIB/PIB23-310_VYr0_Bay3prisma/study7/PIB23-310.MR.HEAD_PERLMUTTER.0007.0001.2024.01.11.10.35.56.39318.14515700.IMA Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName PIB23-310 Date and time StudyDate 20240111 StudyTime 090647.059000 SeriesTime 091730.974000 AcqTime 090921.977500 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol t1_mpr_0p9mm PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.18 InversionTime 1000 RepetitionTime 2400 PhEncFOV 230 ReadoutFOV 230 Image information RunNo 6 SeriesNo 7 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 83.7375 126.3569 121.6507 VolRes 0.8984 0.8984 0.9000 VolDim 256 256 208 Vc 0.0631 -0.9920 -0.1090 Vr -0.0037 0.1090 -0.9940 Vs -0.9980 -0.0631 -0.0032 VolCenter -2.8405 18.9017 -5.5050 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=2400.00, TE=3.18, TI=1000.00, flip angle=8.00 i_ras = (0.0631113, -0.992032, -0.10904) j_ras = (-0.00367852, 0.109026, -0.994032) k_ras = (-0.998, -0.0631358, -0.00323154) writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig/001.mgz... @#@FSTIME 2024:10:08:12:29:22 mri_convert N 2 e 17.95 S 4.71 U 9.01 P 76% M 36020 F 0 R 58038 W 0 c 1715 w 14815 I 98176 O 25912 L 55.17 35.50 25.02 @#@FSLOADPOST 2024:10:08:12:29:40 mri_convert N 2 55.23 36.55 25.54 #-------------------------------------------- #@# MotionCor Tue Oct 8 12:29:41 CDT 2024 Found 1 runs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig/001.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz mri_info /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz type: MGH dimensions: 256 x 256 x 208 voxel sizes: 0.898438, 0.898438, 0.900000 type: SHORT (4) fov: 230.000 dof: 1 xstart: -115.0, xend: 115.0 ystart: -115.0, yend: 115.0 zstart: -93.6, zend: 93.6 TR: 2400.00 msec, TE: 3.18 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.0631, y_r = -0.0037, z_r = -0.9980, c_r = -2.8405 : x_a = -0.9920, y_a = 0.1090, z_a = -0.0631, c_a = 18.9017 : x_s = -0.1090, y_s = -0.9940, z_s = -0.0032, c_s = -5.5050 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.0567 -0.0033 -0.8982 83.7375 -0.8913 0.0980 -0.0568 126.3569 -0.0980 -0.8931 -0.0029 121.6507 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.726471 ras to voxel transform: 0.0702 -1.1042 -0.1214 148.4022 -0.0041 0.1214 -1.1064 119.6039 -1.1089 -0.0702 -0.0036 102.1564 -0.0000 -0.0000 -0.0000 1.0000 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma mri_convert /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz --conform mri_convert /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz --conform reading from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz... TR=2400.00, TE=3.18, TI=1000.00, flip angle=8.00 i_ras = (0.0631113, -0.992032, -0.10904) j_ras = (-0.00367852, 0.109026, -0.994032) k_ras = (-0.998, -0.0631358, -0.00323154) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 815 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz... @#@FSTIME 2024:10:08:12:29:45 mri_convert N 3 e 8.69 S 0.10 U 8.72 P 101% M 47632 F 1 R 45650 W 0 c 884 w 178 I 0 O 11896 L 59.21 37.68 25.97 @#@FSLOADPOST 2024:10:08:12:29:53 mri_convert N 3 63.09 39.17 26.57 mri_add_xform_to_header -c /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/talairach.xfm /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2024:10:08:12:29:53 mri_add_xform_to_header N 4 e 1.25 S 0.02 U 1.88 P 152% M 23372 F 0 R 4580 W 0 c 178 w 199 I 0 O 11904 L 63.09 39.17 26.57 @#@FSLOADPOST 2024:10:08:12:29:55 mri_add_xform_to_header N 4 63.09 39.17 26.57 mri_info /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz orig.mgz ======================================== Volume information for /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2400.00 msec, TE: 3.18 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -2.8405 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 18.9017 : x_s = -0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -5.5050 talairach xfm : /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 -0.0000 -0.0000 125.1595 0.0000 0.0000 1.0000 -109.0983 -0.0000 -1.0000 0.0000 122.4950 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 0.0000 125.1595 0.0000 0.0000 -1.0000 122.4950 -0.0000 1.0000 0.0000 109.0983 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Tue Oct 8 12:29:55 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Tue Oct 8 12:29:55 CDT 2024 tmpdir is ./tmp.mri_nu_correct.mni.2123196 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2123196/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.2123196/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2123196/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2123196/nu0.mgz... TR=2400.00, TE=3.18, TI=1000.00, flip angle=8.00 i_ras = (-1, 0, -2.32831e-10) j_ras = (-2.32831e-10, 8.33825e-09, -1) k_ras = (-7.45058e-09, 1, 6.51926e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Tue Oct 8 12:33:54 CDT 2024 mri_nu_correct.mni done @#@FSTIME 2024:10:08:12:29:55 mri_nu_correct.mni N 12 e 238.96 S 0.56 U 232.58 P 97% M 507096 F 1 R 189440 W 0 c 22730 w 619 I 0 O 22392 L 63.09 39.17 26.57 @#@FSLOADPOST 2024:10:08:12:33:54 mri_nu_correct.mni N 12 49.02 43.80 31.28 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... mv -f /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt Started at Tue Oct 8 12:33:54 CDT 2024 Ended at Tue Oct 8 12:34:24 CDT 2024 talairach_avi done @#@FSTIME 2024:10:08:12:33:54 talairach_avi N 6 e 29.85 S 1.72 U 19.92 P 72% M 255680 F 0 R 419327 W 0 c 2296 w 5734 I 0 O 296032 L 49.02 43.80 31.28 @#@FSLOADPOST 2024:10:08:12:34:24 talairach_avi N 6 56.27 46.10 32.45 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.3.2 --src: orig.mgz src image (geometry). --trg: /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.07321 0.04987 0.00651 1.17262; -0.06555 0.97719 0.30468 -32.46613; -0.01185 -0.23500 1.08964 20.33221; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Tue Oct 8 12:34:26 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7286, pval=0.6675 >= threshold=0.0050) @#@FSTIME 2024:10:08:12:34:26 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 75% M 5920 F 0 R 227 W 0 c 0 w 9 I 0 O 0 L 56.27 46.10 32.45 @#@FSLOADPOST 2024:10:08:12:34:26 talairach_afd N 4 56.27 46.10 32.45 awk -f /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/extract_talairach_avi_QA.awk /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/talairach_avi.log tal_QC_AZS /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/talairach_avi.log TalAviQA: 0.94686 z-score: -7 #-------------------------------------------- #@# Nu Intensity Correction Tue Oct 8 12:34:26 CDT 2024 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 --ants-n4 /usr/bin/bc /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 --ants-n4 nIters 1 mri_nu_correct.mni 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Tue Oct 8 12:34:26 CDT 2024 tmpdir is ./tmp.mri_nu_correct.mni.2188933 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2188933/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.2188933/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2188933/ones.mgz 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.2188933/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2188933/ones.mgz sysname Linux hostname chopin machine x86_64 user grossens input ./tmp.mri_nu_correct.mni.2188933/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2188933/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.2188933/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2188933/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2188933/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2188933/input.mean.dat 7.3.2 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2188933/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2188933/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2188933/input.mean.dat sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2188933/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.2188933/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2188933/ones.mgz --i ./tmp.mri_nu_correct.mni.2188933/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2188933/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2188933/output.mean.dat 7.3.2 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2188933/ones.mgz --i ./tmp.mri_nu_correct.mni.2188933/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2188933/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2188933/output.mean.dat sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2188933/ones.mgz Loading ./tmp.mri_nu_correct.mni.2188933/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.2188933/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2188933/nu0.mgz ./tmp.mri_nu_correct.mni.2188933/nu0.mgz mul 1.20178096156627096382 Saving result to './tmp.mri_nu_correct.mni.2188933/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2188933/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.2188933/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.2188933/nu0.mgz... TR=2400.00, TE=3.18, TI=1000.00, flip angle=8.00 i_ras = (-1, 0, -2.32831e-10) j_ras = (-2.32831e-10, 8.33825e-09, -1) k_ras = (-7.45058e-09, 1, 6.51926e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 4, i2 = 50 #mri_make_uchar# mapping 10 125 to 3 110 : b -6.79348 m 0.932464 : thresh 7.28551 maxsat 280.754 : nzero 12806556 nsat 0 Tue Oct 8 12:39:02 CDT 2024 mri_nu_correct.mni done @#@FSTIME 2024:10:08:12:34:26 mri_nu_correct.mni N 13 e 275.49 S 1.98 U 274.02 P 100% M 614052 F 2 R 862915 W 0 c 27216 w 2025 I 17136 O 63624 L 56.27 46.10 32.45 @#@FSLOADPOST 2024:10:08:12:39:02 mri_nu_correct.mni N 13 61.23 57.85 41.05 mri_add_xform_to_header -c /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2024:10:08:12:39:02 mri_add_xform_to_header N 4 e 0.77 S 0.00 U 1.39 P 180% M 23396 F 0 R 4580 W 0 c 173 w 114 I 0 O 7200 L 61.23 57.85 41.05 @#@FSLOADPOST 2024:10:08:12:39:03 mri_add_xform_to_header N 4 61.23 57.85 41.05 #-------------------------------------------- #@# Intensity Normalization Tue Oct 8 12:39:03 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.07321 0.04987 0.00651 1.17262; -0.06555 0.97719 0.30468 -32.46613; -0.01185 -0.23500 1.08964 20.33221; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 62 (62), valley at 13 (13) csf peak at 13, setting threshold to 45 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 66 (66) csf peak at 26, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 16 seconds. @#@FSTIME 2024:10:08:12:39:03 mri_normalize N 7 e 137.11 S 1.06 U 147.08 P 108% M 583892 F 1 R 633625 W 0 c 14351 w 222 I 0 O 7088 L 61.23 57.85 41.05 @#@FSLOADPOST 2024:10:08:12:41:20 mri_normalize N 7 56.11 57.55 43.24 #-------------------------------------------- #@# Skull Stripping Tue Oct 8 12:41:20 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_em_register -skull nu.mgz /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 48, 30) --> (205, 245, 233) finding center of left hemi white matter using (99, 114, 132) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (79,90,107) --> (118, 138,157) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 8.5 after smoothing, mri peak at 104, scaling input intensities by 1.038 scaling channel 0 by 1.03846 initial log_p = -4.699 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.639106 @ (10.526, -10.526, -10.526) max log p = -4.493193 @ (-15.789, -5.263, -5.263) max log p = -4.451532 @ (2.632, 7.895, -2.632) max log p = -4.409405 @ (3.947, -1.316, -1.316) max log p = -4.409405 @ (0.000, 0.000, 0.000) max log p = -4.398708 @ (-1.645, -0.987, 0.329) max log p = -4.398708 @ (0.000, 0.000, 0.000) max log p = -4.398708 @ (0.000, 0.000, 0.000) Found translation: (-0.3, -10.2, -19.4): log p = -4.399 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.316, old_max_log_p =-4.399 (thresh=-4.4) 1.07500 0.00000 0.00000 -9.73631; 0.00000 1.22567 0.14032 -55.39094; 0.00000 -0.15011 0.99144 4.57133; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 45 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.316, old_max_log_p =-4.316 (thresh=-4.3) 1.07500 0.00000 0.00000 -9.73631; 0.00000 1.22567 0.14032 -55.39094; 0.00000 -0.15011 0.99144 4.57133; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 43 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.223, old_max_log_p =-4.316 (thresh=-4.3) 1.02914 -0.01926 -0.09947 11.73099; 0.03139 1.22011 0.16958 -62.30980; 0.10596 -0.19261 1.00009 -5.49801; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 37 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.220, old_max_log_p =-4.223 (thresh=-4.2) 1.03253 0.01438 -0.06111 1.34878; -0.00235 1.19742 0.16846 -56.48405; 0.07224 -0.19187 1.00281 0.14887; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 26 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.204, old_max_log_p =-4.220 (thresh=-4.2) 1.03120 0.00772 -0.07885 4.33759; 0.00608 1.19612 0.16762 -57.24102; 0.08905 -0.19139 1.00049 -1.73307; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 22 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.202, old_max_log_p =-4.204 (thresh=-4.2) 1.03310 0.00608 -0.07076 3.75752; 0.00680 1.19311 0.17559 -57.45457; 0.08047 -0.20099 0.99853 0.55381; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03310 0.00608 -0.07076 3.75752; 0.00680 1.19311 0.17559 -57.45457; 0.08047 -0.20099 0.99853 0.55381; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.03310 0.00608 -0.07076 3.75752; 0.00680 1.19311 0.17559 -57.45457; 0.08047 -0.20099 0.99853 0.55381; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03310 0.00608 -0.07076 3.75752; 0.00680 1.19311 0.17559 -57.45457; 0.08047 -0.20099 0.99853 0.55381; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.202 (old=-4.699) transform before final EM align: 1.03310 0.00608 -0.07076 3.75752; 0.00680 1.19311 0.17559 -57.45457; 0.08047 -0.20099 0.99853 0.55381; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03310 0.00608 -0.07076 3.75752; 0.00680 1.19311 0.17559 -57.45457; 0.08047 -0.20099 0.99853 0.55381; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.03310 0.00608 -0.07076 3.75752; 0.00680 1.19311 0.17559 -57.45457; 0.08047 -0.20099 0.99853 0.55381; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.5 tol 0.000000 final transform: 1.03310 0.00608 -0.07076 3.75752; 0.00680 1.19311 0.17559 -57.45457; 0.08047 -0.20099 0.99853 0.55381; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 811008 FSRUNTIME@ mri_em_register 0.0720 hours 4 threads registration took 4 minutes and 19 seconds. @#@FSTIME 2024:10:08:12:41:20 mri_em_register N 4 e 259.23 S 2.41 U 840.27 P 325% M 629292 F 1 R 1806490 W 0 c 82302 w 2929 I 0 O 24 L 56.11 57.55 43.24 @#@FSLOADPOST 2024:10:08:12:45:39 mri_em_register N 4 35.86 53.62 45.81 mri_watershed -T1 -brain_atlas /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=125 y=131 z=127 r=79 first estimation of the main basin volume: 2116206 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=160, y=115, z=112, Imax=255 CSF=16, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=1701117792486273 voxels, voxel volume =1.000 = 1701117792486273 mmm3 = 1701117763256.320 cm3 done. PostAnalyze...Basin Prior 25 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=131, z=121, r=10265 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=46 , nb = 44928 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = 3294 LEFT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=40 , nb = 3186 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=15, CSF_MAX=45 , nb = 18666 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=44 , nb = 18774 OTHER CSF_MIN=12, CSF_intensity=22, CSF_MAX=35 , nb = 1008 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 46, 48, 50, 80 after analyzing : 46, 49, 50, 56 RIGHT_CER before analyzing : 36, 36, 37, 80 after analyzing : 27, 36, 37, 47 LEFT_CER before analyzing : 40, 45, 50, 81 after analyzing : 40, 48, 50, 56 RIGHT_BRAIN before analyzing : 45, 47, 50, 80 after analyzing : 45, 49, 50, 56 LEFT_BRAIN before analyzing : 44, 47, 51, 78 after analyzing : 44, 49, 51, 56 OTHER before analyzing : 35, 50, 72, 91 after analyzing : 35, 64, 72, 70 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...71 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 67.730, std = 7.983 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.77, sigma = 4.69 after rotation: sse = 2.77, sigma = 4.69 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.01, its var is 4.41 before Erosion-Dilatation 0.82% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...47 iterations mri_strip_skull: done peeling brain Brain Size = 1612375 voxels, voxel volume = 1.000 mm3 = 1612375 mmm3 = 1612.375 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed done @#@FSTIME 2024:10:08:12:45:39 mri_watershed N 6 e 19.25 S 0.65 U 25.55 P 136% M 810176 F 0 R 452058 W 0 c 2323 w 915 I 0 O 2728 L 35.86 53.62 45.81 @#@FSLOADPOST 2024:10:08:12:45:59 mri_watershed N 6 33.07 51.85 45.40 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Oct 8 12:46:00 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (56, 76, 43) --> (193, 210, 212) finding center of left hemi white matter using (102, 121, 128) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (85,105,107) --> (118, 137,148) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 6.0 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.360 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.236873 @ (-10.526, -10.526, -10.526) max log p = -4.133078 @ (15.789, -5.263, -5.263) max log p = -4.014200 @ (-7.895, 7.895, -2.632) max log p = -3.930688 @ (3.947, -3.947, -1.316) max log p = -3.920048 @ (-0.658, 0.658, -0.658) max log p = -3.920048 @ (0.000, 0.000, 0.000) max log p = -3.920048 @ (0.000, 0.000, 0.000) max log p = -3.920048 @ (0.000, 0.000, 0.000) Found translation: (0.7, -11.2, -20.4): log p = -3.920 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.908, old_max_log_p =-3.920 (thresh=-3.9) 1.07500 0.00000 0.00000 -8.80294; 0.00000 1.03837 0.27823 -51.19630; 0.00000 -0.25882 0.96593 25.16160; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 25 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.908, old_max_log_p =-3.908 (thresh=-3.9) 1.07500 0.00000 0.00000 -8.80294; 0.00000 1.03837 0.27823 -51.19630; 0.00000 -0.25882 0.96593 25.16160; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.841, old_max_log_p =-3.908 (thresh=-3.9) 1.01545 -0.00274 0.00186 -3.26387; 0.00226 1.06541 0.24968 -53.67073; 0.00254 -0.22166 0.95584 19.32011; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 24 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.841, old_max_log_p =-3.841 (thresh=-3.8) 1.01545 -0.00274 0.00186 -3.26387; 0.00226 1.06541 0.24968 -53.67073; 0.00254 -0.22166 0.95584 19.32011; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.805, old_max_log_p =-3.841 (thresh=-3.8) 1.01297 0.01471 0.00567 -4.80409; -0.01434 1.06405 0.24936 -50.84034; 0.00282 -0.22187 0.95697 19.62993; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 23 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.803, old_max_log_p =-3.805 (thresh=-3.8) 1.01307 -0.00276 0.00185 -2.49488; 0.00220 1.06888 0.23404 -52.21682; 0.00258 -0.20391 0.95868 17.05883; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01307 -0.00276 0.00185 -2.49488; 0.00220 1.06888 0.23404 -52.21682; 0.00258 -0.20391 0.95868 17.05883; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.01307 -0.00276 0.00185 -2.49488; 0.00220 1.06888 0.23404 -52.21682; 0.00258 -0.20391 0.95868 17.05883; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01307 -0.00276 0.00185 -2.49488; 0.00220 1.06888 0.23404 -52.21682; 0.00258 -0.20391 0.95868 17.05883; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.803 (old=-4.360) transform before final EM align: 1.01307 -0.00276 0.00185 -2.49488; 0.00220 1.06888 0.23404 -52.21682; 0.00258 -0.20391 0.95868 17.05883; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01307 -0.00276 0.00185 -2.49488; 0.00220 1.06888 0.23404 -52.21682; 0.00258 -0.20391 0.95868 17.05883; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.01307 -0.00276 0.00185 -2.49488; 0.00220 1.06888 0.23404 -52.21682; 0.00258 -0.20391 0.95868 17.05883; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 4.2 after pass:transform: ( 1.01, -0.00, 0.00, -2.49) ( 0.00, 1.07, 0.23, -52.22) ( 0.00, -0.20, 0.96, 17.06) dfp_em_step_func: 010: -log(p) = 4.2 after pass:transform: ( 1.01, -0.00, 0.00, -2.49) ( 0.00, 1.07, 0.23, -52.22) ( 0.00, -0.20, 0.96, 17.06) dfp_em_step_func: 011: -log(p) = 4.2 after pass:transform: ( 1.01, -0.00, 0.00, -2.49) ( 0.00, 1.07, 0.23, -52.22) ( 0.00, -0.20, 0.96, 17.06) dfp_em_step_func: 012: -log(p) = 4.2 after pass:transform: ( 1.01, -0.00, 0.00, -2.49) ( 0.00, 1.07, 0.23, -52.22) ( 0.00, -0.20, 0.96, 17.06) dfp_em_step_func: 013: -log(p) = 4.2 after pass:transform: ( 1.01, -0.00, 0.00, -2.49) ( 0.00, 1.07, 0.23, -52.22) ( 0.00, -0.20, 0.96, 17.06) dfp_em_step_func: 014: -log(p) = 4.2 after pass:transform: ( 1.01, -0.00, 0.00, -2.49) ( 0.00, 1.07, 0.23, -52.22) ( 0.00, -0.20, 0.96, 17.06) dfp_em_step_func: 015: -log(p) = 4.2 after pass:transform: ( 1.01, -0.00, 0.00, -2.49) ( 0.00, 1.07, 0.23, -52.22) ( 0.00, -0.20, 0.96, 17.06) dfp_em_step_func: 016: -log(p) = 4.2 after pass:transform: ( 1.01, -0.00, 0.00, -2.49) ( 0.00, 1.07, 0.23, -52.22) ( 0.00, -0.20, 0.96, 17.06) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 018: -log(p) = 4.2 tol 0.000000 final transform: 1.01356 -0.00221 0.00230 -2.49488; 0.00289 1.06970 0.23475 -52.21682; 0.00263 -0.20392 0.95871 17.05883; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 798460 FSRUNTIME@ mri_em_register 0.0660 hours 4 threads registration took 3 minutes and 58 seconds. @#@FSTIME 2024:10:08:12:46:00 mri_em_register N 7 e 237.55 S 1.43 U 711.34 P 300% M 616448 F 0 R 1060860 W 0 c 65462 w 420 I 0 O 72 L 33.07 51.85 45.40 @#@FSLOADPOST 2024:10:08:12:49:57 mri_em_register N 7 43.90 46.02 44.35 #-------------------------------------- #@# CA Normalize Tue Oct 8 12:49:57 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (56, 76, 43) --> (193, 210, 212) finding center of left hemi white matter using (102, 121, 128) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (85,105,107) --> (118, 137,148) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 6.0 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 246437 sample points... INFO: compute sample coordinates transform 1.01356 -0.00221 0.00230 -2.49488; 0.00289 1.06970 0.23475 -52.21682; 0.00263 -0.20392 0.95871 17.05883; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 72, 42) --> (192, 179, 211) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 0 of 186 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (64, 73, 41) --> (129, 177, 211) Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0 2 of 245 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (129, 153, 71) --> (176, 196, 126) Left_Cerebellum_White_Matter: limiting intensities to 107.0 --> 132.0 0 of 18 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (84, 153, 68) --> (127, 195, 127) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 144, 108) --> (145, 208, 137) Brain_Stem: limiting intensities to 102.0 --> 132.0 9 of 58 (15.5%) samples deleted using 519 total control points for intensity normalization... bias field = 0.897 +- 0.069 0 of 508 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 72, 42) --> (192, 179, 211) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 1 of 308 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (64, 73, 41) --> (129, 177, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 453 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (129, 153, 71) --> (176, 196, 126) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 70 (5.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (84, 153, 68) --> (127, 195, 127) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 66 (13.6%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 144, 108) --> (145, 208, 137) Brain_Stem: limiting intensities to 88.0 --> 132.0 45 of 151 (29.8%) samples deleted using 1048 total control points for intensity normalization... bias field = 1.004 +- 0.063 0 of 986 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 72, 42) --> (192, 179, 211) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 379 (3.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (64, 73, 41) --> (129, 177, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 506 (3.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (129, 153, 71) --> (176, 196, 126) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 56 of 155 (36.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (84, 153, 68) --> (127, 195, 127) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 46 of 94 (48.9%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 144, 108) --> (145, 208, 137) Brain_Stem: limiting intensities to 88.0 --> 132.0 186 of 236 (78.8%) samples deleted using 1370 total control points for intensity normalization... bias field = 1.005 +- 0.048 2 of 1025 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 14 seconds. @#@FSTIME 2024:10:08:12:49:58 mri_ca_normalize N 8 e 73.80 S 1.42 U 76.27 P 105% M 681664 F 0 R 835671 W 0 c 7278 w 317 I 0 O 3616 L 43.90 46.02 44.35 @#@FSLOADPOST 2024:10:08:12:51:11 mri_ca_normalize N 8 41.23 44.50 43.92 #-------------------------------------- #@# CA Reg Tue Oct 8 12:51:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 1.04754 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.945308) vs oldopt=(dt=369.92,rms=0.971649) #GCMRL# 0 dt 221.952000 rms 0.945 9.759% neg 0 invalid 762 tFOTS 16.0060 tGradient 8.6390 tsec 25.9310 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.895355) vs oldopt=(dt=369.92,rms=0.896844) #GCMRL# 1 dt 443.904000 rms 0.895 5.284% neg 0 invalid 762 tFOTS 18.3330 tGradient 10.3590 tsec 30.1900 #FOTS# QuadFit found better minimum quadopt=(dt=239.158,rms=0.878682) vs oldopt=(dt=369.92,rms=0.882754) #GCMRL# 2 dt 239.157895 rms 0.879 1.862% neg 0 invalid 762 tFOTS 16.5420 tGradient 8.1300 tsec 25.9830 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.864126) vs oldopt=(dt=369.92,rms=0.864432) #GCMRL# 3 dt 443.904000 rms 0.864 1.657% neg 0 invalid 762 tFOTS 16.2490 tGradient 8.1690 tsec 25.9040 #FOTS# QuadFit found better minimum quadopt=(dt=150.805,rms=0.855991) vs oldopt=(dt=92.48,rms=0.857552) #GCMRL# 4 dt 150.804598 rms 0.856 0.941% neg 0 invalid 762 tFOTS 17.2770 tGradient 8.2910 tsec 26.7700 #GCMRL# 5 dt 1479.680000 rms 0.839 2.001% neg 0 invalid 762 tFOTS 15.0270 tGradient 7.5690 tsec 23.8680 #FOTS# QuadFit found better minimum quadopt=(dt=145.291,rms=0.827046) vs oldopt=(dt=92.48,rms=0.828875) #GCMRL# 6 dt 145.291228 rms 0.827 1.408% neg 0 invalid 762 tFOTS 15.5770 tGradient 6.9700 tsec 23.7390 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.826457) vs oldopt=(dt=92.48,rms=0.826568) #GCMRL# 7 dt 129.472000 rms 0.826 0.000% neg 0 invalid 762 tFOTS 19.1310 tGradient 7.8750 tsec 28.9740 #GCMRL# 8 dt 129.472000 rms 0.826 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7070 tsec 10.3890 #GCMRL# 9 dt 129.472000 rms 0.824 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1160 tsec 8.4070 #GCMRL# 10 dt 129.472000 rms 0.822 0.245% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1010 tsec 8.2370 #GCMRL# 11 dt 129.472000 rms 0.820 0.310% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1530 tsec 8.2270 #GCMRL# 12 dt 129.472000 rms 0.817 0.366% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6300 tsec 9.0210 #GCMRL# 13 dt 129.472000 rms 0.813 0.428% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5450 tsec 8.7570 #GCMRL# 14 dt 129.472000 rms 0.809 0.486% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5020 tsec 7.7150 #GCMRL# 15 dt 129.472000 rms 0.805 0.518% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9750 tsec 10.4190 #GCMRL# 16 dt 129.472000 rms 0.801 0.514% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.1270 tsec 9.4700 #GCMRL# 17 dt 129.472000 rms 0.797 0.500% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3790 tsec 8.5460 #GCMRL# 18 dt 129.472000 rms 0.793 0.467% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.0540 tsec 9.4580 #GCMRL# 19 dt 129.472000 rms 0.790 0.413% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4300 tsec 9.7180 #GCMRL# 20 dt 129.472000 rms 0.787 0.372% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2140 tsec 8.5490 #GCMRL# 21 dt 129.472000 rms 0.784 0.337% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3560 tsec 10.6600 #GCMRL# 22 dt 129.472000 rms 0.782 0.296% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0010 tsec 10.4290 #GCMRL# 23 dt 129.472000 rms 0.780 0.260% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1760 tsec 10.8620 #GCMRL# 24 dt 129.472000 rms 0.778 0.235% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.8490 tsec 12.6100 #GCMRL# 25 dt 129.472000 rms 0.776 0.219% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7670 tsec 8.9060 #GCMRL# 26 dt 129.472000 rms 0.775 0.218% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0850 tsec 8.3220 #GCMRL# 27 dt 129.472000 rms 0.773 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2480 tsec 8.4890 #GCMRL# 28 dt 129.472000 rms 0.772 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5830 tsec 8.7970 #GCMRL# 29 dt 129.472000 rms 0.770 0.166% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6240 tsec 8.8210 #GCMRL# 30 dt 129.472000 rms 0.769 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6350 tsec 8.9530 #GCMRL# 31 dt 129.472000 rms 0.768 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9470 tsec 6.9360 #GCMRL# 32 dt 129.472000 rms 0.768 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4540 tsec 7.6770 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.767451) vs oldopt=(dt=369.92,rms=0.767464) #GCMRL# 33 dt 517.888000 rms 0.767 0.000% neg 0 invalid 762 tFOTS 15.6410 tGradient 7.3060 tsec 24.2790 #GCAMreg# pass 0 level1 5 level2 1 tsec 479.201 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.767974 #GCMRL# 35 dt 92.480000 rms 0.767 0.082% neg 0 invalid 762 tFOTS 16.2920 tGradient 8.1720 tsec 25.7330 #GCMRL# 36 dt 0.090313 rms 0.767 0.000% neg 0 invalid 762 tFOTS 18.1240 tGradient 8.1360 tsec 27.6370 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.789422 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.788759) vs oldopt=(dt=6.48,rms=0.788788) #GCMRL# 38 dt 9.072000 rms 0.789 0.084% neg 0 invalid 762 tFOTS 17.0340 tGradient 6.2180 tsec 24.5390 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.788681) vs oldopt=(dt=6.48,rms=0.788693) #GCMRL# 39 dt 9.072000 rms 0.789 0.000% neg 0 invalid 762 tFOTS 16.4480 tGradient 5.9720 tsec 23.8650 #GCMRL# 40 dt 9.072000 rms 0.789 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2080 tsec 7.4840 #GCAMreg# pass 0 level1 4 level2 1 tsec 69.331 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.789121 #GCMRL# 42 dt 0.000000 rms 0.789 0.064% neg 0 invalid 762 tFOTS 15.3580 tGradient 6.4090 tsec 22.8780 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.858343 #FOTS# QuadFit found better minimum quadopt=(dt=15.6435,rms=0.837621) vs oldopt=(dt=8,rms=0.842004) #GCMRL# 44 dt 15.643454 rms 0.838 2.414% neg 0 invalid 762 tFOTS 14.5460 tGradient 4.8620 tsec 20.6070 #FOTS# QuadFit found better minimum quadopt=(dt=23.3846,rms=0.832289) vs oldopt=(dt=8,rms=0.833988) #GCMRL# 45 dt 23.384615 rms 0.832 0.637% neg 0 invalid 762 tFOTS 16.1620 tGradient 6.4310 tsec 23.9710 #GCMRL# 46 dt 32.000000 rms 0.830 0.000% neg 0 invalid 762 tFOTS 17.8920 tGradient 8.2710 tsec 27.9260 #GCAMreg# pass 0 level1 3 level2 1 tsec 86.358 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.831065 #GCMRL# 48 dt 0.000000 rms 0.830 0.069% neg 0 invalid 762 tFOTS 17.7810 tGradient 6.1220 tsec 25.2020 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.896159 #GCMRL# 50 dt 0.000000 rms 0.896 0.059% neg 0 invalid 762 tFOTS 17.3980 tGradient 5.7690 tsec 24.7530 #GCAMreg# pass 0 level1 2 level2 1 tsec 52.024 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.896159 #GCMRL# 52 dt 0.000000 rms 0.896 0.059% neg 0 invalid 762 tFOTS 16.6980 tGradient 4.9820 tsec 22.9560 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 1.02079 #FOTS# QuadFit found better minimum quadopt=(dt=0.509091,rms=1.01201) vs oldopt=(dt=0.32,rms=1.01355) #GCMRL# 54 dt 0.509091 rms 1.012 0.861% neg 0 invalid 762 tFOTS 20.8180 tGradient 6.5710 tsec 29.1620 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=1.00777) vs oldopt=(dt=0.32,rms=1.00804) #GCMRL# 55 dt 0.448000 rms 1.008 0.418% neg 0 invalid 762 tFOTS 18.5700 tGradient 7.3140 tsec 27.5670 #GCMRL# 56 dt 0.320000 rms 1.004 0.343% neg 0 invalid 762 tFOTS 16.4910 tGradient 6.2030 tsec 24.2490 #GCMRL# 57 dt 0.320000 rms 1.002 0.000% neg 0 invalid 762 tFOTS 16.5480 tGradient 6.6830 tsec 24.9480 #GCMRL# 58 dt 0.320000 rms 1.000 0.223% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2290 tsec 7.5810 #GCMRL# 59 dt 0.320000 rms 0.997 0.256% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9040 tsec 8.3500 #GCMRL# 60 dt 0.320000 rms 0.996 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2390 tsec 8.9540 #GCMRL# 61 dt 0.320000 rms 0.995 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5560 tsec 8.2280 #GCMRL# 62 dt 0.320000 rms 0.994 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7760 tsec 9.7960 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.991841) vs oldopt=(dt=0.32,rms=0.992202) #GCMRL# 63 dt 0.448000 rms 0.992 0.217% neg 0 invalid 762 tFOTS 17.1870 tGradient 6.7660 tsec 25.2880 #GCMRL# 64 dt 0.320000 rms 0.990 0.000% neg 0 invalid 762 tFOTS 14.7880 tGradient 4.9950 tsec 21.0170 #GCMRL# 65 dt 0.320000 rms 0.990 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4550 tsec 6.5770 #GCMRL# 66 dt 0.320000 rms 0.989 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6890 tsec 7.1220 #GCMRL# 67 dt 0.320000 rms 0.987 0.147% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5790 tsec 6.7880 #GCMRL# 68 dt 0.320000 rms 0.986 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5540 tsec 6.6590 #GCMRL# 69 dt 0.320000 rms 0.986 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7610 tsec 6.3420 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.985502) vs oldopt=(dt=0.32,rms=0.985573) #GCMRL# 70 dt 0.256000 rms 0.986 0.046% neg 0 invalid 762 tFOTS 16.8100 tGradient 6.9700 tsec 25.2680 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.985325) vs oldopt=(dt=0.32,rms=0.985341) #GCMRL# 71 dt 0.256000 rms 0.985 0.000% neg 0 invalid 762 tFOTS 17.3030 tGradient 7.0320 tsec 25.7650 #GCMRL# 72 dt 0.256000 rms 0.985 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3980 tsec 8.6950 #GCMRL# 73 dt 0.256000 rms 0.985 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3030 tsec 8.6880 #GCMRL# 74 dt 0.256000 rms 0.984 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5110 tsec 8.9890 #GCMRL# 75 dt 0.256000 rms 0.984 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9380 tsec 8.2260 #GCMRL# 76 dt 0.256000 rms 0.984 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2460 tsec 6.6110 #GCAMreg# pass 0 level1 1 level2 1 tsec 333.424 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.983886 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.983015) vs oldopt=(dt=0.32,rms=0.983016) #GCMRL# 78 dt 0.384000 rms 0.983 0.089% neg 0 invalid 762 tFOTS 15.3240 tGradient 5.8050 tsec 22.0280 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.932521 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.926315) vs oldopt=(dt=0.32,rms=0.926544) #GCMRL# 80 dt 0.256000 rms 0.926 0.666% neg 0 invalid 762 tFOTS 16.3680 tGradient 3.5910 tsec 21.1070 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.925949) vs oldopt=(dt=0.02,rms=0.925986) #GCMRL# 81 dt 0.028000 rms 0.926 0.000% neg 0 invalid 762 tFOTS 13.9600 tGradient 3.5990 tsec 18.8450 #GCAMreg# pass 0 level1 0 level2 1 tsec 49.627 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.926549 #GCMRL# 83 dt 0.020000 rms 0.926 0.077% neg 0 invalid 762 tFOTS 15.1020 tGradient 3.2850 tsec 19.6400 #FOTS# QuadFit found better minimum quadopt=(dt=0.004,rms=0.925831) vs oldopt=(dt=0.005,rms=0.925831) #GCMRL# 84 dt 0.004000 rms 0.926 0.000% neg 0 invalid 762 tFOTS 15.2740 tGradient 3.6060 tsec 20.5050 GCAMregister done in 23.1061 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.13974 (24) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (2793 voxels, overlap=0.541) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (2793 voxels, peak = 19), gca=19.1 gca peak = 0.17690 (16) mri peak = 0.14881 (25) Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (2034 voxels, overlap=0.378) Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (2034 voxels, peak = 23), gca=23.3 gca peak = 0.28275 (96) mri peak = 0.09307 (103) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (960 voxels, overlap=0.107) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (960 voxels, peak = 103), gca=103.2 gca peak = 0.18948 (93) mri peak = 0.09253 (102) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (839 voxels, overlap=0.277) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (839 voxels, peak = 99), gca=99.0 gca peak = 0.20755 (55) mri peak = 0.05768 (87) Right_Hippocampus (53): linear fit = 1.47 x + 0.0 (910 voxels, overlap=0.031) Right_Hippocampus (53): linear fit = 1.47 x + 0.0 (910 voxels, peak = 81), gca=80.6 gca peak = 0.31831 (58) mri peak = 0.09328 (72) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (799 voxels, overlap=0.016) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (799 voxels, peak = 71), gca=71.1 gca peak = 0.11957 (102) mri peak = 0.08273 (106) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (61133 voxels, overlap=0.773) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (61133 voxels, peak = 107), gca=106.6 gca peak = 0.11429 (102) mri peak = 0.07860 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (64175 voxels, overlap=0.729) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (64175 voxels, peak = 107), gca=106.6 gca peak = 0.14521 (59) mri peak = 0.04010 (79) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (21753 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (21753 voxels, peak = 79), gca=79.4 gca peak = 0.14336 (58) mri peak = 0.04109 (79) Right_Cerebral_Cortex (42): linear fit = 1.38 x + 0.0 (23930 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.38 x + 0.0 (23930 voxels, peak = 80), gca=79.8 gca peak = 0.13305 (70) mri peak = 0.12564 (88) Right_Caudate (50): linear fit = 1.30 x + 0.0 (977 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.30 x + 0.0 (977 voxels, peak = 91), gca=91.3 gca peak = 0.15761 (71) mri peak = 0.10053 (84) Left_Caudate (11): linear fit = 1.17 x + 0.0 (764 voxels, overlap=0.076) Left_Caudate (11): linear fit = 1.17 x + 0.0 (764 voxels, peak = 83), gca=83.4 gca peak = 0.13537 (57) mri peak = 0.04372 (72) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (14226 voxels, overlap=0.009) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (14226 voxels, peak = 72), gca=72.1 gca peak = 0.13487 (56) mri peak = 0.04156 (71) Right_Cerebellum_Cortex (47): linear fit = 1.30 x + 0.0 (17877 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.30 x + 0.0 (17877 voxels, peak = 73), gca=73.1 gca peak = 0.19040 (84) mri peak = 0.08620 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (10031 voxels, overlap=0.305) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (10031 voxels, peak = 89), gca=89.5 gca peak = 0.18871 (83) mri peak = 0.06233 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8330 voxels, overlap=0.668) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8330 voxels, peak = 87), gca=86.7 gca peak = 0.24248 (57) mri peak = 0.15645 (75) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (384 voxels, overlap=0.045) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (384 voxels, peak = 74), gca=73.8 gca peak = 0.35833 (56) mri peak = 0.10487 (71) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (388 voxels, overlap=0.043) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (388 voxels, peak = 73), gca=72.5 gca peak = 0.12897 (85) mri peak = 0.07808 (93) Left_Thalamus (10): linear fit = 1.10 x + 0.0 (4338 voxels, overlap=0.830) Left_Thalamus (10): linear fit = 1.10 x + 0.0 (4338 voxels, peak = 93), gca=93.1 gca peak = 0.13127 (83) mri peak = 0.07353 (86) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (3340 voxels, overlap=0.859) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (3340 voxels, peak = 84), gca=84.2 gca peak = 0.12974 (78) mri peak = 0.09652 (95) Left_Putamen (12): linear fit = 1.20 x + 0.0 (2666 voxels, overlap=0.007) Left_Putamen (12): linear fit = 1.20 x + 0.0 (2666 voxels, peak = 93), gca=93.2 gca peak = 0.17796 (79) mri peak = 0.07415 (93) Right_Putamen (51): linear fit = 1.20 x + 0.0 (2529 voxels, overlap=0.015) Right_Putamen (51): linear fit = 1.20 x + 0.0 (2529 voxels, peak = 94), gca=94.4 gca peak = 0.10999 (80) mri peak = 0.12950 (82) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12232 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12232 voxels, peak = 84), gca=84.4 gca peak = 0.13215 (88) mri peak = 0.08188 (88) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1548 voxels, overlap=0.652) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1548 voxels, peak = 94), gca=93.7 gca peak = 0.11941 (89) mri peak = 0.07436 (91) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1500 voxels, overlap=0.660) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1500 voxels, peak = 95), gca=94.8 gca peak = 0.20775 (25) mri peak = 0.16759 (24) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (95 voxels, overlap=0.870) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (95 voxels, peak = 25), gca=24.6 gca peak = 0.13297 (21) mri peak = 0.16967 (22) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (507 voxels, overlap=0.551) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (507 voxels, peak = 24), gca=24.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 1.33 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.20 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 6.45743 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 1.02558 #FOTS# QuadFit found better minimum quadopt=(dt=170.385,rms=0.966229) vs oldopt=(dt=92.48,rms=0.978942) #GCMRL# 86 dt 170.384906 rms 0.966 5.787% neg 0 invalid 762 tFOTS 15.0350 tGradient 5.2120 tsec 21.4140 #FOTS# QuadFit found better minimum quadopt=(dt=543.779,rms=0.921381) vs oldopt=(dt=369.92,rms=0.92637) #GCMRL# 87 dt 543.779310 rms 0.921 4.642% neg 0 invalid 762 tFOTS 16.2940 tGradient 6.1940 tsec 23.7180 #FOTS# QuadFit found better minimum quadopt=(dt=272.674,rms=0.902269) vs oldopt=(dt=369.92,rms=0.903981) #GCMRL# 88 dt 272.674330 rms 0.902 2.074% neg 0 invalid 762 tFOTS 16.5050 tGradient 6.1420 tsec 23.9720 #FOTS# QuadFit found better minimum quadopt=(dt=286.093,rms=0.888721) vs oldopt=(dt=369.92,rms=0.889758) #GCMRL# 89 dt 286.092715 rms 0.889 1.502% neg 0 invalid 762 tFOTS 16.5460 tGradient 6.5050 tsec 24.0400 #FOTS# QuadFit found better minimum quadopt=(dt=160.582,rms=0.882373) vs oldopt=(dt=92.48,rms=0.88395) #GCMRL# 90 dt 160.581818 rms 0.882 0.714% neg 0 invalid 762 tFOTS 15.9020 tGradient 6.8770 tsec 23.9030 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.866582) vs oldopt=(dt=1479.68,rms=0.867284) #GCMRL# 91 dt 1183.744000 rms 0.867 1.790% neg 0 invalid 762 tFOTS 14.0390 tGradient 7.0390 tsec 22.1590 #FOTS# QuadFit found better minimum quadopt=(dt=137.035,rms=0.854476) vs oldopt=(dt=92.48,rms=0.856012) #GCMRL# 92 dt 137.035294 rms 0.854 1.397% neg 0 invalid 762 tFOTS 13.8860 tGradient 7.0150 tsec 22.3370 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.848555) vs oldopt=(dt=1479.68,rms=0.849429) #GCMRL# 93 dt 1183.744000 rms 0.849 0.693% neg 0 invalid 762 tFOTS 14.6490 tGradient 7.5470 tsec 23.3350 #FOTS# QuadFit found better minimum quadopt=(dt=139.333,rms=0.840967) vs oldopt=(dt=92.48,rms=0.842066) #GCMRL# 94 dt 139.333333 rms 0.841 0.894% neg 0 invalid 762 tFOTS 15.8500 tGradient 6.9030 tsec 24.0840 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.838213) vs oldopt=(dt=369.92,rms=0.838334) #GCMRL# 95 dt 443.904000 rms 0.838 0.328% neg 0 invalid 762 tFOTS 15.9630 tGradient 6.7340 tsec 23.8320 #FOTS# QuadFit found better minimum quadopt=(dt=145.723,rms=0.834951) vs oldopt=(dt=92.48,rms=0.83565) #GCMRL# 96 dt 145.723077 rms 0.835 0.389% neg 0 invalid 762 tFOTS 16.9850 tGradient 6.8750 tsec 25.0940 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.832862) vs oldopt=(dt=369.92,rms=0.833031) #GCMRL# 97 dt 517.888000 rms 0.833 0.250% neg 0 invalid 762 tFOTS 17.3390 tGradient 8.6950 tsec 27.3860 #FOTS# QuadFit found better minimum quadopt=(dt=149.015,rms=0.829414) vs oldopt=(dt=92.48,rms=0.830184) #GCMRL# 98 dt 149.014925 rms 0.829 0.414% neg 0 invalid 762 tFOTS 18.5090 tGradient 7.6710 tsec 27.3080 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.82765) vs oldopt=(dt=369.92,rms=0.827683) #GCMRL# 99 dt 443.904000 rms 0.828 0.213% neg 0 invalid 762 tFOTS 16.0920 tGradient 6.0760 tsec 23.5220 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.82506) vs oldopt=(dt=92.48,rms=0.825533) #GCMRL# 100 dt 129.472000 rms 0.825 0.313% neg 0 invalid 762 tFOTS 15.2090 tGradient 6.4980 tsec 23.1050 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.81833) vs oldopt=(dt=1479.68,rms=0.818628) #GCMRL# 101 dt 1775.616000 rms 0.818 0.816% neg 0 invalid 762 tFOTS 17.7400 tGradient 7.2240 tsec 26.4530 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.812577) vs oldopt=(dt=92.48,rms=0.813016) #GCMRL# 102 dt 129.472000 rms 0.813 0.703% neg 0 invalid 762 tFOTS 20.0990 tGradient 9.1640 tsec 31.0260 #GCMRL# 103 dt 369.920000 rms 0.812 0.120% neg 0 invalid 762 tFOTS 18.6880 tGradient 9.2900 tsec 29.7270 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.810097) vs oldopt=(dt=92.48,rms=0.810373) #GCMRL# 104 dt 129.472000 rms 0.810 0.185% neg 0 invalid 762 tFOTS 23.0970 tGradient 9.3590 tsec 34.3550 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.806436) vs oldopt=(dt=1479.68,rms=0.806452) #GCMRL# 105 dt 1775.616000 rms 0.806 0.452% neg 0 invalid 762 tFOTS 19.2010 tGradient 8.4090 tsec 29.2330 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.80157) vs oldopt=(dt=92.48,rms=0.802031) #GCMRL# 106 dt 129.472000 rms 0.802 0.603% neg 0 invalid 762 tFOTS 19.2530 tGradient 9.6460 tsec 30.3930 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.800855) vs oldopt=(dt=369.92,rms=0.800914) #GCMRL# 107 dt 295.936000 rms 0.801 0.089% neg 0 invalid 762 tFOTS 20.2820 tGradient 8.7490 tsec 30.6360 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.799913) vs oldopt=(dt=92.48,rms=0.800096) #GCMRL# 108 dt 129.472000 rms 0.800 0.118% neg 0 invalid 762 tFOTS 18.3580 tGradient 7.8200 tsec 27.6210 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.79677) vs oldopt=(dt=1479.68,rms=0.796897) #GCMRL# 109 dt 1775.616000 rms 0.797 0.393% neg 0 invalid 762 tFOTS 20.1320 tGradient 8.6060 tsec 30.0510 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.79354) vs oldopt=(dt=92.48,rms=0.793777) #GCMRL# 110 dt 129.472000 rms 0.794 0.405% neg 0 invalid 762 tFOTS 15.6770 tGradient 6.7450 tsec 23.6760 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.793186) vs oldopt=(dt=92.48,rms=0.793256) #GCMRL# 111 dt 129.472000 rms 0.793 0.000% neg 0 invalid 762 tFOTS 14.6010 tGradient 5.6730 tsec 21.6320 #GCMRL# 112 dt 129.472000 rms 0.793 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9670 tsec 7.0950 #GCMRL# 113 dt 129.472000 rms 0.792 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0800 tsec 8.4050 #GCMRL# 114 dt 129.472000 rms 0.791 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8670 tsec 6.8440 #GCMRL# 115 dt 129.472000 rms 0.790 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8660 tsec 7.3280 #GCMRL# 116 dt 129.472000 rms 0.789 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2470 tsec 7.2540 #GCMRL# 117 dt 129.472000 rms 0.787 0.183% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0780 tsec 8.4330 #GCMRL# 118 dt 129.472000 rms 0.786 0.197% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8750 tsec 9.3190 #GCMRL# 119 dt 129.472000 rms 0.784 0.204% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.1120 tsec 9.8660 #GCMRL# 120 dt 129.472000 rms 0.783 0.208% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2880 tsec 8.7150 #GCMRL# 121 dt 129.472000 rms 0.781 0.207% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0190 tsec 10.3380 #GCMRL# 122 dt 129.472000 rms 0.779 0.203% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4850 tsec 9.7740 #GCMRL# 123 dt 129.472000 rms 0.778 0.201% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.4780 tsec 10.6990 #GCMRL# 124 dt 129.472000 rms 0.776 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8360 tsec 11.5690 #GCMRL# 125 dt 129.472000 rms 0.775 0.191% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.1080 tsec 11.5880 #GCMRL# 126 dt 129.472000 rms 0.773 0.184% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.2440 tsec 9.6530 #GCMRL# 127 dt 129.472000 rms 0.772 0.175% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.1140 tsec 9.8360 #GCMRL# 128 dt 129.472000 rms 0.771 0.164% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9450 tsec 10.3470 #GCMRL# 129 dt 129.472000 rms 0.770 0.164% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2550 tsec 10.6670 #GCMRL# 130 dt 129.472000 rms 0.768 0.157% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.1920 tsec 9.4040 #GCMRL# 131 dt 129.472000 rms 0.767 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.4060 tsec 10.9670 #GCMRL# 132 dt 129.472000 rms 0.766 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7100 tsec 11.2080 #GCMRL# 133 dt 129.472000 rms 0.765 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.3990 tsec 12.9210 #GCMRL# 134 dt 129.472000 rms 0.764 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.4750 tsec 12.9480 #GCMRL# 135 dt 129.472000 rms 0.763 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.9230 tsec 11.3280 #GCMRL# 136 dt 129.472000 rms 0.762 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.9120 tsec 11.3560 #GCMRL# 137 dt 129.472000 rms 0.762 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8960 tsec 11.4810 #GCMRL# 138 dt 129.472000 rms 0.761 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.9960 tsec 11.6600 #GCMRL# 139 dt 129.472000 rms 0.760 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0340 tsec 10.0790 #GCMRL# 140 dt 129.472000 rms 0.759 0.106% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2070 tsec 8.5290 #GCMRL# 141 dt 129.472000 rms 0.758 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.0280 tsec 9.3860 #GCMRL# 142 dt 129.472000 rms 0.758 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3700 tsec 11.9890 #GCMRL# 143 dt 129.472000 rms 0.757 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.5340 tsec 12.1050 #GCMRL# 144 dt 129.472000 rms 0.756 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.9990 tsec 13.8830 #GCMRL# 145 dt 129.472000 rms 0.756 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.3050 tsec 13.3080 #GCMRL# 146 dt 129.472000 rms 0.755 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.8770 tsec 12.7230 #GCMRL# 147 dt 129.472000 rms 0.754 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.3450 tsec 13.2430 #GCMRL# 148 dt 129.472000 rms 0.754 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.4190 tsec 13.4950 #GCMRL# 149 dt 129.472000 rms 0.753 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.6950 tsec 13.6490 #GCMRL# 150 dt 129.472000 rms 0.753 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.0500 tsec 14.0240 #GCMRL# 151 dt 129.472000 rms 0.752 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.2020 tsec 14.3180 #GCMRL# 152 dt 129.472000 rms 0.752 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.2510 tsec 14.2740 #GCMRL# 153 dt 129.472000 rms 0.751 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.3000 tsec 14.3270 #GCMRL# 154 dt 129.472000 rms 0.751 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1160 tsec 13.9200 #GCMRL# 155 dt 129.472000 rms 0.751 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.7050 tsec 13.5410 #GCMRL# 156 dt 129.472000 rms 0.750 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.2800 tsec 14.4610 #GCMRL# 157 dt 129.472000 rms 0.750 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.9520 tsec 15.5930 #GCMRL# 158 dt 129.472000 rms 0.749 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1350 tsec 14.9340 #GCMRL# 159 dt 129.472000 rms 0.749 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.4270 tsec 14.2300 #GCMRL# 160 dt 129.472000 rms 0.749 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.6390 tsec 15.4800 #GCMRL# 161 dt 129.472000 rms 0.748 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7610 tsec 14.6930 #GCMRL# 162 dt 129.472000 rms 0.748 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.1110 tsec 12.4850 #GCMRL# 163 dt 129.472000 rms 0.748 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5970 tsec 9.9040 #GCMRL# 164 dt 129.472000 rms 0.747 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.1210 tsec 9.2680 #GCMRL# 165 dt 129.472000 rms 0.747 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7280 tsec 9.9060 #GCMRL# 166 dt 129.472000 rms 0.747 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3510 tsec 9.7120 #GCMRL# 167 dt 129.472000 rms 0.746 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7660 tsec 9.9650 #GCMRL# 168 dt 129.472000 rms 0.746 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5850 tsec 9.6900 #GCMRL# 169 dt 129.472000 rms 0.746 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0880 tsec 10.4280 #GCMRL# 170 dt 129.472000 rms 0.745 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.1540 tsec 10.7630 #GCMRL# 171 dt 129.472000 rms 0.745 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6620 tsec 9.9590 #GCMRL# 172 dt 129.472000 rms 0.745 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9410 tsec 10.2070 #GCMRL# 173 dt 129.472000 rms 0.744 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7970 tsec 10.4460 #GCMRL# 174 dt 129.472000 rms 0.744 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7270 tsec 11.4070 #GCMRL# 175 dt 129.472000 rms 0.744 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.1380 tsec 9.8200 #GCMRL# 176 dt 129.472000 rms 0.743 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.6110 tsec 11.4650 #GCMRL# 177 dt 129.472000 rms 0.743 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.1760 tsec 11.8000 #GCMRL# 178 dt 129.472000 rms 0.743 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7500 tsec 11.4820 #GCMRL# 179 dt 129.472000 rms 0.742 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.6230 tsec 12.5190 #GCMRL# 180 dt 129.472000 rms 0.742 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.2260 tsec 12.4350 #GCMRL# 181 dt 129.472000 rms 0.742 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7860 tsec 11.6480 #GCMRL# 182 dt 129.472000 rms 0.741 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3650 tsec 12.0200 #GCMRL# 183 dt 129.472000 rms 0.741 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.3450 tsec 11.4820 #GCMRL# 184 dt 129.472000 rms 0.741 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.6730 tsec 11.1750 #GCMRL# 185 dt 129.472000 rms 0.741 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.4730 tsec 13.0200 #GCMRL# 186 dt 129.472000 rms 0.740 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.9160 tsec 13.6170 #GCMRL# 187 dt 129.472000 rms 0.740 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.0920 tsec 12.7650 #GCMRL# 188 dt 129.472000 rms 0.740 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.6790 tsec 12.9680 #GCMRL# 189 dt 129.472000 rms 0.739 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.8570 tsec 12.8470 #GCMRL# 190 dt 129.472000 rms 0.739 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.2170 tsec 13.2690 #GCMRL# 191 dt 129.472000 rms 0.739 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.0480 tsec 12.4470 #GCMRL# 192 dt 129.472000 rms 0.738 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.9610 tsec 11.3500 #GCMRL# 193 dt 129.472000 rms 0.738 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.2860 tsec 9.5700 #GCMRL# 194 dt 129.472000 rms 0.738 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8310 tsec 11.4620 #GCMRL# 195 dt 129.472000 rms 0.737 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0490 tsec 10.7070 #GCMRL# 196 dt 129.472000 rms 0.737 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4790 tsec 10.0450 #GCMRL# 197 dt 129.472000 rms 0.737 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.0360 tsec 9.2620 #GCMRL# 198 dt 129.472000 rms 0.737 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4530 tsec 8.5760 #GCMRL# 199 dt 129.472000 rms 0.736 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4880 tsec 8.7460 #GCMRL# 200 dt 129.472000 rms 0.736 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6750 tsec 10.5680 #GCMRL# 201 dt 129.472000 rms 0.736 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8490 tsec 11.2600 #GCMRL# 202 dt 129.472000 rms 0.736 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3870 tsec 11.8840 #GCMRL# 203 dt 129.472000 rms 0.735 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7590 tsec 10.4380 #GCMRL# 204 dt 129.472000 rms 0.735 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.4280 tsec 13.2070 #GCMRL# 205 dt 129.472000 rms 0.735 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.5630 tsec 14.4110 #GCMRL# 206 dt 129.472000 rms 0.735 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.5120 tsec 14.1710 #GCMRL# 207 dt 129.472000 rms 0.734 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1400 tsec 15.1410 #GCMRL# 208 dt 129.472000 rms 0.734 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.9600 tsec 13.6440 #GCMRL# 209 dt 129.472000 rms 0.734 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1110 tsec 15.0100 #GCMRL# 210 dt 129.472000 rms 0.734 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.6480 tsec 14.5090 #GCMRL# 211 dt 129.472000 rms 0.733 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1880 tsec 14.4520 #GCMRL# 212 dt 129.472000 rms 0.733 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1840 tsec 14.0660 #GCMRL# 213 dt 129.472000 rms 0.733 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7560 tsec 14.8960 #GCMRL# 214 dt 129.472000 rms 0.733 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.1190 tsec 13.8380 #GCMRL# 215 dt 129.472000 rms 0.732 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0150 tsec 15.0450 #GCMRL# 216 dt 129.472000 rms 0.732 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7270 tsec 14.4800 #GCMRL# 217 dt 129.472000 rms 0.732 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3140 tsec 15.6000 #GCMRL# 218 dt 129.472000 rms 0.732 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.7590 tsec 18.2080 #GCMRL# 219 dt 129.472000 rms 0.732 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.5780 tsec 14.7450 #GCMRL# 220 dt 129.472000 rms 0.731 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.5470 tsec 14.4020 #GCMRL# 221 dt 129.472000 rms 0.731 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.0090 tsec 12.2210 #GCMRL# 222 dt 129.472000 rms 0.731 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.9770 tsec 12.7840 #GCMRL# 223 dt 129.472000 rms 0.731 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.4560 tsec 12.5450 #GCMRL# 224 dt 129.472000 rms 0.731 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.5830 tsec 13.3660 #GCMRL# 225 dt 129.472000 rms 0.730 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8590 tsec 9.3510 #GCMRL# 226 dt 129.472000 rms 0.730 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.9260 tsec 10.5710 #GCMRL# 227 dt 129.472000 rms 0.730 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.5040 tsec 13.5010 #GCMRL# 228 dt 129.472000 rms 0.730 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.9300 tsec 13.1290 #GCMRL# 229 dt 129.472000 rms 0.730 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.0220 tsec 11.8990 #GCMRL# 230 dt 129.472000 rms 0.729 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8430 tsec 15.0400 #GCMRL# 231 dt 129.472000 rms 0.729 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.2720 tsec 11.6120 #GCMRL# 232 dt 129.472000 rms 0.729 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3560 tsec 15.9500 #GCMRL# 233 dt 129.472000 rms 0.729 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3210 tsec 12.2130 #GCMRL# 234 dt 129.472000 rms 0.729 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9010 tsec 14.7290 #GCMRL# 235 dt 129.472000 rms 0.728 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3210 tsec 12.2030 #GCMRL# 236 dt 129.472000 rms 0.728 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5300 tsec 10.2970 #GCMRL# 237 dt 129.472000 rms 0.728 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.6510 tsec 14.0180 #GCMRL# 238 dt 129.472000 rms 0.728 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.5100 tsec 13.5010 #GCMRL# 239 dt 129.472000 rms 0.728 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 11.7100 tsec 14.0070 #GCMRL# 240 dt 129.472000 rms 0.727 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.3470 tsec 14.4790 #GCMRL# 241 dt 129.472000 rms 0.727 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.9780 tsec 13.4190 #GCMRL# 242 dt 129.472000 rms 0.727 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.3210 tsec 14.2780 #GCMRL# 243 dt 129.472000 rms 0.727 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2260 tsec 15.4460 #GCMRL# 244 dt 129.472000 rms 0.727 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.6760 tsec 15.6510 #GCMRL# 245 dt 129.472000 rms 0.726 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7320 tsec 15.0680 #GCMRL# 246 dt 129.472000 rms 0.726 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.2240 tsec 14.3370 #FOTS# QuadFit found better minimum quadopt=(dt=28409.9,rms=0.724831) vs oldopt=(dt=23674.9,rms=0.724896) #GCMRL# 247 dt 28409.856000 rms 0.725 0.205% neg 0 invalid 762 tFOTS 24.7740 tGradient 11.7450 tsec 38.3170 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.723918) vs oldopt=(dt=92.48,rms=0.724043) #GCMRL# 248 dt 129.472000 rms 0.724 0.126% neg 0 invalid 762 tFOTS 22.5750 tGradient 9.8280 tsec 34.2800 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.722638) vs oldopt=(dt=369.92,rms=0.722833) #GCMRL# 249 dt 517.888000 rms 0.723 0.177% neg 0 invalid 762 tFOTS 19.1120 tGradient 9.7910 tsec 30.5680 #GCMRL# 250 dt 0.850000 rms 0.723 0.000% neg 0 invalid 762 tFOTS 24.5230 tGradient 10.4740 tsec 38.5250 #GCAMreg# pass 0 level1 5 level2 1 tsec 2471.68 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.723575 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.722629) vs oldopt=(dt=23.12,rms=0.722634) #GCMRL# 252 dt 32.368000 rms 0.723 0.131% neg 0 invalid 762 tFOTS 22.4690 tGradient 10.5960 tsec 35.0860 #FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.722612) vs oldopt=(dt=5.78,rms=0.722612) #GCMRL# 253 dt 8.092000 rms 0.723 0.000% neg 0 invalid 762 tFOTS 24.5670 tGradient 10.4160 tsec 37.1940 #GCMRL# 254 dt 8.092000 rms 0.723 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.6290 tsec 12.5470 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.727743 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.704686) vs oldopt=(dt=414.72,rms=0.706368) #GCMRL# 256 dt 580.608000 rms 0.705 3.168% neg 0 invalid 762 tFOTS 23.7120 tGradient 8.4810 tsec 33.9670 #FOTS# QuadFit found better minimum quadopt=(dt=93.762,rms=0.686435) vs oldopt=(dt=103.68,rms=0.686655) #GCMRL# 257 dt 93.762035 rms 0.686 2.590% neg 0 invalid 762 tFOTS 17.1450 tGradient 8.2230 tsec 26.8610 #FOTS# QuadFit found better minimum quadopt=(dt=73.771,rms=0.683213) vs oldopt=(dt=103.68,rms=0.683671) #GCMRL# 258 dt 73.770992 rms 0.683 0.469% neg 0 invalid 762 tFOTS 15.2860 tGradient 5.9220 tsec 22.3980 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.677228) vs oldopt=(dt=414.72,rms=0.678589) #GCMRL# 259 dt 248.832000 rms 0.677 0.876% neg 0 invalid 762 tFOTS 14.2690 tGradient 5.5640 tsec 21.0660 #FOTS# QuadFit found better minimum quadopt=(dt=78,rms=0.673792) vs oldopt=(dt=25.92,rms=0.674834) #GCMRL# 260 dt 78.000000 rms 0.674 0.507% neg 0 invalid 762 tFOTS 16.4970 tGradient 6.3840 tsec 24.2450 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.670582) vs oldopt=(dt=103.68,rms=0.670661) #GCMRL# 261 dt 124.416000 rms 0.671 0.476% neg 0 invalid 762 tFOTS 15.8450 tGradient 6.2440 tsec 23.2180 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.668777) vs oldopt=(dt=103.68,rms=0.669307) #GCMRL# 262 dt 62.208000 rms 0.669 0.269% neg 0 invalid 762 tFOTS 16.1360 tGradient 6.5640 tsec 23.9010 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.662827) vs oldopt=(dt=414.72,rms=0.662947) #GCMRL# 263 dt 497.664000 rms 0.663 0.890% neg 0 invalid 762 tFOTS 16.2570 tGradient 7.6770 tsec 25.2440 #FOTS# QuadFit found better minimum quadopt=(dt=70.0759,rms=0.657916) vs oldopt=(dt=25.92,rms=0.659297) #GCMRL# 264 dt 70.075949 rms 0.658 0.741% neg 0 invalid 762 tFOTS 15.6300 tGradient 7.5370 tsec 24.3750 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.655865) vs oldopt=(dt=103.68,rms=0.655903) #GCMRL# 265 dt 124.416000 rms 0.656 0.312% neg 0 invalid 762 tFOTS 15.6150 tGradient 8.1280 tsec 24.9790 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.654972) vs oldopt=(dt=25.92,rms=0.655141) #GCMRL# 266 dt 36.288000 rms 0.655 0.136% neg 0 invalid 762 tFOTS 16.8360 tGradient 7.5650 tsec 25.7770 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.652967) vs oldopt=(dt=414.72,rms=0.653121) #GCMRL# 267 dt 331.776000 rms 0.653 0.306% neg 0 invalid 762 tFOTS 13.7780 tGradient 6.4700 tsec 21.4090 #FOTS# QuadFit found better minimum quadopt=(dt=63.8871,rms=0.64989) vs oldopt=(dt=103.68,rms=0.650723) #GCMRL# 268 dt 63.887125 rms 0.650 0.471% neg 0 invalid 762 tFOTS 16.0040 tGradient 4.8840 tsec 21.9540 #GCMRL# 269 dt 103.680000 rms 0.649 0.104% neg 0 invalid 762 tFOTS 17.1420 tGradient 5.8650 tsec 24.3550 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.647655) vs oldopt=(dt=103.68,rms=0.647707) #GCMRL# 270 dt 124.416000 rms 0.648 0.240% neg 0 invalid 762 tFOTS 17.8800 tGradient 5.8220 tsec 24.9250 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.647063) vs oldopt=(dt=25.92,rms=0.647175) #GCMRL# 271 dt 36.288000 rms 0.647 0.091% neg 0 invalid 762 tFOTS 14.2180 tGradient 6.6270 tsec 22.1590 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.64549) vs oldopt=(dt=414.72,rms=0.645538) #GCMRL# 272 dt 331.776000 rms 0.645 0.243% neg 0 invalid 762 tFOTS 12.8410 tGradient 5.5480 tsec 19.4070 #FOTS# QuadFit found better minimum quadopt=(dt=65.5238,rms=0.64316) vs oldopt=(dt=103.68,rms=0.643723) #GCMRL# 273 dt 65.523810 rms 0.643 0.361% neg 0 invalid 762 tFOTS 11.7430 tGradient 4.8560 tsec 17.5830 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.642771) vs oldopt=(dt=103.68,rms=0.642787) #GCMRL# 274 dt 82.944000 rms 0.643 0.060% neg 0 invalid 762 tFOTS 10.0480 tGradient 5.6550 tsec 16.6450 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.641297) vs oldopt=(dt=103.68,rms=0.641554) #GCMRL# 275 dt 145.152000 rms 0.641 0.229% neg 0 invalid 762 tFOTS 11.2600 tGradient 4.0080 tsec 16.2500 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.640959) vs oldopt=(dt=25.92,rms=0.641025) #GCMRL# 276 dt 36.288000 rms 0.641 0.053% neg 0 invalid 762 tFOTS 12.1860 tGradient 4.3600 tsec 17.3720 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.638813) vs oldopt=(dt=414.72,rms=0.638995) #GCMRL# 277 dt 580.608000 rms 0.639 0.335% neg 0 invalid 762 tFOTS 10.9390 tGradient 4.0770 tsec 15.8320 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.636587) vs oldopt=(dt=25.92,rms=0.637061) #GCMRL# 278 dt 36.288000 rms 0.637 0.348% neg 0 invalid 762 tFOTS 11.9930 tGradient 4.7340 tsec 17.5690 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.63559) vs oldopt=(dt=103.68,rms=0.635605) #GCMRL# 279 dt 124.416000 rms 0.636 0.157% neg 0 invalid 762 tFOTS 10.5060 tGradient 4.8380 tsec 16.1970 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.635222) vs oldopt=(dt=25.92,rms=0.63529) #GCMRL# 280 dt 36.288000 rms 0.635 0.058% neg 0 invalid 762 tFOTS 11.7280 tGradient 4.0960 tsec 16.5140 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.634629) vs oldopt=(dt=103.68,rms=0.63474) #GCMRL# 281 dt 145.152000 rms 0.635 0.093% neg 0 invalid 762 tFOTS 14.4950 tGradient 4.4310 tsec 19.8150 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.633584) vs oldopt=(dt=103.68,rms=0.633673) #GCMRL# 282 dt 145.152000 rms 0.634 0.165% neg 0 invalid 762 tFOTS 14.5340 tGradient 4.8960 tsec 20.3540 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.633263) vs oldopt=(dt=25.92,rms=0.633315) #GCMRL# 283 dt 36.288000 rms 0.633 0.051% neg 0 invalid 762 tFOTS 11.6750 tGradient 4.4130 tsec 17.0190 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.63274) vs oldopt=(dt=103.68,rms=0.632834) #GCMRL# 284 dt 145.152000 rms 0.633 0.083% neg 0 invalid 762 tFOTS 14.3710 tGradient 4.7050 tsec 20.3130 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.631871) vs oldopt=(dt=103.68,rms=0.631931) #GCMRL# 285 dt 145.152000 rms 0.632 0.137% neg 0 invalid 762 tFOTS 12.5630 tGradient 4.5030 tsec 18.1180 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.631535) vs oldopt=(dt=25.92,rms=0.631584) #GCMRL# 286 dt 36.288000 rms 0.632 0.053% neg 0 invalid 762 tFOTS 13.1350 tGradient 4.5130 tsec 18.8240 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.631074) vs oldopt=(dt=103.68,rms=0.631159) #GCMRL# 287 dt 145.152000 rms 0.631 0.073% neg 0 invalid 762 tFOTS 13.5680 tGradient 4.7530 tsec 19.4160 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.630205) vs oldopt=(dt=103.68,rms=0.630257) #GCMRL# 288 dt 145.152000 rms 0.630 0.138% neg 0 invalid 762 tFOTS 12.6770 tGradient 4.8120 tsec 18.6180 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.629918) vs oldopt=(dt=25.92,rms=0.62996) #GCMRL# 289 dt 36.288000 rms 0.630 0.000% neg 0 invalid 762 tFOTS 13.0910 tGradient 5.4860 tsec 19.7340 #GCMRL# 290 dt 36.288000 rms 0.630 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5120 tsec 6.5080 #GCMRL# 291 dt 36.288000 rms 0.629 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3030 tsec 6.3120 #GCMRL# 292 dt 36.288000 rms 0.629 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4720 tsec 6.5790 #GCMRL# 293 dt 36.288000 rms 0.628 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7550 tsec 5.7660 #GCMRL# 294 dt 36.288000 rms 0.628 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6650 tsec 6.7060 #GCMRL# 295 dt 36.288000 rms 0.627 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5560 tsec 6.5430 #GCMRL# 296 dt 36.288000 rms 0.626 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5680 tsec 6.8010 #GCMRL# 297 dt 36.288000 rms 0.625 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1440 tsec 8.3860 #GCMRL# 298 dt 36.288000 rms 0.624 0.147% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6820 tsec 6.8480 #GCMRL# 299 dt 36.288000 rms 0.624 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8850 tsec 5.8690 #GCMRL# 300 dt 36.288000 rms 0.623 0.149% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1660 tsec 7.2840 #GCMRL# 301 dt 36.288000 rms 0.622 0.153% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6340 tsec 6.5400 #GCMRL# 302 dt 36.288000 rms 0.621 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1230 tsec 7.2420 #GCMRL# 303 dt 36.288000 rms 0.620 0.149% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9640 tsec 7.0490 #GCMRL# 304 dt 36.288000 rms 0.619 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.5620 tsec 7.4980 #GCMRL# 305 dt 36.288000 rms 0.618 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0350 tsec 5.9010 #GCMRL# 306 dt 36.288000 rms 0.617 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5470 tsec 6.6080 #GCMRL# 307 dt 36.288000 rms 0.616 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2290 tsec 6.3040 #GCMRL# 308 dt 36.288000 rms 0.616 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0380 tsec 7.1290 #GCMRL# 309 dt 36.288000 rms 0.615 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1250 tsec 7.3700 #GCMRL# 310 dt 36.288000 rms 0.614 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4210 tsec 5.3060 #GCMRL# 311 dt 36.288000 rms 0.613 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7560 tsec 6.7650 #GCMRL# 312 dt 36.288000 rms 0.612 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1240 tsec 6.1870 #GCMRL# 313 dt 36.288000 rms 0.612 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3990 tsec 6.3240 #GCMRL# 314 dt 18.144000 rms 0.612 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4980 tsec 6.1600 #GCMRL# 315 dt 9.072000 rms 0.612 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1580 tsec 7.0400 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.61156) vs oldopt=(dt=1.62,rms=0.611561) #GCMRL# 316 dt 2.268000 rms 0.612 0.000% neg 0 invalid 762 tFOTS 10.2600 tGradient 4.3320 tsec 15.5380 #GCMRL# 317 dt 2.268000 rms 0.612 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8810 tsec 6.9000 #GCMRL# 318 dt 0.141750 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4900 tsec 9.0680 #GCMRL# 319 dt 0.070875 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8580 tsec 6.8970 #GCMRL# 320 dt 0.035437 rms 0.612 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0650 tsec 6.8220 #GCAMreg# pass 0 level1 4 level2 1 tsec 948.593 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.612698 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.611084) vs oldopt=(dt=103.68,rms=0.611178) #GCMRL# 322 dt 62.208000 rms 0.611 0.263% neg 0 invalid 762 tFOTS 11.4450 tGradient 4.7730 tsec 17.0550 #GCMRL# 323 dt 103.680000 rms 0.611 0.056% neg 0 invalid 762 tFOTS 10.9270 tGradient 3.9150 tsec 15.6980 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.610609) vs oldopt=(dt=103.68,rms=0.610613) #GCMRL# 324 dt 124.416000 rms 0.611 0.000% neg 0 invalid 762 tFOTS 11.2400 tGradient 4.3690 tsec 16.6230 #GCMRL# 325 dt 124.416000 rms 0.610 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0030 tsec 5.9220 #GCMRL# 326 dt 124.416000 rms 0.610 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8560 tsec 5.8620 #GCMRL# 327 dt 124.416000 rms 0.610 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1370 tsec 6.0270 #GCMRL# 328 dt 124.416000 rms 0.609 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5220 tsec 6.3880 #GCMRL# 329 dt 124.416000 rms 0.608 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3660 tsec 6.3680 #GCMRL# 330 dt 124.416000 rms 0.607 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3570 tsec 6.4280 #GCMRL# 331 dt 124.416000 rms 0.607 0.145% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8930 tsec 6.9040 #GCMRL# 332 dt 124.416000 rms 0.606 0.166% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4150 tsec 6.3830 #GCMRL# 333 dt 124.416000 rms 0.604 0.220% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2070 tsec 5.9750 #GCMRL# 334 dt 124.416000 rms 0.603 0.147% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4530 tsec 5.3060 #GCMRL# 335 dt 124.416000 rms 0.602 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4750 tsec 5.3030 #GCMRL# 336 dt 124.416000 rms 0.601 0.196% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1770 tsec 5.0180 #GCMRL# 337 dt 124.416000 rms 0.600 0.185% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4300 tsec 5.2190 #GCMRL# 338 dt 124.416000 rms 0.599 0.167% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6900 tsec 5.4890 #GCMRL# 339 dt 124.416000 rms 0.598 0.221% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8480 tsec 4.7580 #GCMRL# 340 dt 124.416000 rms 0.597 0.185% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8520 tsec 4.6400 #GCMRL# 341 dt 124.416000 rms 0.596 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0960 tsec 4.8630 #GCMRL# 342 dt 124.416000 rms 0.595 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8930 tsec 4.6650 #GCMRL# 343 dt 124.416000 rms 0.594 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8020 tsec 4.6390 #GCMRL# 344 dt 124.416000 rms 0.594 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9830 tsec 4.8070 #GCMRL# 345 dt 124.416000 rms 0.592 0.189% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1070 tsec 4.8360 #GCMRL# 346 dt 124.416000 rms 0.592 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9450 tsec 4.8810 #GCMRL# 347 dt 124.416000 rms 0.591 0.173% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0120 tsec 4.8090 #GCMRL# 348 dt 124.416000 rms 0.590 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0390 tsec 4.8130 #GCMRL# 349 dt 124.416000 rms 0.590 -0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0630 tsec 5.5830 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.589833) vs oldopt=(dt=25.92,rms=0.589835) #GCMRL# 350 dt 31.104000 rms 0.590 0.008% neg 0 invalid 762 tFOTS 9.7350 tGradient 4.6800 tsec 15.3330 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.58974) vs oldopt=(dt=103.68,rms=0.589755) #GCMRL# 351 dt 82.944000 rms 0.590 0.016% neg 0 invalid 762 tFOTS 10.8530 tGradient 4.4920 tsec 16.1290 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.589501) vs oldopt=(dt=103.68,rms=0.589526) #GCMRL# 352 dt 145.152000 rms 0.590 0.041% neg 0 invalid 762 tFOTS 9.9590 tGradient 4.4600 tsec 15.1560 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.605848 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.601548) vs oldopt=(dt=32,rms=0.601754) #GCMRL# 354 dt 44.800000 rms 0.602 0.710% neg 0 invalid 762 tFOTS 9.4730 tGradient 3.8550 tsec 13.9620 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.593408) vs oldopt=(dt=32,rms=0.595512) #GCMRL# 355 dt 44.800000 rms 0.593 1.353% neg 0 invalid 762 tFOTS 9.5540 tGradient 3.2430 tsec 13.5090 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.590055) vs oldopt=(dt=32,rms=0.590864) #GCMRL# 356 dt 44.800000 rms 0.590 0.565% neg 0 invalid 762 tFOTS 9.0500 tGradient 3.2710 tsec 12.9820 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.584607) vs oldopt=(dt=32,rms=0.585956) #GCMRL# 357 dt 44.800000 rms 0.585 0.923% neg 0 invalid 762 tFOTS 8.9350 tGradient 3.4950 tsec 13.0610 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.582577) vs oldopt=(dt=32,rms=0.58294) #GCMRL# 358 dt 44.800000 rms 0.583 0.347% neg 0 invalid 762 tFOTS 9.4460 tGradient 3.1920 tsec 13.3930 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.578859) vs oldopt=(dt=32,rms=0.57929) #GCMRL# 359 dt 38.400000 rms 0.579 0.638% neg 0 invalid 762 tFOTS 9.3950 tGradient 3.2880 tsec 13.3430 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.576911) vs oldopt=(dt=32,rms=0.577223) #GCMRL# 360 dt 44.800000 rms 0.577 0.336% neg 0 invalid 762 tFOTS 8.7190 tGradient 3.1350 tsec 12.4890 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.573938) vs oldopt=(dt=32,rms=0.574408) #GCMRL# 361 dt 44.800000 rms 0.574 0.515% neg 0 invalid 762 tFOTS 8.7150 tGradient 3.1900 tsec 12.6260 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.572531) vs oldopt=(dt=32,rms=0.572565) #GCMRL# 362 dt 38.400000 rms 0.573 0.245% neg 0 invalid 762 tFOTS 9.5260 tGradient 3.3110 tsec 13.5770 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.569884) vs oldopt=(dt=32,rms=0.570303) #GCMRL# 363 dt 44.800000 rms 0.570 0.462% neg 0 invalid 762 tFOTS 9.3420 tGradient 3.6420 tsec 13.6750 #GCMRL# 364 dt 32.000000 rms 0.569 0.155% neg 0 invalid 762 tFOTS 9.3850 tGradient 2.9660 tsec 13.0840 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.566849) vs oldopt=(dt=32,rms=0.567292) #GCMRL# 365 dt 44.800000 rms 0.567 0.378% neg 0 invalid 762 tFOTS 9.0830 tGradient 3.2530 tsec 13.0290 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.566205) vs oldopt=(dt=32,rms=0.566213) #GCMRL# 366 dt 38.400000 rms 0.566 0.114% neg 0 invalid 762 tFOTS 9.3890 tGradient 2.9420 tsec 13.1590 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.565971) vs oldopt=(dt=2,rms=0.566023) #GCMRL# 367 dt 2.800000 rms 0.566 0.000% neg 0 invalid 762 tFOTS 8.3130 tGradient 3.4270 tsec 12.7450 #GCMRL# 368 dt 2.800000 rms 0.566 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7540 tsec 4.6430 #GCMRL# 369 dt 1.400000 rms 0.566 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1540 tsec 4.4190 #GCMRL# 370 dt 0.350000 rms 0.566 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3070 tsec 5.3110 #FOTS# QuadFit found better minimum quadopt=(dt=0.175,rms=0.565684) vs oldopt=(dt=0.125,rms=0.565686) #GCMRL# 371 dt 0.175000 rms 0.566 0.000% neg 0 invalid 762 tFOTS 7.9980 tGradient 4.2110 tsec 13.0520 #GCMRL# 372 dt 0.087500 rms 0.566 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0090 tsec 4.5840 #GCMRL# 373 dt 0.043750 rms 0.566 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3090 tsec 5.1030 #GCMRL# 374 dt 0.021875 rms 0.566 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7460 tsec 5.6450 #GCAMreg# pass 0 level1 3 level2 1 tsec 237.105 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.566423 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.564802) vs oldopt=(dt=32,rms=0.564856) #GCMRL# 376 dt 25.600000 rms 0.565 0.286% neg 0 invalid 762 tFOTS 10.3580 tGradient 3.9030 tsec 15.0140 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.563994) vs oldopt=(dt=32,rms=0.564094) #GCMRL# 377 dt 44.800000 rms 0.564 0.143% neg 0 invalid 762 tFOTS 11.5960 tGradient 3.6380 tsec 15.9760 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.562658) vs oldopt=(dt=32,rms=0.562982) #GCMRL# 378 dt 44.800000 rms 0.563 0.237% neg 0 invalid 762 tFOTS 11.8230 tGradient 3.9740 tsec 16.7630 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.561989) vs oldopt=(dt=32,rms=0.562074) #GCMRL# 379 dt 44.800000 rms 0.562 0.119% neg 0 invalid 762 tFOTS 11.2000 tGradient 4.5860 tsec 16.6610 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.560774) vs oldopt=(dt=32,rms=0.560854) #GCMRL# 380 dt 44.800000 rms 0.561 0.216% neg 0 invalid 762 tFOTS 12.4490 tGradient 5.1280 tsec 18.3010 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.560205) vs oldopt=(dt=32,rms=0.560282) #GCMRL# 381 dt 25.600000 rms 0.560 0.102% neg 0 invalid 762 tFOTS 11.5470 tGradient 4.5910 tsec 17.0490 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.559131) vs oldopt=(dt=32,rms=0.559322) #GCMRL# 382 dt 44.800000 rms 0.559 0.192% neg 0 invalid 762 tFOTS 12.3420 tGradient 4.8950 tsec 18.1400 #GCMRL# 383 dt 32.000000 rms 0.559 0.083% neg 0 invalid 762 tFOTS 12.3360 tGradient 3.9400 tsec 17.3580 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.557767) vs oldopt=(dt=32,rms=0.557781) #GCMRL# 384 dt 38.400000 rms 0.558 0.161% neg 0 invalid 762 tFOTS 12.5100 tGradient 4.4370 tsec 18.0510 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.557437) vs oldopt=(dt=8,rms=0.557521) #GCMRL# 385 dt 11.200000 rms 0.557 0.059% neg 0 invalid 762 tFOTS 12.0490 tGradient 4.8710 tsec 17.7550 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.556746) vs oldopt=(dt=32,rms=0.556843) #GCMRL# 386 dt 44.800000 rms 0.557 0.124% neg 0 invalid 762 tFOTS 11.7370 tGradient 3.9960 tsec 16.8160 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.555843) vs oldopt=(dt=32,rms=0.555857) #GCMRL# 387 dt 38.400000 rms 0.556 0.162% neg 0 invalid 762 tFOTS 13.8620 tGradient 5.0350 tsec 19.9140 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.555376) vs oldopt=(dt=32,rms=0.555432) #GCMRL# 388 dt 25.600000 rms 0.555 0.084% neg 0 invalid 762 tFOTS 12.7170 tGradient 4.5110 tsec 18.0740 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.55436) vs oldopt=(dt=32,rms=0.554517) #GCMRL# 389 dt 44.800000 rms 0.554 0.183% neg 0 invalid 762 tFOTS 13.8880 tGradient 4.5190 tsec 19.3650 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.55405) vs oldopt=(dt=32,rms=0.554091) #GCMRL# 390 dt 25.600000 rms 0.554 0.056% neg 0 invalid 762 tFOTS 12.7460 tGradient 5.1990 tsec 18.9780 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.553131) vs oldopt=(dt=32,rms=0.553259) #GCMRL# 391 dt 44.800000 rms 0.553 0.166% neg 0 invalid 762 tFOTS 11.8820 tGradient 4.9260 tsec 17.9990 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.552835) vs oldopt=(dt=32,rms=0.552903) #GCMRL# 392 dt 19.200000 rms 0.553 0.053% neg 0 invalid 762 tFOTS 11.8030 tGradient 5.0230 tsec 17.7330 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.551945) vs oldopt=(dt=32,rms=0.552156) #GCMRL# 393 dt 44.800000 rms 0.552 0.161% neg 0 invalid 762 tFOTS 11.1200 tGradient 4.2400 tsec 16.2050 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.551523) vs oldopt=(dt=32,rms=0.551607) #GCMRL# 394 dt 44.800000 rms 0.552 0.076% neg 0 invalid 762 tFOTS 11.6460 tGradient 4.1850 tsec 16.7870 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.551138) vs oldopt=(dt=8,rms=0.551235) #GCMRL# 395 dt 11.200000 rms 0.551 0.070% neg 0 invalid 762 tFOTS 10.9520 tGradient 4.4470 tsec 16.2470 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.551064) vs oldopt=(dt=2,rms=0.551078) #GCMRL# 396 dt 2.800000 rms 0.551 0.000% neg 0 invalid 762 tFOTS 10.1810 tGradient 4.2230 tsec 15.2790 #GCMRL# 397 dt 2.800000 rms 0.551 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7080 tsec 5.9080 #GCMRL# 398 dt 0.350000 rms 0.551 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4830 tsec 7.2240 #GCMRL# 399 dt 0.087500 rms 0.551 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0890 tsec 6.5470 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.585859 #GCMRL# 401 dt 0.000000 rms 0.585 0.110% neg 0 invalid 762 tFOTS 10.7120 tGradient 4.6210 tsec 16.2460 #GCMRL# 402 dt 0.150000 rms 0.585 0.000% neg 0 invalid 762 tFOTS 11.1790 tGradient 4.3270 tsec 17.3480 #GCAMreg# pass 0 level1 2 level2 1 tsec 43.247 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.585859 #GCMRL# 404 dt 0.000000 rms 0.585 0.110% neg 0 invalid 762 tFOTS 11.8950 tGradient 4.8660 tsec 17.5950 #GCMRL# 405 dt 0.150000 rms 0.585 0.000% neg 0 invalid 762 tFOTS 12.9350 tGradient 4.5070 tsec 19.1240 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.652551 #FOTS# QuadFit found better minimum quadopt=(dt=1.024,rms=0.650623) vs oldopt=(dt=1.28,rms=0.650812) #GCMRL# 407 dt 1.024000 rms 0.651 0.295% neg 0 invalid 762 tFOTS 12.6950 tGradient 4.8530 tsec 18.4670 #GCMRL# 408 dt 0.100000 rms 0.651 0.000% neg 0 invalid 762 tFOTS 12.0970 tGradient 4.5090 tsec 17.8080 #GCAMreg# pass 0 level1 1 level2 1 tsec 45.972 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.651209 #GCMRL# 410 dt 0.320000 rms 0.650 0.112% neg 0 invalid 762 tFOTS 11.7350 tGradient 3.9500 tsec 16.7890 #FOTS# QuadFit found better minimum quadopt=(dt=0.016,rms=0.650484) vs oldopt=(dt=0.02,rms=0.650484) #GCMRL# 411 dt 0.016000 rms 0.650 0.000% neg 0 invalid 762 tFOTS 11.0130 tGradient 3.8830 tsec 16.7150 #GCMRL# 412 dt 0.016000 rms 0.650 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2040 tsec 5.0140 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.549517 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.532013) vs oldopt=(dt=0.32,rms=0.536667) #GCMRL# 414 dt 0.448000 rms 0.532 3.185% neg 0 invalid 762 tFOTS 10.6540 tGradient 2.5600 tsec 14.2690 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.52653) vs oldopt=(dt=0.32,rms=0.528087) #GCMRL# 415 dt 0.448000 rms 0.527 1.031% neg 0 invalid 762 tFOTS 12.7230 tGradient 3.2210 tsec 16.7570 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.52333) vs oldopt=(dt=0.32,rms=0.524239) #GCMRL# 416 dt 0.448000 rms 0.523 0.608% neg 0 invalid 762 tFOTS 11.0620 tGradient 2.4380 tsec 14.3990 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.521268) vs oldopt=(dt=0.32,rms=0.521843) #GCMRL# 417 dt 0.448000 rms 0.521 0.394% neg 0 invalid 762 tFOTS 11.2020 tGradient 2.8540 tsec 14.9050 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.51975) vs oldopt=(dt=0.32,rms=0.520169) #GCMRL# 418 dt 0.448000 rms 0.520 0.291% neg 0 invalid 762 tFOTS 10.5270 tGradient 2.3860 tsec 13.9070 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.518783) vs oldopt=(dt=0.32,rms=0.518934) #GCMRL# 419 dt 0.384000 rms 0.519 0.186% neg 0 invalid 762 tFOTS 10.9890 tGradient 2.4530 tsec 14.4630 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.517984) vs oldopt=(dt=0.32,rms=0.518109) #GCMRL# 420 dt 0.384000 rms 0.518 0.154% neg 0 invalid 762 tFOTS 11.7160 tGradient 2.2230 tsec 14.9970 #FOTS# QuadFit found better minimum quadopt=(dt=0.333333,rms=0.51743) vs oldopt=(dt=0.32,rms=0.51745) #GCMRL# 421 dt 0.333333 rms 0.517 0.107% neg 0 invalid 762 tFOTS 11.0190 tGradient 2.1020 tsec 14.2910 #GCMRL# 422 dt 0.320000 rms 0.517 0.098% neg 0 invalid 762 tFOTS 11.5660 tGradient 2.5330 tsec 14.9400 #GCMRL# 423 dt 0.320000 rms 0.517 0.079% neg 0 invalid 762 tFOTS 10.5830 tGradient 2.0710 tsec 13.5840 #GCMRL# 424 dt 0.320000 rms 0.516 0.072% neg 0 invalid 762 tFOTS 10.2270 tGradient 2.4820 tsec 13.6920 #GCMRL# 425 dt 0.320000 rms 0.516 0.062% neg 0 invalid 762 tFOTS 10.5290 tGradient 2.1180 tsec 13.2500 #GCMRL# 426 dt 0.320000 rms 0.516 0.058% neg 0 invalid 762 tFOTS 10.2640 tGradient 1.8580 tsec 12.8970 #GCMRL# 427 dt 0.320000 rms 0.515 0.000% neg 0 invalid 762 tFOTS 9.7600 tGradient 2.0430 tsec 12.6590 #GCMRL# 428 dt 0.320000 rms 0.515 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9990 tsec 3.0060 #GCMRL# 429 dt 0.320000 rms 0.515 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8400 tsec 2.7270 #GCMRL# 430 dt 0.320000 rms 0.514 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6260 tsec 4.1150 #GCMRL# 431 dt 0.320000 rms 0.514 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8420 tsec 2.7440 #GCMRL# 432 dt 0.320000 rms 0.514 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0280 tsec 3.2520 #GCMRL# 433 dt 0.320000 rms 0.514 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9830 tsec 2.9400 #GCMRL# 434 dt 0.320000 rms 0.514 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0520 tsec 3.6970 #GCMRL# 435 dt 0.320000 rms 0.513 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8810 tsec 3.1920 #GCMRL# 436 dt 0.320000 rms 0.513 0.000% neg 0 invalid 762 tFOTS 9.7370 tGradient 1.9640 tsec 12.5780 #GCMRL# 437 dt 0.320000 rms 0.513 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0130 tsec 2.7870 #GCMRL# 438 dt 0.320000 rms 0.513 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1050 tsec 2.9360 #GCMRL# 439 dt 0.160000 rms 0.513 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9400 tsec 3.7450 #GCMRL# 440 dt 0.160000 rms 0.513 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1920 tsec 2.8840 #GCMRL# 441 dt 0.160000 rms 0.513 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1330 tsec 3.0740 #GCMRL# 442 dt 0.160000 rms 0.513 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0030 tsec 2.9160 #GCMRL# 443 dt 0.160000 rms 0.513 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4730 tsec 3.2750 #GCMRL# 444 dt 0.160000 rms 0.512 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7060 tsec 2.3900 #GCMRL# 445 dt 0.160000 rms 0.512 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8500 tsec 2.6150 #GCMRL# 446 dt 0.160000 rms 0.512 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6420 tsec 2.2820 #GCMRL# 447 dt 0.160000 rms 0.512 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8690 tsec 2.5920 #GCMRL# 448 dt 0.160000 rms 0.512 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7990 tsec 3.3460 #GCMRL# 449 dt 0.160000 rms 0.512 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0320 tsec 2.7990 #GCMRL# 450 dt 0.160000 rms 0.512 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3080 tsec 3.1380 #GCMRL# 451 dt 0.160000 rms 0.512 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8810 tsec 2.6520 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.5119) vs oldopt=(dt=0.08,rms=0.511902) #GCAMreg# pass 0 level1 0 level2 1 tsec 296.845 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.512485 #FOTS# QuadFit found better minimum quadopt=(dt=0.21875,rms=0.509653) vs oldopt=(dt=0.08,rms=0.511067) #GCMRL# 453 dt 0.218750 rms 0.510 0.553% neg 0 invalid 762 tFOTS 8.5370 tGradient 1.9970 tsec 11.1270 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.508985) vs oldopt=(dt=0.08,rms=0.509172) #GCMRL# 454 dt 0.112000 rms 0.509 0.131% neg 0 invalid 762 tFOTS 7.9150 tGradient 2.3030 tsec 10.8350 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.508483) vs oldopt=(dt=0.08,rms=0.508629) #GCMRL# 455 dt 0.112000 rms 0.508 0.099% neg 0 invalid 762 tFOTS 8.2390 tGradient 1.8420 tsec 11.0810 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.508077) vs oldopt=(dt=0.08,rms=0.50819) #GCMRL# 456 dt 0.112000 rms 0.508 0.080% neg 0 invalid 762 tFOTS 8.8650 tGradient 1.9150 tsec 11.4540 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.507781) vs oldopt=(dt=0.08,rms=0.507868) #GCMRL# 457 dt 0.112000 rms 0.508 0.058% neg 0 invalid 762 tFOTS 8.0020 tGradient 1.4470 tsec 10.1280 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.50755) vs oldopt=(dt=0.08,rms=0.507617) #GCMRL# 458 dt 0.112000 rms 0.508 0.000% neg 0 invalid 762 tFOTS 8.5660 tGradient 2.0270 tsec 11.3710 #GCMRL# 459 dt 0.112000 rms 0.507 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6770 tsec 2.4160 #GCMRL# 460 dt 0.112000 rms 0.507 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9410 tsec 2.7410 #GCMRL# 461 dt 0.112000 rms 0.507 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0250 tsec 2.8520 #GCMRL# 462 dt 0.112000 rms 0.506 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8530 tsec 2.7370 #GCMRL# 463 dt 0.112000 rms 0.506 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1570 tsec 2.9470 #GCMRL# 464 dt 0.112000 rms 0.506 -0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7480 tsec 3.2050 GCAMregister done in 83.2016 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.504136 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.503486) vs oldopt=(dt=23.12,rms=0.503493) #GCMRL# 466 dt 32.368000 rms 0.503 0.129% neg 0 invalid 762 tFOTS 13.0360 tGradient 3.5610 tsec 17.3320 #FOTS# QuadFit found better minimum quadopt=(dt=18.496,rms=0.503484) vs oldopt=(dt=23.12,rms=0.503485) #GCMRL# 467 dt 18.496000 rms 0.503 0.000% neg 0 invalid 762 tFOTS 11.5840 tGradient 4.0210 tsec 16.2980 #GCAMreg# pass 0 level1 5 level2 1 tsec 42.716 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.504077 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.503057) vs oldopt=(dt=92.48,rms=0.503135) #GCMRL# 469 dt 129.472000 rms 0.503 0.202% neg 0 invalid 762 tFOTS 11.5640 tGradient 3.8090 tsec 16.1880 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.502703) vs oldopt=(dt=369.92,rms=0.502784) #GCMRL# 470 dt 221.952000 rms 0.503 0.000% neg 0 invalid 762 tFOTS 10.5230 tGradient 4.2910 tsec 15.5470 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.503335 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.501648) vs oldopt=(dt=25.92,rms=0.501847) #GCMRL# 472 dt 36.288000 rms 0.502 0.335% neg 0 invalid 762 tFOTS 12.2510 tGradient 4.0600 tsec 16.9740 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.500879) vs oldopt=(dt=103.68,rms=0.500976) #GCMRL# 473 dt 82.944000 rms 0.501 0.000% neg 0 invalid 762 tFOTS 10.8720 tGradient 2.9500 tsec 14.5620 #GCMRL# 474 dt 82.944000 rms 0.500 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3540 tsec 4.0070 #GCMRL# 475 dt 82.944000 rms 0.499 0.171% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0770 tsec 3.7150 #GCMRL# 476 dt 82.944000 rms 0.499 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8970 tsec 3.7780 #GCMRL# 477 dt 82.944000 rms 0.499 -0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6880 tsec 4.2190 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.498016) vs oldopt=(dt=103.68,rms=0.498198) #GCMRL# 478 dt 145.152000 rms 0.498 0.200% neg 0 invalid 762 tFOTS 10.9550 tGradient 3.0840 tsec 14.7750 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.497591) vs oldopt=(dt=25.92,rms=0.497666) #GCAMreg# pass 0 level1 4 level2 1 tsec 80.486 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.498213 #FOTS# QuadFit found better minimum quadopt=(dt=99.3502,rms=0.495058) vs oldopt=(dt=103.68,rms=0.495066) #GCMRL# 480 dt 99.350181 rms 0.495 0.633% neg 0 invalid 762 tFOTS 11.1470 tGradient 3.3570 tsec 15.3220 #FOTS# QuadFit found better minimum quadopt=(dt=79.7538,rms=0.494171) vs oldopt=(dt=103.68,rms=0.494243) #GCMRL# 481 dt 79.753846 rms 0.494 0.000% neg 0 invalid 762 tFOTS 11.5200 tGradient 3.8070 tsec 16.1060 #GCMRL# 482 dt 79.753846 rms 0.494 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1540 tsec 3.8570 #GCMRL# 483 dt 79.753846 rms 0.493 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3300 tsec 4.2270 #GCMRL# 484 dt 79.753846 rms 0.492 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0590 tsec 3.7220 #GCMRL# 485 dt 79.753846 rms 0.492 0.111% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1370 tsec 3.9340 #GCMRL# 486 dt 79.753846 rms 0.491 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9940 tsec 3.6440 #GCMRL# 487 dt 79.753846 rms 0.491 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0030 tsec 3.5940 #GCMRL# 488 dt 79.753846 rms 0.490 0.164% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6710 tsec 3.2420 #GCMRL# 489 dt 79.753846 rms 0.490 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6280 tsec 3.2870 #GCMRL# 490 dt 79.753846 rms 0.489 0.201% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7960 tsec 3.5550 #GCMRL# 491 dt 79.753846 rms 0.488 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3560 tsec 4.0670 #GCMRL# 492 dt 79.753846 rms 0.488 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6740 tsec 4.5790 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.487378) vs oldopt=(dt=25.92,rms=0.487428) #GCMRL# 493 dt 36.288000 rms 0.487 0.080% neg 0 invalid 762 tFOTS 10.1650 tGradient 3.2850 tsec 14.2690 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.487356) vs oldopt=(dt=25.92,rms=0.487358) #GCMRL# 494 dt 36.288000 rms 0.487 0.000% neg 0 invalid 762 tFOTS 10.0210 tGradient 3.1400 tsec 14.1940 #GCMRL# 495 dt 36.288000 rms 0.487 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3800 tsec 4.1510 #GCMRL# 496 dt 36.288000 rms 0.487 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2190 tsec 3.8690 #GCMRL# 497 dt 36.288000 rms 0.487 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4730 tsec 3.0400 #GCMRL# 498 dt 36.288000 rms 0.487 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8660 tsec 3.5620 #GCMRL# 499 dt 36.288000 rms 0.487 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1200 tsec 3.7980 #GCMRL# 500 dt 36.288000 rms 0.487 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9870 tsec 3.6220 #GCMRL# 501 dt 36.288000 rms 0.487 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8180 tsec 3.4640 #GCMRL# 502 dt 36.288000 rms 0.487 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6990 tsec 3.3420 #GCMRL# 503 dt 36.288000 rms 0.487 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9030 tsec 3.5800 #GCMRL# 504 dt 36.288000 rms 0.487 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2620 tsec 4.1260 #GCMRL# 505 dt 36.288000 rms 0.487 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4650 tsec 4.3320 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.487824 #GCMRL# 507 dt 32.000000 rms 0.485 0.480% neg 0 invalid 762 tFOTS 12.3680 tGradient 3.2430 tsec 16.5260 #FOTS# QuadFit found better minimum quadopt=(dt=88.2162,rms=0.483366) vs oldopt=(dt=128,rms=0.48387) iter 0, gcam->neg = 45 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 508 dt 88.216216 rms 0.484 0.404% neg 0 invalid 762 tFOTS 12.7620 tGradient 4.0350 tsec 35.1160 iter 0, gcam->neg = 8 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 509 dt 32.000000 rms 0.482 0.000% neg 0 invalid 762 tFOTS 11.3320 tGradient 2.5790 tsec 27.6400 iter 0, gcam->neg = 5 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 510 dt 32.000000 rms 0.481 0.218% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9200 tsec 15.3170 iter 0, gcam->neg = 59 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 511 dt 32.000000 rms 0.480 0.317% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4270 tsec 16.9800 iter 0, gcam->neg = 29 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 512 dt 32.000000 rms 0.479 0.226% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0840 tsec 21.0700 iter 0, gcam->neg = 120 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 513 dt 32.000000 rms 0.477 0.304% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0340 tsec 21.5840 iter 0, gcam->neg = 228 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 514 dt 32.000000 rms 0.476 0.257% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9560 tsec 20.6610 iter 0, gcam->neg = 377 after 33 iterations, nbhd size=2, neg = 0 #GCMRL# 515 dt 32.000000 rms 0.476 -0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7670 tsec 33.8080 #FOTS# QuadFit found better minimum quadopt=(dt=23.2038,rms=0.475403) vs oldopt=(dt=32,rms=0.475588) iter 0, gcam->neg = 29 after 20 iterations, nbhd size=2, neg = 0 #GCMRL# 516 dt 23.203791 rms 0.476 0.075% neg 0 invalid 762 tFOTS 12.2580 tGradient 3.4960 tsec 32.1970 iter 0, gcam->neg = 18 after 16 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 271.307 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.476263 #FOTS# QuadFit found better minimum quadopt=(dt=44.5517,rms=0.472451) vs oldopt=(dt=32,rms=0.472616) iter 0, gcam->neg = 16 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 518 dt 44.551724 rms 0.472 0.798% neg 0 invalid 762 tFOTS 10.2160 tGradient 2.8660 tsec 25.4430 #FOTS# QuadFit found better minimum quadopt=(dt=24.7407,rms=0.471278) vs oldopt=(dt=32,rms=0.471421) iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 519 dt 24.740741 rms 0.471 0.251% neg 0 invalid 762 tFOTS 9.1970 tGradient 2.6620 tsec 16.4640 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.470443) vs oldopt=(dt=32,rms=0.470453) #GCMRL# 520 dt 25.600000 rms 0.470 0.000% neg 0 invalid 762 tFOTS 10.1940 tGradient 2.9880 tsec 13.9200 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 521 dt 25.600000 rms 0.470 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3660 tsec 5.2560 iter 0, gcam->neg = 13 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 522 dt 25.600000 rms 0.469 0.187% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8010 tsec 12.7740 iter 0, gcam->neg = 40 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 523 dt 25.600000 rms 0.468 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8450 tsec 15.2290 iter 0, gcam->neg = 72 after 25 iterations, nbhd size=1, neg = 0 #GCMRL# 524 dt 25.600000 rms 0.468 -0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6480 tsec 20.3910 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.468252) vs oldopt=(dt=8,rms=0.468268) iter 0, gcam->neg = 3 after 12 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.474011 #FOTS# QuadFit found better minimum quadopt=(dt=5,rms=0.472956) vs oldopt=(dt=2.88,rms=0.47303) iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 526 dt 5.000000 rms 0.473 0.182% neg 0 invalid 762 tFOTS 10.9070 tGradient 2.8240 tsec 23.6730 #FOTS# QuadFit found better minimum quadopt=(dt=8.25806,rms=0.472523) vs oldopt=(dt=11.52,rms=0.47263) iter 0, gcam->neg = 18 after 21 iterations, nbhd size=1, neg = 0 #GCMRL# 527 dt 8.258065 rms 0.473 0.000% neg 0 invalid 762 tFOTS 10.9710 tGradient 2.6030 tsec 28.2900 iter 0, gcam->neg = 45 after 10 iterations, nbhd size=0, neg = 0 #GCMRL# 528 dt 8.258065 rms 0.472 0.207% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4510 tsec 11.1520 iter 0, gcam->neg = 188 after 23 iterations, nbhd size=1, neg = 0 #GCMRL# 529 dt 8.258065 rms 0.472 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1910 tsec 18.7960 iter 0, gcam->neg = 167 after 22 iterations, nbhd size=1, neg = 0 #GCMRL# 530 dt 8.258065 rms 0.471 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4590 tsec 18.4290 iter 0, gcam->neg = 229 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 531 dt 8.258065 rms 0.470 0.260% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3360 tsec 16.3930 iter 0, gcam->neg = 387 after 22 iterations, nbhd size=1, neg = 0 #GCMRL# 532 dt 8.258065 rms 0.469 0.235% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7050 tsec 17.9740 iter 0, gcam->neg = 488 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 533 dt 8.258065 rms 0.467 0.448% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8310 tsec 16.7110 iter 0, gcam->neg = 555 after 26 iterations, nbhd size=1, neg = 0 #GCMRL# 534 dt 8.258065 rms 0.466 0.268% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7730 tsec 22.8330 iter 0, gcam->neg = 602 after 24 iterations, nbhd size=1, neg = 0 #GCMRL# 535 dt 8.258065 rms 0.465 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7930 tsec 22.3740 iter 0, gcam->neg = 675 after 21 iterations, nbhd size=1, neg = 0 #GCMRL# 536 dt 8.258065 rms 0.464 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0160 tsec 18.1130 iter 0, gcam->neg = 815 after 24 iterations, nbhd size=1, neg = 0 #GCMRL# 537 dt 8.258065 rms 0.464 -0.267% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1290 tsec 22.1830 #FOTS# QuadFit found better minimum quadopt=(dt=7.74194,rms=0.464155) vs oldopt=(dt=11.52,rms=0.464238) iter 0, gcam->neg = 84 after 18 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 270.483 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.465022 #FOTS# QuadFit found better minimum quadopt=(dt=12.2822,rms=0.462519) vs oldopt=(dt=11.52,rms=0.462528) iter 0, gcam->neg = 102 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 539 dt 12.282158 rms 0.463 0.503% neg 0 invalid 762 tFOTS 10.3050 tGradient 2.7080 tsec 25.4250 #FOTS# QuadFit found better minimum quadopt=(dt=16.128,rms=0.461426) vs oldopt=(dt=11.52,rms=0.461544) iter 0, gcam->neg = 125 after 22 iterations, nbhd size=1, neg = 0 #GCMRL# 540 dt 16.128000 rms 0.463 0.000% neg 0 invalid 762 tFOTS 9.3380 tGradient 2.7160 tsec 28.8420 iter 0, gcam->neg = 203 after 21 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.471396 #GCMRL# 542 dt 0.000000 rms 0.471 0.125% neg 0 invalid 762 tFOTS 9.1240 tGradient 3.1080 tsec 12.8580 #GCAMreg# pass 0 level1 1 level2 1 tsec 30.208 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.471396 #GCMRL# 544 dt 0.000000 rms 0.471 0.125% neg 0 invalid 762 tFOTS 9.0880 tGradient 2.5330 tsec 12.3580 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.457762 #FOTS# QuadFit found better minimum quadopt=(dt=1.58685,rms=0.43158) vs oldopt=(dt=1.28,rms=0.432671) iter 0, gcam->neg = 1934 after 24 iterations, nbhd size=1, neg = 0 #GCMRL# 546 dt 1.586854 rms 0.431 5.843% neg 0 invalid 762 tFOTS 10.5670 tGradient 1.4220 tsec 30.6400 #GCMRL# 547 dt 0.000013 rms 0.431 0.000% neg 0 invalid 762 tFOTS 14.2190 tGradient 1.5220 tsec 16.6410 #GCAMreg# pass 0 level1 0 level2 1 tsec 53.316 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.431582 #GCMRL# 549 dt 0.000000 rms 0.431 0.149% neg 0 invalid 762 tFOTS 9.8260 tGradient 1.7470 tsec 12.3640 label assignment complete, 0 changed (0.00%) GCAMregister done in 20.0547 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.419938 #GCAMreg# pass 0 level1 5 level2 1 tsec 14.429 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.419938 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.419888) vs oldopt=(dt=92.48,rms=0.419888) #GCMRL# 552 dt 73.984000 rms 0.420 0.012% neg 0 invalid 762 tFOTS 8.2120 tGradient 2.1750 tsec 11.0160 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.41986) vs oldopt=(dt=92.48,rms=0.419864) iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 553 dt 129.472000 rms 0.420 0.000% neg 0 invalid 762 tFOTS 8.8280 tGradient 2.2290 tsec 12.5860 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 554 dt 129.472000 rms 0.420 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4300 tsec 4.1430 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.41998 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.41993) vs oldopt=(dt=6.48,rms=0.419939) iter 0, gcam->neg = 10 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 556 dt 9.072000 rms 0.420 0.010% neg 0 invalid 762 tFOTS 9.0650 tGradient 2.2170 tsec 13.6430 #FOTS# QuadFit found better minimum quadopt=(dt=7.776,rms=0.419923) vs oldopt=(dt=6.48,rms=0.419923) iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 557 dt 7.776000 rms 0.420 0.000% neg 0 invalid 762 tFOTS 7.4570 tGradient 1.7210 tsec 14.4910 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 4 level2 1 tsec 35.412 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.419919 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.419297) vs oldopt=(dt=103.68,rms=0.419322) iter 0, gcam->neg = 32 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 559 dt 124.416000 rms 0.419 0.115% neg 0 invalid 762 tFOTS 7.7430 tGradient 2.3750 tsec 19.2460 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.419222) vs oldopt=(dt=103.68,rms=0.41925) iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 560 dt 82.944000 rms 0.419 0.000% neg 0 invalid 762 tFOTS 7.8420 tGradient 2.2250 tsec 12.5340 iter 0, gcam->neg = 11 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 561 dt 82.944000 rms 0.419 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.8160 tsec 6.9410 iter 0, gcam->neg = 15 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 562 dt 82.944000 rms 0.419 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7010 tsec 4.8620 iter 0, gcam->neg = 17 after 13 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.419216 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.418024) vs oldopt=(dt=32,rms=0.418127) iter 0, gcam->neg = 111 after 22 iterations, nbhd size=1, neg = 0 #GCMRL# 564 dt 25.600000 rms 0.419 0.061% neg 0 invalid 762 tFOTS 8.7090 tGradient 1.5710 tsec 22.6290 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.418137) vs oldopt=(dt=32,rms=0.418162) iter 0, gcam->neg = 127 after 22 iterations, nbhd size=1, neg = 0 #GCMRL# 565 dt 38.400000 rms 0.419 0.000% neg 0 invalid 762 tFOTS 7.3930 tGradient 1.5900 tsec 20.7980 iter 0, gcam->neg = 135 after 18 iterations, nbhd size=1, neg = 0 #GCMRL# 566 dt 38.400000 rms 0.419 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4500 tsec 10.5240 iter 0, gcam->neg = 252 after 24 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 71.008 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.418841 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.416121) vs oldopt=(dt=32,rms=0.416269) iter 0, gcam->neg = 67 after 23 iterations, nbhd size=1, neg = 0 #GCMRL# 568 dt 44.800000 rms 0.416 0.573% neg 0 invalid 762 tFOTS 7.2620 tGradient 1.4530 tsec 20.1310 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.415209) vs oldopt=(dt=32,rms=0.41536) iter 0, gcam->neg = 55 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 569 dt 44.800000 rms 0.416 0.000% neg 0 invalid 762 tFOTS 7.0000 tGradient 1.4860 tsec 18.2400 iter 0, gcam->neg = 40 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 570 dt 44.800000 rms 0.415 0.205% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7530 tsec 15.4670 iter 0, gcam->neg = 130 after 26 iterations, nbhd size=1, neg = 0 #GCMRL# 571 dt 44.800000 rms 0.415 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5200 tsec 17.6500 iter 0, gcam->neg = 178 after 25 iterations, nbhd size=1, neg = 0 #GCMRL# 572 dt 44.800000 rms 0.415 -0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3170 tsec 20.3680 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.414349) vs oldopt=(dt=32,rms=0.414354) iter 0, gcam->neg = 40 after 35 iterations, nbhd size=2, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.417523 #FOTS# QuadFit found better minimum quadopt=(dt=13.3571,rms=0.415161) vs oldopt=(dt=11.52,rms=0.415206) iter 0, gcam->neg = 156 after 27 iterations, nbhd size=1, neg = 0 #GCMRL# 574 dt 13.357143 rms 0.416 0.330% neg 0 invalid 762 tFOTS 10.4380 tGradient 1.8070 tsec 31.3000 #FOTS# QuadFit found better minimum quadopt=(dt=17.3435,rms=0.413915) vs oldopt=(dt=11.52,rms=0.414176) iter 0, gcam->neg = 279 after 26 iterations, nbhd size=1, neg = 0 #GCMRL# 575 dt 17.343511 rms 0.415 0.000% neg 0 invalid 762 tFOTS 8.8440 tGradient 2.0280 tsec 26.0660 iter 0, gcam->neg = 416 after 22 iterations, nbhd size=1, neg = 0 #GCMRL# 576 dt 17.343511 rms 0.415 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6000 tsec 15.8870 iter 0, gcam->neg = 973 after 27 iterations, nbhd size=1, neg = 0 #GCMRL# 577 dt 17.343511 rms 0.414 0.194% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5530 tsec 17.1100 iter 0, gcam->neg = 1485 after 31 iterations, nbhd size=1, neg = 0 #GCMRL# 578 dt 17.343511 rms 0.414 -0.488% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1020 tsec 22.6020 #FOTS# QuadFit found better minimum quadopt=(dt=10.0455,rms=0.413358) vs oldopt=(dt=11.52,rms=0.413377) iter 0, gcam->neg = 174 after 25 iterations, nbhd size=1, neg = 0 #GCMRL# 579 dt 10.045455 rms 0.414 0.007% neg 0 invalid 762 tFOTS 9.0280 tGradient 1.6780 tsec 30.2660 #FOTS# QuadFit found better minimum quadopt=(dt=14.4615,rms=0.413056) vs oldopt=(dt=11.52,rms=0.413108) iter 0, gcam->neg = 228 after 29 iterations, nbhd size=1, neg = 0 #GCMRL# 580 dt 14.461538 rms 0.413 0.227% neg 0 invalid 762 tFOTS 9.9070 tGradient 1.5880 tsec 32.9170 #FOTS# QuadFit found better minimum quadopt=(dt=8.4,rms=0.412964) vs oldopt=(dt=2.88,rms=0.413041) iter 0, gcam->neg = 112 after 42 iterations, nbhd size=2, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 218.634 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.413213 #FOTS# QuadFit found better minimum quadopt=(dt=13.1687,rms=0.410884) vs oldopt=(dt=11.52,rms=0.410931) iter 0, gcam->neg = 198 after 39 iterations, nbhd size=2, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.420802 #FOTS# QuadFit found better minimum quadopt=(dt=6.25e-05,rms=0.420802) vs oldopt=(dt=7.8125e-05,rms=0.420802) #GCMRL# 583 dt 0.000063 rms 0.421 0.000% neg 0 invalid 762 tFOTS 11.5310 tGradient 1.6750 tsec 13.7170 #GCAMreg# pass 0 level1 1 level2 1 tsec 26.051 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.420802 #FOTS# QuadFit found better minimum quadopt=(dt=0.096,rms=0.420797) vs oldopt=(dt=0.08,rms=0.420797) #GCMRL# 585 dt 0.096000 rms 0.421 0.001% neg 0 invalid 762 tFOTS 9.1670 tGradient 1.5530 tsec 11.2570 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.420797) vs oldopt=(dt=0.02,rms=0.420797) #GCMRL# 586 dt 0.028000 rms 0.421 0.000% neg 0 invalid 762 tFOTS 10.0620 tGradient 2.0590 tsec 12.7460 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.408385 #FOTS# QuadFit found better minimum quadopt=(dt=0.824324,rms=0.400296) vs oldopt=(dt=0.32,rms=0.403323) iter 0, gcam->neg = 1256 after 27 iterations, nbhd size=1, neg = 0 #GCMRL# 588 dt 0.824324 rms 0.402 1.498% neg 0 invalid 762 tFOTS 10.0140 tGradient 1.1010 tsec 30.6140 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.40224) vs oldopt=(dt=0.02,rms=0.402243) #GCMRL# 589 dt 0.028000 rms 0.402 0.000% neg 0 invalid 762 tFOTS 9.8360 tGradient 0.9860 tsec 11.4470 #GCMRL# 590 dt 0.028000 rms 0.402 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8270 tsec 1.4030 #GCAMreg# pass 0 level1 0 level2 1 tsec 48.216 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.402231 iter 0, gcam->neg = 8 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 592 dt 0.320000 rms 0.401 0.216% neg 0 invalid 762 tFOTS 9.4500 tGradient 1.2900 tsec 15.8630 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.399971) vs oldopt=(dt=0.32,rms=0.40014) iter 0, gcam->neg = 68 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 593 dt 0.448000 rms 0.400 0.343% neg 0 invalid 762 tFOTS 10.2430 tGradient 0.8250 tsec 19.0040 iter 0, gcam->neg = 26 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 594 dt 0.320000 rms 0.399 0.000% neg 0 invalid 762 tFOTS 8.7870 tGradient 0.7190 tsec 13.0800 iter 0, gcam->neg = 12 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 595 dt 0.320000 rms 0.399 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1420 tsec 3.5450 iter 0, gcam->neg = 49 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 596 dt 0.320000 rms 0.398 0.213% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8040 tsec 6.4640 iter 0, gcam->neg = 73 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 597 dt 0.320000 rms 0.397 0.171% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.1250 tsec 10.3330 iter 0, gcam->neg = 114 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 598 dt 0.320000 rms 0.397 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8760 tsec 7.9930 iter 0, gcam->neg = 145 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 599 dt 0.320000 rms 0.396 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.6840 tsec 11.5080 iter 0, gcam->neg = 184 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 600 dt 0.320000 rms 0.396 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.0190 tsec 12.4720 iter 0, gcam->neg = 192 after 19 iterations, nbhd size=1, neg = 0 #GCMRL# 601 dt 0.320000 rms 0.396 -0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.8650 tsec 14.1670 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.396065) vs oldopt=(dt=0.32,rms=0.396133) #GCMRL# 602 dt 0.192000 rms 0.396 0.057% neg 0 invalid 762 tFOTS 8.7990 tGradient 0.8530 tsec 10.3440 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.395846) vs oldopt=(dt=0.32,rms=0.395851) iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 GCAMregister done in 14.0512 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4870 tmin = 14.3184 Calls to gcamLabelEnergy 4218 tmin = 4.06585 Calls to gcamJacobianEnergy 4870 tmin = 6.51523 Calls to gcamSmoothnessEnergy 4870 tmin = 11.4697 Calls to gcamLogLikelihoodTerm 604 tmin = 3.3172 Calls to gcamLabelTerm 551 tmin = 20.3018 Calls to gcamJacobianTerm 604 tmin = 5.23742 Calls to gcamSmoothnessTerm 604 tmin = 1.74872 Calls to gcamComputeGradient 604 tmin = 57.9377 Calls to gcamComputeMetricProperties 7902 tmin = 14.9332 mri_ca_register took 2 hours, 27 minutes and 29 seconds. #VMPC# mri_ca_register VmPeak 2308956 FSRUNTIME@ mri_ca_register 2.4582 hours 4 threads @#@FSTIME 2024:10:08:12:51:11 mri_ca_register N 9 e 8849.46 S 122.52 U 17574.62 P 199% M 1335200 F 1 R 110932655 W 0 c 2027777 w 143121 I 1576 O 66384 L 41.23 44.50 43.92 @#@FSLOADPOST 2024:10:08:15:18:41 mri_ca_register N 9 41.84 43.56 46.39 #-------------------------------------- #@# SubCort Seg Tue Oct 8 15:18:41 CDT 2024 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname chopin machine x86_64 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.35 Atlas used for the 3D morph was /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.15659 (24) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (24846 voxels, overlap=0.859) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (24846 voxels, peak = 22), gca=22.5 gca peak = 0.20380 (13) mri peak = 0.15834 (24) Right_Lateral_Ventricle (43): linear fit = 1.57 x + 0.0 (22170 voxels, overlap=0.338) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (22170 voxels, peak = 20), gca=19.5 gca peak = 0.26283 (96) mri peak = 0.11429 (103) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (608 voxels, overlap=0.320) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (608 voxels, peak = 103), gca=103.2 gca peak = 0.15814 (97) mri peak = 0.11486 (102) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (494 voxels, overlap=0.503) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (494 voxels, peak = 106), gca=106.2 gca peak = 0.27624 (56) mri peak = 0.12764 (72) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (976 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (976 voxels, peak = 69), gca=68.6 gca peak = 0.28723 (59) mri peak = 0.09116 (72) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (822 voxels, overlap=0.020) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (822 voxels, peak = 73), gca=73.5 gca peak = 0.07623 (103) mri peak = 0.10686 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (18604 voxels, overlap=0.665) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (18604 voxels, peak = 106), gca=105.6 gca peak = 0.07837 (105) mri peak = 0.10596 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (20670 voxels, overlap=0.572) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (20670 voxels, peak = 108), gca=107.6 gca peak = 0.10165 (58) mri peak = 0.05469 (79) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (23578 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (23578 voxels, peak = 78), gca=78.0 gca peak = 0.11113 (58) mri peak = 0.05094 (79) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (24987 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (24987 voxels, peak = 78), gca=78.0 gca peak = 0.27796 (67) mri peak = 0.14026 (88) Right_Caudate (50): linear fit = 1.29 x + 0.0 (1285 voxels, overlap=0.021) Right_Caudate (50): linear fit = 1.29 x + 0.0 (1285 voxels, peak = 87), gca=86.8 gca peak = 0.14473 (69) mri peak = 0.11579 (89) Left_Caudate (11): linear fit = 1.17 x + 0.0 (1042 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.17 x + 0.0 (1042 voxels, peak = 81), gca=81.1 gca peak = 0.14301 (56) mri peak = 0.06462 (72) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (18096 voxels, overlap=0.041) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (18096 voxels, peak = 71), gca=70.8 gca peak = 0.14610 (55) mri peak = 0.06829 (72) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (21428 voxels, overlap=0.018) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (21428 voxels, peak = 70), gca=69.6 gca peak = 0.16309 (85) mri peak = 0.13623 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5515 voxels, overlap=0.426) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5515 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.14731 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4966 voxels, overlap=0.505) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4966 voxels, peak = 89), gca=89.5 gca peak = 0.30461 (58) mri peak = 0.10552 (76) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (408 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (408 voxels, peak = 75), gca=75.1 gca peak = 0.32293 (57) mri peak = 0.10200 (75) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (451 voxels, overlap=0.058) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (451 voxels, peak = 74), gca=74.4 gca peak = 0.11083 (90) mri peak = 0.08410 (93) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (3749 voxels, overlap=0.807) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (3749 voxels, peak = 96), gca=95.9 gca peak = 0.11393 (83) mri peak = 0.06714 (90) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3543 voxels, overlap=0.718) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (3543 voxels, peak = 88), gca=88.4 gca peak = 0.08575 (81) mri peak = 0.13559 (94) Left_Putamen (12): linear fit = 1.17 x + 0.0 (1003 voxels, overlap=0.010) Left_Putamen (12): linear fit = 1.17 x + 0.0 (1003 voxels, peak = 95), gca=95.2 gca peak = 0.08618 (78) mri peak = 0.11850 (93) Right_Putamen (51): linear fit = 1.16 x + 0.0 (1173 voxels, overlap=0.019) Right_Putamen (51): linear fit = 1.16 x + 0.0 (1173 voxels, peak = 91), gca=90.9 gca peak = 0.08005 (78) mri peak = 0.10621 (83) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13567 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13567 voxels, peak = 82), gca=82.3 gca peak = 0.12854 (88) mri peak = 0.10413 (97) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1138 voxels, overlap=0.419) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1138 voxels, peak = 95), gca=95.5 gca peak = 0.15703 (87) mri peak = 0.08047 (96) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1031 voxels, overlap=0.487) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1031 voxels, peak = 96), gca=96.1 gca peak = 0.17522 (25) mri peak = 0.18912 (25) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (535 voxels, overlap=0.931) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (535 voxels, peak = 24), gca=23.9 gca peak = 0.17113 (14) mri peak = 0.20318 (22) Fourth_Ventricle (15): linear fit = 1.40 x + 0.0 (780 voxels, overlap=0.418) Fourth_Ventricle (15): linear fit = 1.40 x + 0.0 (780 voxels, peak = 20), gca=19.7 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.29 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.25 x + 0.0 Left_Putamen too bright - rescaling by 1.008 (from 1.175) to 95.9 (was 95.2) Left_Pallidum too bright - rescaling by 0.974 (from 1.095) to 103.4 (was 106.2) Right_Pallidum too bright - rescaling by 1.002 (from 1.075) to 103.4 (was 103.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15076 (21) mri peak = 0.15659 (24) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (24846 voxels, overlap=0.883) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (24846 voxels, peak = 20), gca=20.5 gca peak = 0.16363 (19) mri peak = 0.15834 (24) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (22170 voxels, overlap=0.643) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (22170 voxels, peak = 20), gca=20.4 gca peak = 0.20537 (103) mri peak = 0.11429 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (608 voxels, overlap=0.976) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (608 voxels, peak = 103), gca=103.0 gca peak = 0.17574 (101) mri peak = 0.11486 (102) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (494 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (494 voxels, peak = 101), gca=101.0 gca peak = 0.23288 (68) mri peak = 0.12764 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (976 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (976 voxels, peak = 68), gca=68.0 gca peak = 0.25756 (70) mri peak = 0.09116 (72) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (822 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (822 voxels, peak = 70), gca=70.0 gca peak = 0.07779 (106) mri peak = 0.10686 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (18604 voxels, overlap=0.764) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (18604 voxels, peak = 106), gca=106.0 gca peak = 0.07733 (107) mri peak = 0.10596 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (20670 voxels, overlap=0.685) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (20670 voxels, peak = 108), gca=107.5 gca peak = 0.07328 (78) mri peak = 0.05469 (79) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (23578 voxels, overlap=0.949) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (23578 voxels, peak = 78), gca=78.0 gca peak = 0.08475 (78) mri peak = 0.05094 (79) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (24987 voxels, overlap=0.957) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (24987 voxels, peak = 77), gca=76.8 gca peak = 0.19515 (87) mri peak = 0.14026 (88) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1285 voxels, overlap=0.998) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1285 voxels, peak = 87), gca=87.0 gca peak = 0.15454 (81) mri peak = 0.11579 (89) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1042 voxels, overlap=0.701) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1042 voxels, peak = 82), gca=82.2 gca peak = 0.10890 (70) mri peak = 0.06462 (72) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (18096 voxels, overlap=0.970) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (18096 voxels, peak = 69), gca=69.0 gca peak = 0.12813 (70) mri peak = 0.06829 (72) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21428 voxels, overlap=0.978) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21428 voxels, peak = 70), gca=70.0 gca peak = 0.15236 (90) mri peak = 0.13623 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5515 voxels, overlap=0.880) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5515 voxels, peak = 90), gca=89.6 gca peak = 0.17066 (90) mri peak = 0.14731 (89) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4966 voxels, overlap=0.876) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4966 voxels, peak = 89), gca=88.7 gca peak = 0.28608 (75) mri peak = 0.10552 (76) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (408 voxels, overlap=0.986) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (408 voxels, peak = 75), gca=75.0 gca peak = 0.26946 (75) mri peak = 0.10200 (75) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (451 voxels, overlap=1.014) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (451 voxels, peak = 75), gca=75.0 gca peak = 0.10503 (94) mri peak = 0.08410 (93) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3749 voxels, overlap=0.974) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3749 voxels, peak = 94), gca=93.5 gca peak = 0.09944 (86) mri peak = 0.06714 (90) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3543 voxels, overlap=0.915) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3543 voxels, peak = 86), gca=85.6 gca peak = 0.08031 (96) mri peak = 0.13559 (94) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1003 voxels, overlap=0.740) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1003 voxels, peak = 96), gca=96.0 gca peak = 0.08491 (90) mri peak = 0.11850 (93) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1173 voxels, overlap=0.773) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1173 voxels, peak = 92), gca=92.2 gca peak = 0.08502 (83) mri peak = 0.10621 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (13567 voxels, overlap=0.675) Brain_Stem (16): linear fit = 1.00 x + 0.0 (13567 voxels, peak = 83), gca=82.6 gca peak = 0.11739 (97) mri peak = 0.10413 (97) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1138 voxels, overlap=0.800) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1138 voxels, peak = 98), gca=98.5 gca peak = 0.15891 (96) mri peak = 0.08047 (96) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1031 voxels, overlap=0.859) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1031 voxels, peak = 96), gca=96.5 gca peak = 0.17536 (26) mri peak = 0.18912 (25) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (535 voxels, overlap=0.852) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (535 voxels, peak = 26), gca=25.6 gca peak = 0.15172 (20) mri peak = 0.20318 (22) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (780 voxels, overlap=0.695) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (780 voxels, peak = 20), gca=20.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.14657 (35) gca peak CSF = 0.18810 (45) gca peak Left_Accumbens_area = 0.59454 (73) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.10623 (35) gca peak Right_Inf_Lat_Vent = 0.22619 (28) gca peak Right_Accumbens_area = 0.29105 (84) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13305 (38) gca peak Fifth_Ventricle = 0.77755 (40) gca peak WM_hypointensities = 0.10699 (78) gca peak non_WM_hypointensities = 0.11377 (42) gca peak Optic_Chiasm = 0.60854 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 Left_Putamen too bright - rescaling by 1.001 (from 1.000) to 96.1 (was 96.0) Right_Pallidum too bright - rescaling by 1.005 (from 1.000) to 103.6 (was 103.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 52933 voxels changed in iteration 0 of unlikely voxel relabeling 171 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 55818 gm and wm labels changed (%36 to gray, %64 to white out of all changed labels) 383 hippocampal voxels changed. 1 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 71083 changed. image ll: -2.114, PF=0.500 pass 2: 16410 changed. image ll: -2.112, PF=0.500 pass 3: 4810 changed. 40822 voxels changed in iteration 0 of unlikely voxel relabeling 177 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 16 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5079 voxels changed in iteration 0 of unlikely voxel relabeling 139 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 4924 voxels changed in iteration 0 of unlikely voxel relabeling 70 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4492 voxels changed in iteration 0 of unlikely voxel relabeling 50 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling !!!!!!!!! ventricle segment 4 with volume 55463 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 2190 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 3 with volume 51767 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 1706 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3394.834566 mri_ca_label stimesec 19.561424 mri_ca_label ru_maxrss 2073032 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 19974828 mri_ca_label ru_majflt 7 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 6896 mri_ca_label ru_oublock 696 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 865 mri_ca_label ru_nivcsw 341277 auto-labeling took 57 minutes and 31 seconds. @#@FSTIME 2024:10:08:15:18:41 mri_ca_label N 10 e 3451.50 S 19.75 U 3394.83 P 98% M 2073032 F 7 R 19974849 W 0 c 341297 w 866 I 6896 O 696 L 41.84 43.56 46.39 @#@FSLOADPOST 2024:10:08:16:16:13 mri_ca_label N 10 78.06 77.95 70.51 #-------------------------------------- #@# CC Seg Tue Oct 8 16:16:13 CDT 2024 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/cc_up.lta PIB23-310_VYr0_Bay3prisma will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/cc_up.lta reading aseg from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.auto_noCCseg.mgz reading norm from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/norm.mgz 35566 voxels in left wm, 41675 in right wm, xrange [121, 132] searching rotation angles z=[-8 6], y=[-10 4] searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 global minimum found at slice 125.6, rotations (-3.07, -0.57) final transformation (x=125.6, yr=-3.067, zr=-0.574): 0.99852 0.01002 -0.05350 6.93003; -0.01001 0.99995 0.00054 13.20755; 0.05350 0.00000 0.99857 19.42913; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 130] in xformed coordinates best xformed slice 127 min_x_fornix = 132 min_x_fornix = 133 min_x_fornix = 133 min_x_fornix = 138 min_x_fornix = 135 cc center is found at 127 116 102 eigenvectors: -0.00052 -0.00668 0.99998; -0.03704 -0.99929 -0.00669; 0.99931 -0.03705 0.00027; writing aseg with callosum to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.auto.mgz... corpus callosum segmentation took 0.9 minutes #VMPC# mri_cc VmPeak 461756 mri_cc done @#@FSTIME 2024:10:08:16:16:13 mri_cc N 7 e 53.24 S 0.72 U 52.45 P 99% M 344968 F 15 R 504140 W 0 c 5441 w 101 I 3544 O 680 L 78.06 77.95 70.51 @#@FSLOADPOST 2024:10:08:16:17:06 mri_cc N 7 67.06 75.27 70.01 #-------------------------------------- #@# Merge ASeg Tue Oct 8 16:17:06 CDT 2024 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Oct 8 16:17:06 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 856 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 108 gm peak at 84 (84), valley at 56 (56) csf peak at 23, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 83 (83), valley at 49 (49) csf peak at 23, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 20 seconds. @#@FSTIME 2024:10:08:16:17:06 mri_normalize N 9 e 202.63 S 2.33 U 213.64 P 106% M 1210780 F 25 R 1200315 W 0 c 21209 w 201 I 5888 O 2752 L 67.06 75.27 70.01 @#@FSLOADPOST 2024:10:08:16:20:29 mri_normalize N 9 68.99 70.37 68.87 #-------------------------------------------- #@# Mask BFS Tue Oct 8 16:20:29 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1599286 voxels in mask (pct= 9.53) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:10:08:16:20:29 mri_mask N 5 e 1.41 S 0.06 U 1.68 P 124% M 74296 F 5 R 20206 W 0 c 187 w 72 I 192 O 2736 L 68.99 70.37 68.87 @#@FSLOADPOST 2024:10:08:16:20:31 mri_mask N 5 68.99 70.37 68.87 #-------------------------------------------- #@# WM Segmentation Tue Oct 8 16:20:31 CDT 2024 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2024:10:08:16:20:31 AntsDenoiseImageFs N 4 e 57.75 S 0.40 U 57.15 P 99% M 351264 F 3 R 244290 W 0 c 5607 w 127 I 40 O 2704 L 68.99 70.37 68.87 @#@FSLOADPOST 2024:10:08:16:21:28 AntsDenoiseImageFs N 4 81.88 73.43 70.00 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (101.0): 101.4 +- 5.8 [79.0 --> 125.0] CCS GM (77.0) : 74.2 +- 14.0 [30.0 --> 95.0] white_mean 101.367 white_sigma 5.84241 gray_mean 74.1778 gray_sigma 13.9943 setting bottom of white matter range wm_low to 88.2 setting top of gray matter range gray_hi to 100.4 wm_low 88.1721 wm_hi 125 gray_low 30 gray_hi 100.367 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 88.1721 wm_hi 125 gray_low 30 gray_hi 100.367 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 100.367, wm_low = 88.1721 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=100.367, wmlow=88.1721 164993 voxels processed (0.98%) 84402 voxels white (0.50%) 80591 voxels non-white (0.48%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=83.1721, gray_hi=100.367, wsize=13 328654 voxels tested (1.96%) 55623 voxels changed (0.33%) 48134 multi-scale searches (0.29%) Recovering bright white MRIrecoverBrightWhite() wm_low 88.1721 wm_hi 125 slack 5.84241 pct_thresh 0.33 intensity_thresh 130.842 nvox_thresh 8.58 34 voxels tested (0.00%) 19 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=83.1721, hithr=100.367 smoothing input volume with sigma = 0.250 156743 voxels tested (0.93%) 17480 voxels changed (0.10%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 2651 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 2797 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 4768 filled MRIfindBrightNonWM(): 205 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:10:08:16:21:29 mri_segment N 5 e 105.80 S 0.45 U 102.97 P 97% M 147020 F 4 R 307127 W 0 c 10284 w 61 I 112 O 784 L 81.88 73.43 70.00 @#@FSLOADPOST 2024:10:08:16:23:14 mri_segment N 5 117.00 86.64 75.05 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.72 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 7984 additional wm voxels added 0 additional wm voxels added SEG EDIT: 176383 voxels turned on, 33572 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:10:08:16:23:14 mri_edit_wm_with_aseg N 5 e 43.56 S 0.60 U 45.49 P 105% M 463680 F 11 R 512206 W 0 c 4509 w 160 I 640 O 736 L 117.00 86.64 75.05 @#@FSLOADPOST 2024:10:08:16:23:58 mri_edit_wm_with_aseg N 5 106.30 87.85 75.99 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 36 found - 36 modified | TOTAL: 36 pass 2 (xy+): 0 found - 36 modified | TOTAL: 36 pass 1 (xy-): 45 found - 45 modified | TOTAL: 81 pass 2 (xy-): 0 found - 45 modified | TOTAL: 81 pass 1 (yz+): 52 found - 52 modified | TOTAL: 133 pass 2 (yz+): 0 found - 52 modified | TOTAL: 133 pass 1 (yz-): 44 found - 44 modified | TOTAL: 177 pass 2 (yz-): 0 found - 44 modified | TOTAL: 177 pass 1 (xz+): 26 found - 26 modified | TOTAL: 203 pass 2 (xz+): 0 found - 26 modified | TOTAL: 203 pass 1 (xz-): 40 found - 40 modified | TOTAL: 243 pass 2 (xz-): 0 found - 40 modified | TOTAL: 243 Iteration Number : 1 pass 1 (+++): 24 found - 24 modified | TOTAL: 24 pass 2 (+++): 0 found - 24 modified | TOTAL: 24 pass 1 (+++): 23 found - 23 modified | TOTAL: 47 pass 2 (+++): 0 found - 23 modified | TOTAL: 47 pass 1 (+++): 21 found - 21 modified | TOTAL: 68 pass 2 (+++): 0 found - 21 modified | TOTAL: 68 pass 1 (+++): 7 found - 7 modified | TOTAL: 75 pass 2 (+++): 0 found - 7 modified | TOTAL: 75 Iteration Number : 1 pass 1 (++): 85 found - 85 modified | TOTAL: 85 pass 2 (++): 0 found - 85 modified | TOTAL: 85 pass 1 (+-): 78 found - 78 modified | TOTAL: 163 pass 2 (+-): 1 found - 79 modified | TOTAL: 164 pass 3 (+-): 0 found - 79 modified | TOTAL: 164 pass 1 (--): 110 found - 110 modified | TOTAL: 274 pass 2 (--): 1 found - 111 modified | TOTAL: 275 pass 3 (--): 0 found - 111 modified | TOTAL: 275 pass 1 (-+): 75 found - 75 modified | TOTAL: 350 pass 2 (-+): 0 found - 75 modified | TOTAL: 350 Iteration Number : 2 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 6 found - 6 modified | TOTAL: 19 pass 2 (xy-): 0 found - 6 modified | TOTAL: 19 pass 1 (yz+): 7 found - 7 modified | TOTAL: 26 pass 2 (yz+): 0 found - 7 modified | TOTAL: 26 pass 1 (yz-): 8 found - 8 modified | TOTAL: 34 pass 2 (yz-): 0 found - 8 modified | TOTAL: 34 pass 1 (xz+): 7 found - 7 modified | TOTAL: 41 pass 2 (xz+): 0 found - 7 modified | TOTAL: 41 pass 1 (xz-): 5 found - 5 modified | TOTAL: 46 pass 2 (xz-): 0 found - 5 modified | TOTAL: 46 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 3 found - 3 modified | TOTAL: 7 pass 2 (+-): 0 found - 3 modified | TOTAL: 7 pass 1 (--): 3 found - 3 modified | TOTAL: 10 pass 2 (--): 0 found - 3 modified | TOTAL: 10 pass 1 (-+): 1 found - 1 modified | TOTAL: 11 pass 2 (-+): 0 found - 1 modified | TOTAL: 11 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 738 (out of 539229: 0.136862) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:10:08:16:23:58 mri_pretess N 4 e 6.83 S 0.05 U 8.42 P 123% M 57348 F 5 R 35852 W 0 c 933 w 52 I 136 O 736 L 106.30 87.85 75.99 @#@FSLOADPOST 2024:10:08:16:24:05 mri_pretess N 4 101.15 87.09 75.81 #-------------------------------------------- #@# Fill Tue Oct 8 16:24:05 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/SubCorticalMassLUT.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01356 -0.00221 0.00230 -2.49489; 0.00289 1.06970 0.23475 -52.21680; 0.00263 -0.20392 0.95871 17.05884; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01356 -0.00221 0.00230 -2.49489; 0.00289 1.06970 0.23475 -52.21680; 0.00263 -0.20392 0.95871 17.05884; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1898 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) need search nearby using seed (127, 120, 155), TAL = (1.0, 27.0, 8.0) talairach voxel to voxel transform 0.98662 0.00151 -0.00274 2.58727; -0.00198 0.89314 -0.21869 50.36283; -0.00313 0.18997 0.99656 -7.08817; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 120, 155) --> (1.0, 27.0, 8.0) done. filling took 1.6 minutes talairach cc position changed to (1.00, 27.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 27.00, 8.00) SRC: (109.89, 123.43, 169.83) search lh wm seed point around talairach space (-17.00, 27.00, 8.00), SRC: (145.40, 123.36, 169.72) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2024:10:08:16:24:05 mri_fill N 10 e 99.15 S 2.41 U 95.95 P 99% M 988476 F 0 R 1348129 W 0 c 10065 w 47 I 8 O 240 L 101.15 87.09 75.81 @#@FSLOADPOST 2024:10:08:16:25:44 mri_fill N 10 62.92 80.08 74.61 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Tue Oct 8 16:25:44 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 4 found - 4 modified | TOTAL: 7 pass 2 (yz+): 0 found - 4 modified | TOTAL: 7 pass 1 (yz-): 7 found - 7 modified | TOTAL: 14 pass 2 (yz-): 0 found - 7 modified | TOTAL: 14 pass 1 (xz+): 0 found - 0 modified | TOTAL: 14 pass 1 (xz-): 2 found - 2 modified | TOTAL: 16 pass 2 (xz-): 0 found - 2 modified | TOTAL: 16 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 2 found - 2 modified | TOTAL: 5 pass 2 (+-): 0 found - 2 modified | TOTAL: 5 pass 1 (--): 1 found - 1 modified | TOTAL: 6 pass 2 (--): 0 found - 1 modified | TOTAL: 6 pass 1 (-+): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 25 (out of 261121: 0.009574) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:10:08:16:25:44 mri_pretess N 4 e 3.99 S 0.05 U 5.83 P 147% M 40540 F 0 R 17427 W 0 c 577 w 50 I 0 O 232 L 62.92 80.08 74.61 @#@FSLOADPOST 2024:10:08:16:25:48 mri_pretess N 4 61.89 79.58 74.47 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.3.2 7.3.2 slice 50: 1208 vertices, 1320 faces slice 60: 6557 vertices, 6796 faces slice 70: 14756 vertices, 15050 faces slice 80: 23387 vertices, 23689 faces slice 90: 32085 vertices, 32375 faces slice 100: 40469 vertices, 40830 faces slice 110: 49985 vertices, 50361 faces slice 120: 59437 vertices, 59810 faces slice 130: 68544 vertices, 68909 faces slice 140: 77329 vertices, 77708 faces slice 150: 86154 vertices, 86516 faces slice 160: 93388 vertices, 93682 faces slice 170: 99820 vertices, 100104 faces slice 180: 105447 vertices, 105683 faces slice 190: 109876 vertices, 110095 faces slice 200: 112575 vertices, 112714 faces slice 210: 112988 vertices, 113064 faces slice 220: 112988 vertices, 113064 faces slice 230: 112988 vertices, 113064 faces slice 240: 112988 vertices, 113064 faces slice 250: 112988 vertices, 113064 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:10:08:16:25:48 mri_tessellate N 3 e 2.54 S 0.00 U 3.27 P 128% M 35740 F 3 R 9388 W 0 c 316 w 88 I 136 O 5304 L 61.89 79.58 74.47 @#@FSLOADPOST 2024:10:08:16:25:51 mri_tessellate N 3 61.89 79.58 74.47 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 112988 voxel in cpt #1: X=-76 [v=112988,e=339192,f=226128] located at (-25.503611, -10.850152, 1.684931) For the whole surface: X=-76 [v=112988,e=339192,f=226128] One single component has been found nothing to do done @#@FSTIME 2024:10:08:16:25:51 mris_extract_main_component N 2 e 1.12 S 0.14 U 1.14 P 115% M 225696 F 8 R 59472 W 0 c 125 w 118 I 248 O 7952 L 61.89 79.58 74.47 @#@FSLOADPOST 2024:10:08:16:25:52 mris_extract_main_component N 2 61.89 79.58 74.47 #-------------------------------------------- #@# Tessellate rh Tue Oct 8 16:25:52 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 8 found - 8 modified | TOTAL: 10 pass 2 (yz+): 0 found - 8 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 1 found - 1 modified | TOTAL: 13 pass 2 (xz+): 0 found - 1 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 14 (out of 260082: 0.005383) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:10:08:16:25:52 mri_pretess N 4 e 2.79 S 0.06 U 4.21 P 152% M 40532 F 0 R 13170 W 0 c 502 w 37 I 0 O 232 L 61.89 79.58 74.47 @#@FSLOADPOST 2024:10:08:16:25:55 mri_pretess N 4 66.94 80.33 74.74 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 50: 741 vertices, 822 faces slice 60: 6077 vertices, 6300 faces slice 70: 13426 vertices, 13695 faces slice 80: 22730 vertices, 23095 faces slice 90: 31789 vertices, 32080 faces slice 100: 40522 vertices, 40846 faces slice 110: 49760 vertices, 50123 faces slice 120: 59053 vertices, 59417 faces slice 130: 68130 vertices, 68494 faces slice 140: 76993 vertices, 77356 faces slice 150: 86002 vertices, 86356 faces slice 160: 94325 vertices, 94652 faces slice 170: 101298 vertices, 101574 faces slice 180: 107552 vertices, 107796 faces slice 190: 112142 vertices, 112357 faces slice 200: 115868 vertices, 116035 faces slice 210: 117128 vertices, 117200 faces slice 220: 117128 vertices, 117200 faces slice 230: 117128 vertices, 117200 faces slice 240: 117128 vertices, 117200 faces slice 250: 117128 vertices, 117200 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:10:08:16:25:55 mri_tessellate N 3 e 2.42 S 0.05 U 3.26 P 136% M 36048 F 0 R 8609 W 0 c 330 w 129 I 0 O 5496 L 66.94 80.33 74.74 @#@FSLOADPOST 2024:10:08:16:25:58 mri_tessellate N 3 64.86 79.68 74.56 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 117128 voxel in cpt #1: X=-72 [v=117128,e=351600,f=234400] located at (29.170771, -8.194898, 2.955715) For the whole surface: X=-72 [v=117128,e=351600,f=234400] One single component has been found nothing to do done @#@FSTIME 2024:10:08:16:25:58 mris_extract_main_component N 2 e 1.11 S 0.17 U 1.16 P 119% M 233552 F 1 R 61724 W 0 c 154 w 315 I 0 O 8248 L 64.86 79.68 74.56 @#@FSLOADPOST 2024:10:08:16:25:59 mris_extract_main_component N 2 64.86 79.68 74.56 #-------------------------------------------- #@# Smooth1 lh Tue Oct 8 16:25:59 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Tue Oct 8 16:25:59 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 2894053 of (2894053 2894056) to complete... Waiting for PID 2894056 of (2894053 2894056) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (2894053 2894056) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Tue Oct 8 16:26:03 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Tue Oct 8 16:26:03 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 2894984 of (2894984 2894987) to complete... Waiting for PID 2894987 of (2894984 2894987) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.8 mm, total surface area = 60879 mm^2 step 000: RMS=0.154 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.070 (target=0.015) step 025: RMS=0.064 (target=0.015) step 030: RMS=0.059 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.055 (target=0.015) step 045: RMS=0.053 (target=0.015) step 050: RMS=0.051 (target=0.015) step 055: RMS=0.052 (target=0.015) step 060: RMS=0.052 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 36.719529 mris_inflate stimesec 1.648615 mris_inflate ru_maxrss 180912 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 721882 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7976 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 13893 mris_inflate ru_nivcsw 3928 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.2 mm, total surface area = 63369 mm^2 step 000: RMS=0.154 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.064 (target=0.015) step 030: RMS=0.060 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.055 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.052 (target=0.015) step 055: RMS=0.052 (target=0.015) step 060: RMS=0.052 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 36.042576 mris_inflate stimesec 1.698216 mris_inflate ru_maxrss 187184 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 715813 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8248 mris_inflate ru_oublock 8272 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 19694 mris_inflate ru_nivcsw 3808 PIDs (2894984 2894987) completed and logs appended. #-------------------------------------------- #@# QSphere lh Tue Oct 8 16:26:23 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Tue Oct 8 16:26:23 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 2899127 of (2899127 2899130) to complete... Waiting for PID 2899130 of (2899127 2899130) to complete... mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 scaling brain by 0.342... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.08 +- 0.61 (0.00-->6.92) (max @ vno 45916 --> 46823) face area 0.03 +- 0.04 (-0.16-->0.58) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.189, avgs=0 005/300: dt: 0.9000, rms radial error=175.931, avgs=0 010/300: dt: 0.9000, rms radial error=175.377, avgs=0 015/300: dt: 0.9000, rms radial error=174.649, avgs=0 020/300: dt: 0.9000, rms radial error=173.819, avgs=0 025/300: dt: 0.9000, rms radial error=172.932, avgs=0 030/300: dt: 0.9000, rms radial error=172.013, avgs=0 035/300: dt: 0.9000, rms radial error=171.077, avgs=0 040/300: dt: 0.9000, rms radial error=170.133, avgs=0 045/300: dt: 0.9000, rms radial error=169.187, avgs=0 050/300: dt: 0.9000, rms radial error=168.246, avgs=0 055/300: dt: 0.9000, rms radial error=167.308, avgs=0 060/300: dt: 0.9000, rms radial error=166.373, avgs=0 065/300: dt: 0.9000, rms radial error=165.442, avgs=0 070/300: dt: 0.9000, rms radial error=164.515, avgs=0 075/300: dt: 0.9000, rms radial error=163.593, avgs=0 080/300: dt: 0.9000, rms radial error=162.676, avgs=0 085/300: dt: 0.9000, rms radial error=161.763, avgs=0 090/300: dt: 0.9000, rms radial error=160.856, avgs=0 095/300: dt: 0.9000, rms radial error=159.953, avgs=0 100/300: dt: 0.9000, rms radial error=159.055, avgs=0 105/300: dt: 0.9000, rms radial error=158.162, avgs=0 110/300: dt: 0.9000, rms radial error=157.274, avgs=0 115/300: dt: 0.9000, rms radial error=156.391, avgs=0 120/300: dt: 0.9000, rms radial error=155.512, avgs=0 125/300: dt: 0.9000, rms radial error=154.639, avgs=0 130/300: dt: 0.9000, rms radial error=153.770, avgs=0 135/300: dt: 0.9000, rms radial error=152.905, avgs=0 140/300: dt: 0.9000, rms radial error=152.046, avgs=0 145/300: dt: 0.9000, rms radial error=151.191, avgs=0 150/300: dt: 0.9000, rms radial error=150.340, avgs=0 155/300: dt: 0.9000, rms radial error=149.495, avgs=0 160/300: dt: 0.9000, rms radial error=148.654, avgs=0 165/300: dt: 0.9000, rms radial error=147.817, avgs=0 170/300: dt: 0.9000, rms radial error=146.985, avgs=0 175/300: dt: 0.9000, rms radial error=146.158, avgs=0 180/300: dt: 0.9000, rms radial error=145.335, avgs=0 185/300: dt: 0.9000, rms radial error=144.517, avgs=0 190/300: dt: 0.9000, rms radial error=143.704, avgs=0 195/300: dt: 0.9000, rms radial error=142.895, avgs=0 200/300: dt: 0.9000, rms radial error=142.090, avgs=0 205/300: dt: 0.9000, rms radial error=141.290, avgs=0 210/300: dt: 0.9000, rms radial error=140.494, avgs=0 215/300: dt: 0.9000, rms radial error=139.703, avgs=0 220/300: dt: 0.9000, rms radial error=138.916, avgs=0 225/300: dt: 0.9000, rms radial error=138.134, avgs=0 230/300: dt: 0.9000, rms radial error=137.356, avgs=0 235/300: dt: 0.9000, rms radial error=136.582, avgs=0 240/300: dt: 0.9000, rms radial error=135.812, avgs=0 245/300: dt: 0.9000, rms radial error=135.047, avgs=0 250/300: dt: 0.9000, rms radial error=134.286, avgs=0 255/300: dt: 0.9000, rms radial error=133.530, avgs=0 260/300: dt: 0.9000, rms radial error=132.777, avgs=0 265/300: dt: 0.9000, rms radial error=132.029, avgs=0 270/300: dt: 0.9000, rms radial error=131.285, avgs=0 275/300: dt: 0.9000, rms radial error=130.546, avgs=0 280/300: dt: 0.9000, rms radial error=129.810, avgs=0 285/300: dt: 0.9000, rms radial error=129.079, avgs=0 290/300: dt: 0.9000, rms radial error=128.351, avgs=0 295/300: dt: 0.9000, rms radial error=127.628, avgs=0 300/300: dt: 0.9000, rms radial error=126.909, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12720.89 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00051 epoch 2 (K=40.0), pass 1, starting sse = 1907.84 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00082 epoch 3 (K=160.0), pass 1, starting sse = 158.36 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/16 = 0.00992 epoch 4 (K=640.0), pass 1, starting sse = 9.51 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/16 = 0.00476 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0290 hours FSRUNTIME@ mris_sphere 0.0290 hours 4 threads #VMPC# mris_sphere VmPeak 647604 mris_sphere done mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 scaling brain by 0.330... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.06 +- 0.61 (0.00-->9.24) (max @ vno 55993 --> 55994) face area 0.03 +- 0.04 (-0.08-->1.27) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.535, avgs=0 005/300: dt: 0.9000, rms radial error=176.277, avgs=0 010/300: dt: 0.9000, rms radial error=175.723, avgs=0 015/300: dt: 0.9000, rms radial error=174.994, avgs=0 020/300: dt: 0.9000, rms radial error=174.169, avgs=0 025/300: dt: 0.9000, rms radial error=173.287, avgs=0 030/300: dt: 0.9000, rms radial error=172.372, avgs=0 035/300: dt: 0.9000, rms radial error=171.441, avgs=0 040/300: dt: 0.9000, rms radial error=170.502, avgs=0 045/300: dt: 0.9000, rms radial error=169.559, avgs=0 050/300: dt: 0.9000, rms radial error=168.617, avgs=0 055/300: dt: 0.9000, rms radial error=167.677, avgs=0 060/300: dt: 0.9000, rms radial error=166.741, avgs=0 065/300: dt: 0.9000, rms radial error=165.809, avgs=0 070/300: dt: 0.9000, rms radial error=164.881, avgs=0 075/300: dt: 0.9000, rms radial error=163.958, avgs=0 080/300: dt: 0.9000, rms radial error=163.040, avgs=0 085/300: dt: 0.9000, rms radial error=162.127, avgs=0 090/300: dt: 0.9000, rms radial error=161.219, avgs=0 095/300: dt: 0.9000, rms radial error=160.315, avgs=0 100/300: dt: 0.9000, rms radial error=159.416, avgs=0 105/300: dt: 0.9000, rms radial error=158.522, avgs=0 110/300: dt: 0.9000, rms radial error=157.632, avgs=0 115/300: dt: 0.9000, rms radial error=156.748, avgs=0 120/300: dt: 0.9000, rms radial error=155.867, avgs=0 125/300: dt: 0.9000, rms radial error=154.992, avgs=0 130/300: dt: 0.9000, rms radial error=154.121, avgs=0 135/300: dt: 0.9000, rms radial error=153.256, avgs=0 140/300: dt: 0.9000, rms radial error=152.394, avgs=0 145/300: dt: 0.9000, rms radial error=151.538, avgs=0 150/300: dt: 0.9000, rms radial error=150.686, avgs=0 155/300: dt: 0.9000, rms radial error=149.839, avgs=0 160/300: dt: 0.9000, rms radial error=148.996, avgs=0 165/300: dt: 0.9000, rms radial error=148.158, avgs=0 170/300: dt: 0.9000, rms radial error=147.325, avgs=0 175/300: dt: 0.9000, rms radial error=146.496, avgs=0 180/300: dt: 0.9000, rms radial error=145.672, avgs=0 185/300: dt: 0.9000, rms radial error=144.852, avgs=0 190/300: dt: 0.9000, rms radial error=144.037, avgs=0 195/300: dt: 0.9000, rms radial error=143.226, avgs=0 200/300: dt: 0.9000, rms radial error=142.420, avgs=0 205/300: dt: 0.9000, rms radial error=141.618, avgs=0 210/300: dt: 0.9000, rms radial error=140.821, avgs=0 215/300: dt: 0.9000, rms radial error=140.028, avgs=0 220/300: dt: 0.9000, rms radial error=139.240, avgs=0 225/300: dt: 0.9000, rms radial error=138.456, avgs=0 230/300: dt: 0.9000, rms radial error=137.676, avgs=0 235/300: dt: 0.9000, rms radial error=136.901, avgs=0 240/300: dt: 0.9000, rms radial error=136.130, avgs=0 245/300: dt: 0.9000, rms radial error=135.363, avgs=0 250/300: dt: 0.9000, rms radial error=134.600, avgs=0 255/300: dt: 0.9000, rms radial error=133.842, avgs=0 260/300: dt: 0.9000, rms radial error=133.088, avgs=0 265/300: dt: 0.9000, rms radial error=132.339, avgs=0 270/300: dt: 0.9000, rms radial error=131.593, avgs=0 275/300: dt: 0.9000, rms radial error=130.851, avgs=0 280/300: dt: 0.9000, rms radial error=130.114, avgs=0 285/300: dt: 0.9000, rms radial error=129.381, avgs=0 290/300: dt: 0.9000, rms radial error=128.652, avgs=0 295/300: dt: 0.9000, rms radial error=127.926, avgs=0 300/300: dt: 0.9000, rms radial error=127.205, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13373.63 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00031 epoch 2 (K=40.0), pass 1, starting sse = 2076.84 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00076 epoch 3 (K=160.0), pass 1, starting sse = 186.96 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/15 = 0.00856 epoch 4 (K=640.0), pass 1, starting sse = 12.29 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/16 = 0.00216 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0275 hours FSRUNTIME@ mris_sphere 0.0275 hours 4 threads #VMPC# mris_sphere VmPeak 653636 mris_sphere done PIDs (2899127 2899130) completed and logs appended. #@# Fix Topology lh Tue Oct 8 16:28:07 CDT 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma lh #@# Fix Topology rh Tue Oct 8 16:28:08 CDT 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma rh Waiting for PID 2913053 of (2913053 2913058) to complete... Waiting for PID 2913058 of (2913053 2913058) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-76 (nv=112988, nf=226128, ne=339192, g=39) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 4954 ambiguous faces found in tessellation segmenting defects... 59 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 37 into 34 58 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.8056 (-4.4028) -vertex loglikelihood: -6.3146 (-3.1573) -normal dot loglikelihood: -3.5729 (-3.5729) -quad curv loglikelihood: -5.7952 (-2.8976) Total Loglikelihood : -24.4882 CORRECTING DEFECT 0 (vertices=482, convex hull=164, v0=6858) After retessellation of defect 0 (v0=6858), euler #=-56 (110010,328849,218783) : difference with theory (-55) = 1 CORRECTING DEFECT 1 (vertices=70, convex hull=104, v0=8962) After retessellation of defect 1 (v0=8962), euler #=-55 (110054,329027,218918) : difference with theory (-54) = 1 CORRECTING DEFECT 2 (vertices=39, convex hull=73, v0=10037) After retessellation of defect 2 (v0=10037), euler #=-54 (110081,329138,219003) : difference with theory (-53) = 1 CORRECTING DEFECT 3 (vertices=12, convex hull=27, v0=14584) After retessellation of defect 3 (v0=14584), euler #=-53 (110081,329147,219013) : difference with theory (-52) = 1 CORRECTING DEFECT 4 (vertices=35, convex hull=62, v0=17402) After retessellation of defect 4 (v0=17402), euler #=-52 (110096,329221,219073) : difference with theory (-51) = 1 CORRECTING DEFECT 5 (vertices=64, convex hull=29, v0=18325) After retessellation of defect 5 (v0=18325), euler #=-51 (110104,329254,219099) : difference with theory (-50) = 1 CORRECTING DEFECT 6 (vertices=94, convex hull=51, v0=19595) After retessellation of defect 6 (v0=19595), euler #=-50 (110113,329297,219134) : difference with theory (-49) = 1 CORRECTING DEFECT 7 (vertices=29, convex hull=46, v0=21506) After retessellation of defect 7 (v0=21506), euler #=-49 (110131,329369,219189) : difference with theory (-48) = 1 CORRECTING DEFECT 8 (vertices=5, convex hull=23, v0=23518) After retessellation of defect 8 (v0=23518), euler #=-48 (110132,329378,219198) : difference with theory (-47) = 1 CORRECTING DEFECT 9 (vertices=215, convex hull=115, v0=23719) After retessellation of defect 9 (v0=23719), euler #=-47 (110180,329574,219347) : difference with theory (-46) = 1 CORRECTING DEFECT 10 (vertices=14, convex hull=21, v0=24709) After retessellation of defect 10 (v0=24709), euler #=-46 (110185,329594,219363) : difference with theory (-45) = 1 CORRECTING DEFECT 11 (vertices=32, convex hull=49, v0=25325) After retessellation of defect 11 (v0=25325), euler #=-45 (110202,329667,219420) : difference with theory (-44) = 1 CORRECTING DEFECT 12 (vertices=40, convex hull=66, v0=30707) After retessellation of defect 12 (v0=30707), euler #=-44 (110224,329759,219491) : difference with theory (-43) = 1 CORRECTING DEFECT 13 (vertices=29, convex hull=32, v0=31722) After retessellation of defect 13 (v0=31722), euler #=-43 (110231,329793,219519) : difference with theory (-42) = 1 CORRECTING DEFECT 14 (vertices=45, convex hull=70, v0=35818) After retessellation of defect 14 (v0=35818), euler #=-42 (110263,329918,219613) : difference with theory (-41) = 1 CORRECTING DEFECT 15 (vertices=41, convex hull=30, v0=38340) After retessellation of defect 15 (v0=38340), euler #=-41 (110269,329946,219636) : difference with theory (-40) = 1 CORRECTING DEFECT 16 (vertices=37, convex hull=64, v0=39040) After retessellation of defect 16 (v0=39040), euler #=-40 (110286,330023,219697) : difference with theory (-39) = 1 CORRECTING DEFECT 17 (vertices=30, convex hull=70, v0=43202) After retessellation of defect 17 (v0=43202), euler #=-39 (110295,330079,219745) : difference with theory (-38) = 1 CORRECTING DEFECT 18 (vertices=5, convex hull=20, v0=44161) After retessellation of defect 18 (v0=44161), euler #=-38 (110296,330087,219753) : difference with theory (-37) = 1 CORRECTING DEFECT 19 (vertices=33, convex hull=65, v0=45091) After retessellation of defect 19 (v0=45091), euler #=-37 (110313,330160,219810) : difference with theory (-36) = 1 CORRECTING DEFECT 20 (vertices=23, convex hull=59, v0=45741) After retessellation of defect 20 (v0=45741), euler #=-36 (110328,330230,219866) : difference with theory (-35) = 1 CORRECTING DEFECT 21 (vertices=23, convex hull=28, v0=50474) After retessellation of defect 21 (v0=50474), euler #=-35 (110331,330247,219881) : difference with theory (-34) = 1 CORRECTING DEFECT 22 (vertices=174, convex hull=98, v0=52824) After retessellation of defect 22 (v0=52824), euler #=-34 (110341,330320,219945) : difference with theory (-33) = 1 CORRECTING DEFECT 23 (vertices=49, convex hull=28, v0=56798) After retessellation of defect 23 (v0=56798), euler #=-33 (110347,330348,219968) : difference with theory (-32) = 1 CORRECTING DEFECT 24 (vertices=47, convex hull=57, v0=57590) After retessellation of defect 24 (v0=57590), euler #=-32 (110365,330429,220032) : difference with theory (-31) = 1 CORRECTING DEFECT 25 (vertices=55, convex hull=44, v0=63380) After retessellation of defect 25 (v0=63380), euler #=-31 (110375,330476,220070) : difference with theory (-30) = 1 CORRECTING DEFECT 26 (vertices=65, convex hull=117, v0=64351) After retessellation of defect 26 (v0=64351), euler #=-30 (110411,330637,220196) : difference with theory (-29) = 1 CORRECTING DEFECT 27 (vertices=156, convex hull=78, v0=65545) After retessellation of defect 27 (v0=65545), euler #=-29 (110440,330755,220286) : difference with theory (-28) = 1 CORRECTING DEFECT 28 (vertices=13, convex hull=23, v0=66361) After retessellation of defect 28 (v0=66361), euler #=-28 (110444,330774,220302) : difference with theory (-27) = 1 CORRECTING DEFECT 29 (vertices=13, convex hull=14, v0=66955) After retessellation of defect 29 (v0=66955), euler #=-27 (110444,330777,220306) : difference with theory (-26) = 1 CORRECTING DEFECT 30 (vertices=26, convex hull=23, v0=69557) After retessellation of defect 30 (v0=69557), euler #=-26 (110450,330803,220327) : difference with theory (-25) = 1 CORRECTING DEFECT 31 (vertices=27, convex hull=18, v0=73880) After retessellation of defect 31 (v0=73880), euler #=-25 (110454,330820,220341) : difference with theory (-24) = 1 CORRECTING DEFECT 32 (vertices=6, convex hull=22, v0=74848) After retessellation of defect 32 (v0=74848), euler #=-24 (110454,330827,220349) : difference with theory (-23) = 1 CORRECTING DEFECT 33 (vertices=35, convex hull=30, v0=77540) After retessellation of defect 33 (v0=77540), euler #=-23 (110462,330860,220375) : difference with theory (-22) = 1 CORRECTING DEFECT 34 (vertices=94, convex hull=161, v0=78089) After retessellation of defect 34 (v0=78089), euler #=-21 (110482,330995,220492) : difference with theory (-21) = 0 CORRECTING DEFECT 35 (vertices=67, convex hull=76, v0=81121) After retessellation of defect 35 (v0=81121), euler #=-20 (110497,331072,220555) : difference with theory (-20) = 0 CORRECTING DEFECT 36 (vertices=81, convex hull=37, v0=81785) After retessellation of defect 36 (v0=81785), euler #=-19 (110506,331115,220590) : difference with theory (-19) = 0 CORRECTING DEFECT 37 (vertices=16, convex hull=26, v0=82342) After retessellation of defect 37 (v0=82342), euler #=-18 (110512,331141,220611) : difference with theory (-18) = 0 CORRECTING DEFECT 38 (vertices=53, convex hull=116, v0=82374) After retessellation of defect 38 (v0=82374), euler #=-17 (110527,331236,220692) : difference with theory (-17) = 0 CORRECTING DEFECT 39 (vertices=57, convex hull=28, v0=84609) After retessellation of defect 39 (v0=84609), euler #=-16 (110537,331277,220724) : difference with theory (-16) = 0 CORRECTING DEFECT 40 (vertices=22, convex hull=23, v0=84680) After retessellation of defect 40 (v0=84680), euler #=-15 (110542,331298,220741) : difference with theory (-15) = 0 CORRECTING DEFECT 41 (vertices=22, convex hull=55, v0=87473) After retessellation of defect 41 (v0=87473), euler #=-14 (110553,331350,220783) : difference with theory (-14) = 0 CORRECTING DEFECT 42 (vertices=29, convex hull=26, v0=87831) After retessellation of defect 42 (v0=87831), euler #=-13 (110561,331382,220808) : difference with theory (-13) = 0 CORRECTING DEFECT 43 (vertices=25, convex hull=51, v0=88533) After retessellation of defect 43 (v0=88533), euler #=-12 (110570,331428,220846) : difference with theory (-12) = 0 CORRECTING DEFECT 44 (vertices=21, convex hull=40, v0=89066) After retessellation of defect 44 (v0=89066), euler #=-11 (110582,331482,220889) : difference with theory (-11) = 0 CORRECTING DEFECT 45 (vertices=48, convex hull=35, v0=89522) After retessellation of defect 45 (v0=89522), euler #=-10 (110588,331511,220913) : difference with theory (-10) = 0 CORRECTING DEFECT 46 (vertices=47, convex hull=52, v0=90068) After retessellation of defect 46 (v0=90068), euler #=-9 (110598,331561,220954) : difference with theory (-9) = 0 CORRECTING DEFECT 47 (vertices=90, convex hull=40, v0=90493) After retessellation of defect 47 (v0=90493), euler #=-8 (110613,331619,220998) : difference with theory (-8) = 0 CORRECTING DEFECT 48 (vertices=15, convex hull=23, v0=90497) After retessellation of defect 48 (v0=90497), euler #=-7 (110615,331633,221011) : difference with theory (-7) = 0 CORRECTING DEFECT 49 (vertices=24, convex hull=59, v0=91436) After retessellation of defect 49 (v0=91436), euler #=-6 (110627,331690,221057) : difference with theory (-6) = 0 CORRECTING DEFECT 50 (vertices=25, convex hull=70, v0=93136) After retessellation of defect 50 (v0=93136), euler #=-5 (110639,331754,221110) : difference with theory (-5) = 0 CORRECTING DEFECT 51 (vertices=23, convex hull=57, v0=95127) After retessellation of defect 51 (v0=95127), euler #=-4 (110651,331815,221160) : difference with theory (-4) = 0 CORRECTING DEFECT 52 (vertices=37, convex hull=87, v0=95695) After retessellation of defect 52 (v0=95695), euler #=-3 (110665,331900,221232) : difference with theory (-3) = 0 CORRECTING DEFECT 53 (vertices=5, convex hull=25, v0=97959) After retessellation of defect 53 (v0=97959), euler #=-2 (110666,331909,221241) : difference with theory (-2) = 0 CORRECTING DEFECT 54 (vertices=31, convex hull=32, v0=100871) After retessellation of defect 54 (v0=100871), euler #=-1 (110668,331930,221261) : difference with theory (-1) = 0 CORRECTING DEFECT 55 (vertices=17, convex hull=37, v0=107341) After retessellation of defect 55 (v0=107341), euler #=0 (110674,331963,221289) : difference with theory (0) = 0 CORRECTING DEFECT 56 (vertices=107, convex hull=74, v0=110820) After retessellation of defect 56 (v0=110820), euler #=1 (110701,332076,221376) : difference with theory (1) = 0 CORRECTING DEFECT 57 (vertices=24, convex hull=60, v0=111978) After retessellation of defect 57 (v0=111978), euler #=2 (110715,332139,221426) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.06-->8.26) (max @ vno 79396 --> 84965) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.06-->8.26) (max @ vno 79396 --> 84965) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 184 mutations (34.2%), 354 crossovers (65.8%), 153 vertices were eliminated building final representation... 2273 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=110715, nf=221426, ne=332139, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 253 intersecting 001: 13 intersecting terminating search with 0 intersecting topology fixing took 2.3 minutes FSRUNTIME@ mris_fix_topology lh 0.0376 hours 4 threads #VMPC# mris_fix_topology VmPeak 950248 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-72 (nv=117128, nf=234400, ne=351600, g=37) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 6175 ambiguous faces found in tessellation segmenting defects... 56 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 11 -merging segment 21 into 20 -merging segment 24 into 22 -merging segment 41 into 39 -merging segment 42 into 39 -merging segment 54 into 51 50 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.8249 (-4.4124) -vertex loglikelihood: -6.2149 (-3.1074) -normal dot loglikelihood: -3.6380 (-3.6380) -quad curv loglikelihood: -6.1619 (-3.0810) Total Loglikelihood : -24.8397 CORRECTING DEFECT 0 (vertices=74, convex hull=99, v0=5108) After retessellation of defect 0 (v0=5108), euler #=-52 (113366,338656,225238) : difference with theory (-47) = 5 CORRECTING DEFECT 1 (vertices=80, convex hull=84, v0=8145) After retessellation of defect 1 (v0=8145), euler #=-51 (113397,338787,225339) : difference with theory (-46) = 5 CORRECTING DEFECT 2 (vertices=1228, convex hull=303, v0=9250) After retessellation of defect 2 (v0=9250), euler #=-51 (113407,338976,225518) : difference with theory (-45) = 6 CORRECTING DEFECT 3 (vertices=66, convex hull=105, v0=12743) After retessellation of defect 3 (v0=12743), euler #=-50 (113441,339122,225631) : difference with theory (-44) = 6 CORRECTING DEFECT 4 (vertices=23, convex hull=18, v0=16364) After retessellation of defect 4 (v0=16364), euler #=-49 (113444,339138,225645) : difference with theory (-43) = 6 CORRECTING DEFECT 5 (vertices=13, convex hull=32, v0=18847) After retessellation of defect 5 (v0=18847), euler #=-48 (113445,339154,225661) : difference with theory (-42) = 6 CORRECTING DEFECT 6 (vertices=8, convex hull=27, v0=26382) After retessellation of defect 6 (v0=26382), euler #=-47 (113448,339170,225675) : difference with theory (-41) = 6 CORRECTING DEFECT 7 (vertices=8, convex hull=29, v0=33920) After retessellation of defect 7 (v0=33920), euler #=-46 (113449,339181,225686) : difference with theory (-40) = 6 CORRECTING DEFECT 8 (vertices=22, convex hull=33, v0=33947) After retessellation of defect 8 (v0=33947), euler #=-45 (113451,339198,225702) : difference with theory (-39) = 6 CORRECTING DEFECT 9 (vertices=48, convex hull=70, v0=41910) After retessellation of defect 9 (v0=41910), euler #=-44 (113467,339272,225761) : difference with theory (-38) = 6 CORRECTING DEFECT 10 (vertices=146, convex hull=53, v0=42620) After retessellation of defect 10 (v0=42620), euler #=-43 (113481,339334,225810) : difference with theory (-37) = 6 CORRECTING DEFECT 11 (vertices=72, convex hull=112, v0=46673) After retessellation of defect 11 (v0=46673), euler #=-41 (113489,339404,225874) : difference with theory (-36) = 5 CORRECTING DEFECT 12 (vertices=9, convex hull=30, v0=50454) After retessellation of defect 12 (v0=50454), euler #=-40 (113493,339423,225890) : difference with theory (-35) = 5 CORRECTING DEFECT 13 (vertices=6, convex hull=26, v0=53096) After retessellation of defect 13 (v0=53096), euler #=-39 (113495,339435,225901) : difference with theory (-34) = 5 CORRECTING DEFECT 14 (vertices=66, convex hull=101, v0=53321) After retessellation of defect 14 (v0=53321), euler #=-38 (113538,339613,226037) : difference with theory (-33) = 5 CORRECTING DEFECT 15 (vertices=34, convex hull=49, v0=57830) After retessellation of defect 15 (v0=57830), euler #=-37 (113550,339670,226083) : difference with theory (-32) = 5 CORRECTING DEFECT 16 (vertices=31, convex hull=27, v0=58136) After retessellation of defect 16 (v0=58136), euler #=-36 (113555,339694,226103) : difference with theory (-31) = 5 CORRECTING DEFECT 17 (vertices=11, convex hull=27, v0=61113) After retessellation of defect 17 (v0=61113), euler #=-35 (113557,339710,226118) : difference with theory (-30) = 5 CORRECTING DEFECT 18 (vertices=18, convex hull=17, v0=65787) After retessellation of defect 18 (v0=65787), euler #=-34 (113561,339726,226131) : difference with theory (-29) = 5 CORRECTING DEFECT 19 (vertices=101, convex hull=146, v0=69558) After retessellation of defect 19 (v0=69558), euler #=-32 (113597,339914,226285) : difference with theory (-28) = 4 CORRECTING DEFECT 20 (vertices=180, convex hull=155, v0=75126) After retessellation of defect 20 (v0=75126), euler #=-30 (113640,340114,226444) : difference with theory (-27) = 3 CORRECTING DEFECT 21 (vertices=37, convex hull=67, v0=80902) After retessellation of defect 21 (v0=80902), euler #=-29 (113649,340169,226491) : difference with theory (-26) = 3 CORRECTING DEFECT 22 (vertices=15, convex hull=23, v0=85773) After retessellation of defect 22 (v0=85773), euler #=-28 (113652,340188,226508) : difference with theory (-25) = 3 CORRECTING DEFECT 23 (vertices=68, convex hull=82, v0=88571) After retessellation of defect 23 (v0=88571), euler #=-27 (113694,340354,226633) : difference with theory (-24) = 3 CORRECTING DEFECT 24 (vertices=15, convex hull=31, v0=88965) After retessellation of defect 24 (v0=88965), euler #=-26 (113698,340378,226654) : difference with theory (-23) = 3 CORRECTING DEFECT 25 (vertices=6, convex hull=23, v0=89008) After retessellation of defect 25 (v0=89008), euler #=-25 (113701,340393,226667) : difference with theory (-22) = 3 CORRECTING DEFECT 26 (vertices=8, convex hull=23, v0=90541) After retessellation of defect 26 (v0=90541), euler #=-24 (113704,340408,226680) : difference with theory (-21) = 3 CORRECTING DEFECT 27 (vertices=38, convex hull=62, v0=90832) After retessellation of defect 27 (v0=90832), euler #=-23 (113727,340500,226750) : difference with theory (-20) = 3 CORRECTING DEFECT 28 (vertices=27, convex hull=76, v0=92300) After retessellation of defect 28 (v0=92300), euler #=-22 (113736,340556,226798) : difference with theory (-19) = 3 CORRECTING DEFECT 29 (vertices=138, convex hull=204, v0=92521) After retessellation of defect 29 (v0=92521), euler #=-21 (113807,340868,227040) : difference with theory (-18) = 3 CORRECTING DEFECT 30 (vertices=52, convex hull=47, v0=92770) After retessellation of defect 30 (v0=92770), euler #=-20 (113816,340915,227079) : difference with theory (-17) = 3 CORRECTING DEFECT 31 (vertices=34, convex hull=36, v0=92868) After retessellation of defect 31 (v0=92868), euler #=-19 (113823,340949,227107) : difference with theory (-16) = 3 CORRECTING DEFECT 32 (vertices=29, convex hull=30, v0=94424) After retessellation of defect 32 (v0=94424), euler #=-18 (113828,340975,227129) : difference with theory (-15) = 3 CORRECTING DEFECT 33 (vertices=61, convex hull=96, v0=95874) After retessellation of defect 33 (v0=95874), euler #=-17 (113861,341117,227239) : difference with theory (-14) = 3 CORRECTING DEFECT 34 (vertices=26, convex hull=31, v0=96354) After retessellation of defect 34 (v0=96354), euler #=-16 (113869,341149,227264) : difference with theory (-13) = 3 CORRECTING DEFECT 35 (vertices=76, convex hull=48, v0=96564) After retessellation of defect 35 (v0=96564), euler #=-15 (113878,341200,227307) : difference with theory (-12) = 3 CORRECTING DEFECT 36 (vertices=136, convex hull=172, v0=97132) After retessellation of defect 36 (v0=97132), euler #=-12 (113947,341502,227543) : difference with theory (-11) = 1 CORRECTING DEFECT 37 (vertices=107, convex hull=50, v0=99488) After retessellation of defect 37 (v0=99488), euler #=-11 (113958,341555,227586) : difference with theory (-10) = 1 CORRECTING DEFECT 38 (vertices=29, convex hull=57, v0=100634) After retessellation of defect 38 (v0=100634), euler #=-10 (113967,341608,227631) : difference with theory (-9) = 1 CORRECTING DEFECT 39 (vertices=98, convex hull=106, v0=101236) After retessellation of defect 39 (v0=101236), euler #=-9 (114004,341767,227754) : difference with theory (-8) = 1 CORRECTING DEFECT 40 (vertices=37, convex hull=64, v0=101306) After retessellation of defect 40 (v0=101306), euler #=-8 (114021,341839,227810) : difference with theory (-7) = 1 CORRECTING DEFECT 41 (vertices=63, convex hull=58, v0=108033) After retessellation of defect 41 (v0=108033), euler #=-7 (114038,341917,227872) : difference with theory (-6) = 1 CORRECTING DEFECT 42 (vertices=33, convex hull=24, v0=109036) After retessellation of defect 42 (v0=109036), euler #=-6 (114044,341941,227891) : difference with theory (-5) = 1 CORRECTING DEFECT 43 (vertices=138, convex hull=50, v0=109466) After retessellation of defect 43 (v0=109466), euler #=-5 (114053,341988,227930) : difference with theory (-4) = 1 CORRECTING DEFECT 44 (vertices=16, convex hull=48, v0=111212) After retessellation of defect 44 (v0=111212), euler #=-4 (114062,342032,227966) : difference with theory (-3) = 1 CORRECTING DEFECT 45 (vertices=60, convex hull=81, v0=112148) After retessellation of defect 45 (v0=112148), euler #=-3 (114084,342131,228044) : difference with theory (-2) = 1 CORRECTING DEFECT 46 (vertices=96, convex hull=135, v0=113774) After retessellation of defect 46 (v0=113774), euler #=-1 (114122,342307,228184) : difference with theory (-1) = 0 CORRECTING DEFECT 47 (vertices=19, convex hull=25, v0=114386) After retessellation of defect 47 (v0=114386), euler #=0 (114125,342319,228194) : difference with theory (0) = 0 CORRECTING DEFECT 48 (vertices=31, convex hull=56, v0=115767) After retessellation of defect 48 (v0=115767), euler #=1 (114141,342389,228249) : difference with theory (1) = 0 CORRECTING DEFECT 49 (vertices=33, convex hull=71, v0=116897) After retessellation of defect 49 (v0=116897), euler #=2 (114155,342459,228306) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.13-->12.96) (max @ vno 17787 --> 28461) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.13-->12.96) (max @ vno 17787 --> 28461) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 212 mutations (35.7%), 382 crossovers (64.3%), 459 vertices were eliminated building final representation... 2973 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=114155, nf=228306, ne=342459, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 370 intersecting 001: 19 intersecting terminating search with 0 intersecting topology fixing took 3.5 minutes FSRUNTIME@ mris_fix_topology rh 0.0580 hours 4 threads #VMPC# mris_fix_topology VmPeak 954620 PIDs (2913053 2913058) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 110715 - 332139 + 221426 = 2 --> 0 holes F =2V-4: 221426 = 221430-4 (0) 2E=3F: 664278 = 664278 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 114155 - 342459 + 228306 = 2 --> 0 holes F =2V-4: 228306 = 228310-4 (0) 2E=3F: 684918 = 684918 (0) total defect index = 0 Tue Oct 8 16:31:38 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/defect2seg --s PIB23-310_VYr0_Bay3prisma --cortex freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 defect2seg 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2944320 mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 26 non-cortical segments detected only using segment with 9182 vertices erasing segment 0 (vno[0] = 6933) erasing segment 1 (vno[0] = 11968) erasing segment 2 (vno[0] = 13588) erasing segment 3 (vno[0] = 14400) erasing segment 4 (vno[0] = 16044) erasing segment 5 (vno[0] = 18640) erasing segment 6 (vno[0] = 18709) erasing segment 7 (vno[0] = 18745) erasing segment 8 (vno[0] = 19473) erasing segment 9 (vno[0] = 19631) erasing segment 10 (vno[0] = 20453) erasing segment 11 (vno[0] = 21278) erasing segment 13 (vno[0] = 47740) erasing segment 14 (vno[0] = 50419) erasing segment 15 (vno[0] = 63391) erasing segment 16 (vno[0] = 78471) erasing segment 17 (vno[0] = 80779) erasing segment 18 (vno[0] = 80804) erasing segment 19 (vno[0] = 82190) erasing segment 20 (vno[0] = 82493) erasing segment 21 (vno[0] = 83320) erasing segment 22 (vno[0] = 84995) erasing segment 23 (vno[0] = 86551) erasing segment 24 (vno[0] = 87453) erasing segment 25 (vno[0] = 91861) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz 1000 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 528156 mris_defects_pointset done mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 53 non-cortical segments detected only using segment with 8904 vertices erasing segment 0 (vno[0] = 7837) erasing segment 1 (vno[0] = 8537) erasing segment 2 (vno[0] = 10863) erasing segment 3 (vno[0] = 13062) erasing segment 4 (vno[0] = 13207) erasing segment 5 (vno[0] = 17477) erasing segment 6 (vno[0] = 17612) erasing segment 7 (vno[0] = 18269) erasing segment 8 (vno[0] = 19365) erasing segment 9 (vno[0] = 19490) erasing segment 10 (vno[0] = 20213) erasing segment 11 (vno[0] = 21307) erasing segment 12 (vno[0] = 21398) erasing segment 13 (vno[0] = 23587) erasing segment 14 (vno[0] = 24513) erasing segment 15 (vno[0] = 24679) erasing segment 16 (vno[0] = 25340) erasing segment 17 (vno[0] = 25382) erasing segment 18 (vno[0] = 25444) erasing segment 19 (vno[0] = 27148) erasing segment 20 (vno[0] = 28038) erasing segment 21 (vno[0] = 29754) erasing segment 22 (vno[0] = 29767) erasing segment 23 (vno[0] = 30669) erasing segment 24 (vno[0] = 30697) erasing segment 25 (vno[0] = 31562) erasing segment 26 (vno[0] = 32358) erasing segment 27 (vno[0] = 34195) erasing segment 29 (vno[0] = 38246) erasing segment 30 (vno[0] = 40075) erasing segment 31 (vno[0] = 47498) erasing segment 32 (vno[0] = 51425) erasing segment 33 (vno[0] = 58765) erasing segment 34 (vno[0] = 66140) erasing segment 35 (vno[0] = 83877) erasing segment 36 (vno[0] = 84734) erasing segment 37 (vno[0] = 84846) erasing segment 38 (vno[0] = 84864) erasing segment 39 (vno[0] = 85667) erasing segment 40 (vno[0] = 87279) erasing segment 41 (vno[0] = 87355) erasing segment 42 (vno[0] = 88154) erasing segment 43 (vno[0] = 88179) erasing segment 44 (vno[0] = 89039) erasing segment 45 (vno[0] = 92430) erasing segment 46 (vno[0] = 93147) erasing segment 47 (vno[0] = 93234) erasing segment 48 (vno[0] = 93388) erasing segment 49 (vno[0] = 100343) erasing segment 50 (vno[0] = 100351) erasing segment 51 (vno[0] = 101074) erasing segment 52 (vno[0] = 103553) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz 2000 1 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 469440 mris_defects_pointset done Started at Tue Oct 8 16:31:38 CDT 2024 Ended at Tue Oct 8 16:32:29 CDT 2024 Defect2seg-Run-Time-Sec 51 Defect2seg-Run-Time-Min 1.02 Defect2seg-Run-Time-Hours 0.01 tkmeditfv PIB23-310_VYr0_Bay3prisma brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2024:10:08:16:31:38 defect2seg N 3 e 51.18 S 1.69 U 51.70 P 104% M 496344 F 85 R 649183 W 0 c 5247 w 1228 I 34448 O 18832 L 62.97 64.47 69.02 @#@FSLOADPOST 2024:10:08:16:32:29 defect2seg N 3 59.63 63.06 68.28 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.71035 remeshing to edge length 0.71035 with 3 iterations avg qual before : 0.89073 after: 0.970693 Removing intersections Remeshed surface quality stats nv0 = 110715 nv = 115461 1.04287 Area 230918 0.30191 0.03385 0.084984 0.4855 Corner 692754 60.00000 8.87370 16.613728 146.3529 Edge 346377 0.84310 0.08300 0.446294 1.2515 Hinge 346377 9.69530 10.52777 0.000000 129.9230 mris_remesh done @#@FSTIME 2024:10:08:16:32:29 mris_remesh N 7 e 35.61 S 1.12 U 35.99 P 104% M 650208 F 21 R 874922 W 0 c 3599 w 339 I 3584 O 8120 L 59.63 63.06 68.28 @#@FSLOADPOST 2024:10:08:16:33:05 mris_remesh N 7 66.35 64.62 68.62 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.712463 remeshing to edge length 0.712463 with 3 iterations avg qual before : 0.890374 after: 0.971031 Removing intersections Remeshed surface quality stats nv0 = 114155 nv = 119197 1.04417 Area 238390 0.30365 0.03391 0.096144 0.4638 Corner 715170 60.00000 8.82304 20.281964 138.9994 Edge 357585 0.84543 0.08278 0.466458 1.2841 Hinge 357585 9.66402 10.61789 0.000000 156.2937 mris_remesh done @#@FSTIME 2024:10:08:16:33:05 mris_remesh N 7 e 39.71 S 1.31 U 39.54 P 102% M 672124 F 2 R 1063170 W 0 c 3941 w 2331 I 0 O 8384 L 66.35 64.62 68.62 @#@FSLOADPOST 2024:10:08:16:33:45 mris_remesh N 7 64.20 64.04 68.25 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2024:10:08:16:33:45 mris_remove_intersection N 2 e 3.23 S 0.30 U 3.25 P 110% M 301100 F 5 R 189555 W 0 c 324 w 201 I 472 O 8128 L 64.20 64.04 68.25 @#@FSLOADPOST 2024:10:08:16:33:48 mris_remove_intersection N 2 62.18 63.62 68.09 rm -f ../surf/lh.inflated /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2024:10:08:16:33:48 mris_remove_intersection N 2 e 4.06 S 0.26 U 3.97 P 104% M 308112 F 0 R 144930 W 0 c 451 w 83 I 8384 O 8384 L 62.18 63.62 68.09 @#@FSLOADPOST 2024:10:08:16:33:52 mris_remove_intersection N 2 62.18 63.62 68.09 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Tue Oct 8 16:33:52 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 230208 voxels (1.37%) border gray 235342 voxels (1.40%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=25831, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 100.3 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 80.7 +- 12.0 [30.0 --> 110.0] white_mean = 100.251 +/- 6.76465, gray_mean = 80.67 +/- 12.0315 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=206 nbins=207 intensity peaks found at WM=101+-6.1, GM=80+-7.8 white_mode = 101, gray_mode = 80 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 68.0 (was 70.000000) setting MAX_BORDER_WHITE to 107.8 (was 105.000000) setting MIN_BORDER_WHITE to 80.0 (was 85.000000) setting MAX_CSF to 55.9 (was 40.000000) setting MAX_GRAY to 94.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 68.0 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 43.9 (was 40.000000) When placing the white surface white_border_hi = 107.765; white_border_low = 80; white_outside_low = 67.9685; white_inside_hi = 120; white_outside_hi = 107.765; When placing the pial surface pial_border_hi = 67.9685; pial_border_low = 43.9054; pial_outside_low = 10; pial_inside_hi = 94.2353; pial_outside_hi = 61.9527; #VMPC# mris_autodet_gwstats VmPeak 565348 mris_autodet_gwstats done @#@FSTIME 2024:10:08:16:33:52 mris_autodet_gwstats N 8 e 6.69 S 0.34 U 8.26 P 128% M 207748 F 1 R 131407 W 0 c 952 w 122 I 8 O 8 L 62.18 63.62 68.09 @#@FSLOADPOST 2024:10:08:16:33:59 mris_autodet_gwstats N 8 68.14 64.79 68.42 #-------------------------------------------- #@# AutoDetGWStats rh Tue Oct 8 16:33:59 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 230208 voxels (1.37%) border gray 235342 voxels (1.40%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=25831, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 100.3 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 80.7 +- 12.0 [30.0 --> 110.0] white_mean = 100.251 +/- 6.76465, gray_mean = 80.67 +/- 12.0315 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=206 nbins=207 intensity peaks found at WM=103+-5.2, GM=80+-7.8 white_mode = 103, gray_mode = 80 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 68.0 (was 70.000000) setting MAX_BORDER_WHITE to 109.8 (was 105.000000) setting MIN_BORDER_WHITE to 80.0 (was 85.000000) setting MAX_CSF to 55.9 (was 40.000000) setting MAX_GRAY to 96.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 68.0 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 43.9 (was 40.000000) When placing the white surface white_border_hi = 109.765; white_border_low = 80; white_outside_low = 67.9685; white_inside_hi = 120; white_outside_hi = 109.765; When placing the pial surface pial_border_hi = 67.9685; pial_border_low = 43.9054; pial_outside_low = 10; pial_inside_hi = 96.2353; pial_outside_hi = 61.9527; #VMPC# mris_autodet_gwstats VmPeak 568164 mris_autodet_gwstats done @#@FSTIME 2024:10:08:16:33:59 mris_autodet_gwstats N 8 e 6.40 S 0.25 U 7.73 P 124% M 212544 F 1 R 143420 W 0 c 792 w 133 I 0 O 8 L 68.14 64.79 68.42 @#@FSLOADPOST 2024:10:08:16:34:06 mris_autodet_gwstats N 8 65.80 64.36 68.26 #-------------------------------------------- #@# WhitePreAparc lh Tue Oct 8 16:34:06 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface before ripping with 5 iterations Area 230918 0.26766 0.06494 0.000962 0.5786 Corner 692754 60.00000 9.62484 6.596091 155.1700 Edge 346377 0.78965 0.11782 0.036256 1.2668 Hinge 346377 6.22794 6.66518 0.000000 146.7343 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25831, wmmin=5, clip=110 MRIfindBrightNonWM(): 342 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8238, nmarked2=7, nripped=8238 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57731: xyz = (-42.6894,3.40729,26.5254) oxyz = (-42.6894,3.40729,26.5254) wxzy = (-42.6894,3.40729,26.5254) pxyz = (0,0,0) CBVO Creating mask 115461 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8238 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8238, nmarked2=7, nripped=8238 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 107.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 107.7646560; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=2 had to be increased for 207 vertices, nripped=8238 mean border=86.7, 582 (582) missing vertices, mean dist 0.3 [1.1 (%30.7)->0.9 (%69.3))] %27 local maxima, %65 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0512 min Finding expansion regions mean absolute distance = 0.99 +- 1.16 3964 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1814045.5, rms=8.894 001: dt: 0.5000, sse=1005555.1, rms=6.440 (27.592%) 002: dt: 0.5000, sse=614678.0, rms=4.804 (25.399%) 003: dt: 0.5000, sse=431222.9, rms=3.774 (21.457%) 004: dt: 0.5000, sse=347409.9, rms=3.151 (16.488%) 005: dt: 0.5000, sse=300494.8, rms=2.772 (12.023%) 006: dt: 0.5000, sse=285773.3, rms=2.537 (8.504%) 007: dt: 0.5000, sse=264766.0, rms=2.385 (5.999%) 008: dt: 0.5000, sse=258054.6, rms=2.295 (3.734%) rms = 2.2478/2.2955, sse=258939.4/258054.6, time step reduction 1 of 3 to 0.250 0 1 1 009: dt: 0.5000, sse=258939.4, rms=2.248 (2.076%) 010: dt: 0.2500, sse=217121.2, rms=1.708 (24.000%) 011: dt: 0.2500, sse=209694.2, rms=1.623 (5.012%) rms = 1.5976/1.6227, sse=224610.7/209694.2, time step reduction 2 of 3 to 0.125 0 1 1 012: dt: 0.2500, sse=224610.7, rms=1.598 (1.545%) rms = 1.5726/1.5976, sse=215500.9/224610.7, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=215500.9, rms=1.573 (1.566%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8238 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8510, nmarked2=37, nripped=8510 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 107.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 107.7646560; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=1 had to be increased for 277 vertices, nripped=8510 mean border=88.8, 474 (208) missing vertices, mean dist -0.3 [0.6 (%63.8)->0.3 (%36.2))] %47 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0318 min Finding expansion regions mean absolute distance = 0.52 +- 0.84 4396 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=492384.5, rms=3.676 014: dt: 0.5000, sse=321376.6, rms=2.436 (33.724%) 015: dt: 0.5000, sse=294443.2, rms=2.013 (17.384%) 016: dt: 0.5000, sse=272293.7, rms=1.859 (7.625%) rms = 1.8305/1.8594, sse=260184.3/272293.7, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=260184.3, rms=1.830 (1.554%) 018: dt: 0.2500, sse=247732.5, rms=1.356 (25.939%) 019: dt: 0.2500, sse=235796.5, rms=1.272 (6.208%) rms = 1.2551/1.2715, sse=222086.6/235796.5, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=222086.5, rms=1.255 (1.288%) rms = 1.2323/1.2551, sse=231331.6/222086.6, time step reduction 3 of 3 to 0.062 0 1 1 021: dt: 0.1250, sse=231331.6, rms=1.232 (1.821%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8510 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8568, nmarked2=38, nripped=8568 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 107.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 107.7646560; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 381 vertices, nripped=8568 mean border=91.4, 466 (165) missing vertices, mean dist -0.3 [0.4 (%72.9)->0.3 (%27.1))] %71 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0221 min Finding expansion regions mean absolute distance = 0.40 +- 0.50 3577 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=457401.1, rms=3.497 022: dt: 0.5000, sse=288312.7, rms=1.973 (43.580%) 023: dt: 0.5000, sse=256893.9, rms=1.706 (13.526%) rms = 1.7101/1.7061, sse=255762.8/256893.9, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 024: dt: 0.2500, sse=238577.2, rms=1.367 (19.896%) 025: dt: 0.2500, sse=228253.4, rms=1.184 (13.355%) rms = 1.1506/1.1841, sse=227900.3/228253.4, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=227900.3, rms=1.151 (2.831%) rms = 1.1195/1.1506, sse=226776.2/227900.3, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=226776.2, rms=1.120 (2.701%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8568 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8594, nmarked2=37, nripped=8594 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 107.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 107.7646560; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 408 vertices, nripped=8594 mean border=92.3, 488 (141) missing vertices, mean dist -0.1 [0.3 (%60.2)->0.2 (%39.8))] %79 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0116 min Finding expansion regions mean absolute distance = 0.28 +- 0.38 2764 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=255656.3, rms=1.655 028: dt: 0.5000, sse=228028.8, rms=1.193 (27.907%) rms = 1.3966/1.1931, sse=236692.5/228028.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=215587.5, rms=0.972 (18.534%) rms = 0.9312/0.9720, sse=205445.3/215587.5, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=205445.3, rms=0.931 (4.201%) rms = 0.8889/0.9312, sse=229160.1/205445.3, time step reduction 3 of 3 to 0.062 0 1 1 031: dt: 0.1250, sse=229160.1, rms=0.889 (4.538%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 2.81 minutes #VMPC# mris_place_surfaces VmPeak 2077076 mris_place_surface done @#@FSTIME 2024:10:08:16:34:06 mris_place_surface N 18 e 177.39 S 4.05 U 300.91 P 171% M 1640532 F 2 R 3393244 W 0 c 29888 w 2307 I 0 O 8128 L 65.80 64.36 68.26 @#@FSLOADPOST 2024:10:08:16:37:03 mris_place_surface N 18 60.58 62.59 66.90 #-------------------------------------------- #@# WhitePreAparc rh Tue Oct 8 16:37:03 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface before ripping with 5 iterations Area 238390 0.26906 0.06524 0.001281 0.5826 Corner 715170 60.00000 9.61477 5.738822 151.3081 Edge 357585 0.79164 0.11813 0.030327 1.3811 Hinge 357585 6.25738 6.75179 0.000000 158.5848 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25831, wmmin=5, clip=110 MRIfindBrightNonWM(): 342 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 #FML# MRISripMidline(): nmarked=8514, nmarked2=0, nripped=8514 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59599: xyz = (5.9146,5.15132,27.9379) oxyz = (5.9146,5.15132,27.9379) wxzy = (5.9146,5.15132,27.9379) pxyz = (0,0,0) CBVO Creating mask 119197 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8514 #FML# MRISripMidline(): nmarked=8514, nmarked2=0, nripped=8514 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 109.7646560; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=2 had to be increased for 262 vertices, nripped=8514 mean border=86.9, 628 (628) missing vertices, mean dist 0.3 [1.2 (%29.2)->1.0 (%70.8))] %33 local maxima, %59 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0557 min Finding expansion regions mean absolute distance = 1.04 +- 1.22 4380 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1837724.0, rms=8.809 001: dt: 0.5000, sse=1048509.9, rms=6.470 (26.555%) 002: dt: 0.5000, sse=661832.1, rms=4.930 (23.798%) 003: dt: 0.5000, sse=476816.2, rms=3.936 (20.168%) 004: dt: 0.5000, sse=383492.5, rms=3.296 (16.263%) 005: dt: 0.5000, sse=315377.8, rms=2.857 (13.304%) 006: dt: 0.5000, sse=298431.6, rms=2.560 (10.414%) 007: dt: 0.5000, sse=278070.2, rms=2.370 (7.418%) 008: dt: 0.5000, sse=261339.2, rms=2.248 (5.144%) 009: dt: 0.5000, sse=254034.7, rms=2.192 (2.472%) rms = 2.1509/2.1924, sse=260112.1/254034.7, time step reduction 1 of 3 to 0.250 0 1 1 010: dt: 0.5000, sse=260112.1, rms=2.151 (1.895%) 011: dt: 0.2500, sse=205972.5, rms=1.659 (22.855%) 012: dt: 0.2500, sse=204232.7, rms=1.587 (4.353%) rms = 1.5723/1.5870, sse=205990.1/204232.7, time step reduction 2 of 3 to 0.125 0 1 1 013: dt: 0.2500, sse=205990.1, rms=1.572 (0.932%) rms = 1.5517/1.5723, sse=204800.1/205990.1, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=204800.1, rms=1.552 (1.310%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8514 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8760, nmarked2=0, nripped=8760 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 109.7646560; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=1 had to be increased for 312 vertices, nripped=8760 mean border=89.2, 547 (385) missing vertices, mean dist -0.3 [0.7 (%64.5)->0.3 (%35.5))] %51 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0314 min Finding expansion regions mean absolute distance = 0.54 +- 0.87 4284 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=529650.9, rms=3.891 015: dt: 0.5000, sse=361541.2, rms=2.620 (32.678%) 016: dt: 0.5000, sse=313978.0, rms=2.157 (17.662%) 017: dt: 0.5000, sse=296962.8, rms=1.945 (9.847%) 018: dt: 0.5000, sse=287189.4, rms=1.867 (3.978%) rms = 1.8356/1.8673, sse=293607.5/287189.4, time step reduction 1 of 3 to 0.250 0 1 1 019: dt: 0.5000, sse=293607.5, rms=1.836 (1.697%) 020: dt: 0.2500, sse=247431.6, rms=1.356 (26.102%) rms = 1.2742/1.3565, sse=250638.7/247431.6, time step reduction 2 of 3 to 0.125 0 1 0 021: dt: 0.2500, sse=250638.7, rms=1.274 (6.064%) rms = 1.2479/1.2742, sse=247814.3/250638.7, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=247814.3, rms=1.248 (2.068%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8760 removing 1 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8891, nmarked2=0, nripped=8891 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 109.7646560; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 375 vertices, nripped=8891 mean border=91.8, 579 (338) missing vertices, mean dist -0.3 [0.5 (%73.6)->0.3 (%26.4))] %73 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0186 min Finding expansion regions mean absolute distance = 0.42 +- 0.53 3226 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=496642.1, rms=3.615 023: dt: 0.5000, sse=316865.3, rms=2.062 (42.954%) 024: dt: 0.5000, sse=284355.0, rms=1.662 (19.404%) rms = 1.6326/1.6621, sse=263964.3/284355.0, time step reduction 1 of 3 to 0.250 0 0 1 025: dt: 0.5000, sse=263964.3, rms=1.633 (1.775%) 026: dt: 0.2500, sse=231382.9, rms=1.176 (27.962%) 027: dt: 0.2500, sse=230902.9, rms=1.108 (5.778%) rms = 1.0947/1.1081, sse=239613.2/230902.9, time step reduction 2 of 3 to 0.125 0 1 1 028: dt: 0.2500, sse=239613.2, rms=1.095 (1.213%) rms = 1.0769/1.0947, sse=231409.9/239613.2, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=231409.9, rms=1.077 (1.626%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8891 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8911, nmarked2=0, nripped=8911 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 109.7646560; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 395 vertices, nripped=8911 mean border=92.8, 605 (315) missing vertices, mean dist -0.1 [0.3 (%60.7)->0.2 (%39.3))] %81 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0129 min Finding expansion regions mean absolute distance = 0.29 +- 0.39 2790 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=262181.3, rms=1.657 030: dt: 0.5000, sse=241273.2, rms=1.116 (32.645%) rms = 1.2994/1.1159, sse=250431.2/241273.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=235560.2, rms=0.925 (17.089%) rms = 0.8912/0.9252, sse=244096.5/235560.2, time step reduction 2 of 3 to 0.125 0 1 1 032: dt: 0.2500, sse=244096.5, rms=0.891 (3.680%) rms = 0.8588/0.8912, sse=224751.1/244096.5, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=224751.1, rms=0.859 (3.635%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 3.26 minutes #VMPC# mris_place_surfaces VmPeak 2146980 mris_place_surface done @#@FSTIME 2024:10:08:16:37:03 mris_place_surface N 18 e 204.78 S 4.62 U 339.90 P 168% M 1711680 F 3 R 4222958 W 0 c 34151 w 2681 I 8384 O 8384 L 60.58 62.59 66.90 @#@FSLOADPOST 2024:10:08:16:40:28 mris_place_surface N 18 49.22 59.59 65.11 #-------------------------------------------- #@# CortexLabel lh Tue Oct 8 16:40:28 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 10 non-cortical segments detected only using segment with 10043 vertices erasing segment 1 (vno[0] = 54611) erasing segment 2 (vno[0] = 65310) erasing segment 3 (vno[0] = 69968) erasing segment 4 (vno[0] = 73278) erasing segment 5 (vno[0] = 76710) erasing segment 6 (vno[0] = 78179) erasing segment 7 (vno[0] = 95121) erasing segment 8 (vno[0] = 102525) erasing segment 9 (vno[0] = 102526) @#@FSTIME 2024:10:08:16:40:28 mri_label2label N 5 e 22.52 S 0.38 U 23.00 P 103% M 312956 F 1 R 191592 W 0 c 2323 w 320 I 0 O 9144 L 53.53 60.31 65.32 @#@FSLOADPOST 2024:10:08:16:40:51 mri_label2label N 5 58.94 61.20 65.51 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Tue Oct 8 16:40:51 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 10 non-cortical segments detected only using segment with 8672 vertices erasing segment 1 (vno[0] = 35512) erasing segment 2 (vno[0] = 65310) erasing segment 3 (vno[0] = 69968) erasing segment 4 (vno[0] = 73278) erasing segment 5 (vno[0] = 76710) erasing segment 6 (vno[0] = 78179) erasing segment 7 (vno[0] = 95121) erasing segment 8 (vno[0] = 102525) erasing segment 9 (vno[0] = 102526) @#@FSTIME 2024:10:08:16:40:51 mri_label2label N 5 e 20.54 S 0.41 U 20.79 P 103% M 312788 F 2 R 179965 W 0 c 2032 w 329 I 0 O 9264 L 58.94 61.20 65.51 @#@FSLOADPOST 2024:10:08:16:41:12 mri_label2label N 5 70.43 63.61 66.21 #-------------------------------------------- #@# CortexLabel rh Tue Oct 8 16:41:12 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 19 non-cortical segments detected only using segment with 9991 vertices erasing segment 0 (vno[0] = 7687) erasing segment 1 (vno[0] = 8316) erasing segment 2 (vno[0] = 10926) erasing segment 3 (vno[0] = 15027) erasing segment 4 (vno[0] = 24092) erasing segment 6 (vno[0] = 30024) erasing segment 7 (vno[0] = 31446) erasing segment 8 (vno[0] = 37653) erasing segment 9 (vno[0] = 55530) erasing segment 10 (vno[0] = 72795) erasing segment 11 (vno[0] = 74810) erasing segment 12 (vno[0] = 75521) erasing segment 13 (vno[0] = 78876) erasing segment 14 (vno[0] = 82121) erasing segment 15 (vno[0] = 96628) erasing segment 16 (vno[0] = 97222) erasing segment 17 (vno[0] = 101953) erasing segment 18 (vno[0] = 113593) @#@FSTIME 2024:10:08:16:41:12 mri_label2label N 5 e 22.79 S 0.43 U 23.11 P 103% M 355688 F 1 R 172989 W 0 c 2229 w 404 I 8384 O 9264 L 70.43 63.61 66.21 @#@FSLOADPOST 2024:10:08:16:41:35 mri_label2label N 5 66.18 63.07 65.95 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Tue Oct 8 16:41:35 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 18 non-cortical segments detected only using segment with 8460 vertices erasing segment 0 (vno[0] = 7687) erasing segment 1 (vno[0] = 8316) erasing segment 2 (vno[0] = 10926) erasing segment 3 (vno[0] = 15027) erasing segment 4 (vno[0] = 24092) erasing segment 6 (vno[0] = 30024) erasing segment 7 (vno[0] = 31446) erasing segment 8 (vno[0] = 37653) erasing segment 9 (vno[0] = 41500) erasing segment 10 (vno[0] = 72795) erasing segment 11 (vno[0] = 74215) erasing segment 12 (vno[0] = 74810) erasing segment 13 (vno[0] = 75521) erasing segment 14 (vno[0] = 78876) erasing segment 15 (vno[0] = 82121) erasing segment 16 (vno[0] = 97222) erasing segment 17 (vno[0] = 101953) @#@FSTIME 2024:10:08:16:41:35 mri_label2label N 5 e 22.15 S 0.33 U 22.73 P 104% M 351436 F 2 R 178320 W 0 c 2163 w 222 I 0 O 9392 L 66.18 63.07 65.95 @#@FSLOADPOST 2024:10:08:16:41:57 mri_label2label N 5 68.31 63.71 66.10 #-------------------------------------------- #@# Smooth2 lh Tue Oct 8 16:41:57 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Tue Oct 8 16:41:57 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 3101183 of (3101183 3101187) to complete... Waiting for PID 3101187 of (3101183 3101187) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (3101183 3101187) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Tue Oct 8 16:42:00 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Tue Oct 8 16:42:00 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 3101416 of (3101416 3101419) to complete... Waiting for PID 3101419 of (3101416 3101419) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.7 mm, total surface area = 71311 mm^2 step 000: RMS=0.168 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 39.381759 mris_inflate stimesec 0.453349 mris_inflate ru_maxrss 179984 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 224595 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9064 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5223 mris_inflate ru_nivcsw 3850 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 47.1 mm, total surface area = 73650 mm^2 step 000: RMS=0.167 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 40.878733 mris_inflate stimesec 1.308563 mris_inflate ru_maxrss 184388 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 649807 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8384 mris_inflate ru_oublock 9360 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 6479 mris_inflate ru_nivcsw 4175 PIDs (3101416 3101419) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Tue Oct 8 16:42:21 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature -w -seed 1234 lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Tue Oct 8 16:42:21 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf reconbatchjobs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 3107066 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107070 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107073 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107076 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107079 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107082 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107086 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107089 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107092 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107095 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107098 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... Waiting for PID 3107102 of (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 18.302*4pi (229.985) --> -17 handles ICI = 151.7, FI = 1301.2, variation=21250.319 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 134 vertices thresholded to be in k1 ~ [-6.10 0.33], k2 ~ [-0.13 0.12] total integrated curvature = 0.543*4pi (6.818) --> 0 handles ICI = 1.4, FI = 9.1, variation=156.707 107 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 64 vertices thresholded to be in [-1.22 0.16] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.019, std = 0.030 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 19.677*4pi (247.262) --> -19 handles ICI = 153.2, FI = 1417.7, variation=22717.655 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 188 vertices thresholded to be in k1 ~ [-8.18 0.34], k2 ~ [-0.13 0.79] total integrated curvature = 0.513*4pi (6.448) --> 0 handles ICI = 1.5, FI = 11.4, variation=185.739 141 vertices thresholded to be in [-0.09 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 94 vertices thresholded to be in [-1.75 0.16] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.020, std = 0.038 done. PIDs (3107066 3107070 3107073 3107076 3107079 3107082 3107086 3107089 3107092 3107095 3107098 3107102) completed and logs appended. #-------------------------------------------- #@# Sphere lh Tue Oct 8 16:43:10 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Tue Oct 8 16:43:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 3119312 of (3119312 3119315) to complete... Waiting for PID 3119315 of (3119312 3119315) to complete... mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.314... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.24 pass 1: epoch 2 of 3 starting distance error %19.20 unfolding complete - removing small folds... starting distance error %19.15 removing remaining folds... final distance error %19.18 MRISunfold() return, current seed 1234 -01: dt=0.0000, 41 negative triangles VmPeak 774504 176: dt=0.9900, 41 negative triangles 177: dt=0.9900, 24 negative triangles 178: dt=0.9900, 14 negative triangles 179: dt=0.9900, 12 negative triangles 180: dt=0.9900, 16 negative triangles 181: dt=0.9900, 15 negative triangles 182: dt=0.9900, 13 negative triangles 183: dt=0.9900, 11 negative triangles 184: dt=0.9900, 14 negative triangles 185: dt=0.9900, 10 negative triangles 186: dt=0.9900, 9 negative triangles 187: dt=0.9900, 14 negative triangles 188: dt=0.9900, 10 negative triangles 189: dt=0.9900, 9 negative triangles 190: dt=0.9900, 12 negative triangles 191: dt=0.9900, 9 negative triangles 192: dt=0.9900, 9 negative triangles 193: dt=0.9900, 8 negative triangles 194: dt=0.9900, 10 negative triangles 195: dt=0.9900, 11 negative triangles 196: dt=0.9900, 7 negative triangles 197: dt=0.9900, 9 negative triangles 198: dt=0.9900, 9 negative triangles 199: dt=0.9900, 9 negative triangles 200: dt=0.9900, 7 negative triangles 201: dt=0.9900, 6 negative triangles 202: dt=0.9900, 7 negative triangles 203: dt=0.9900, 6 negative triangles 204: dt=0.9900, 6 negative triangles 205: dt=0.9900, 7 negative triangles 206: dt=0.9900, 7 negative triangles 207: dt=0.9900, 6 negative triangles 208: dt=0.9900, 6 negative triangles 209: dt=0.9900, 9 negative triangles 210: dt=0.9900, 5 negative triangles 211: dt=0.9900, 7 negative triangles 212: dt=0.9900, 7 negative triangles 213: dt=0.9900, 6 negative triangles 214: dt=0.9900, 5 negative triangles 215: dt=0.9900, 9 negative triangles 216: dt=0.9900, 4 negative triangles 217: dt=0.9900, 7 negative triangles 218: dt=0.9900, 4 negative triangles 219: dt=0.9900, 6 negative triangles 220: dt=0.9900, 3 negative triangles 221: dt=0.9900, 2 negative triangles 222: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1146 hours FSRUNTIME@ mris_sphere 0.1146 hours 4 threads #VMPC# mris_sphere VmPeak 774504 mris_sphere done mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.304... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.19 pass 1: epoch 2 of 3 starting distance error %19.18 unfolding complete - removing small folds... starting distance error %19.13 removing remaining folds... final distance error %19.13 MRISunfold() return, current seed 1234 -01: dt=0.0000, 295 negative triangles VmPeak 777528 108: dt=0.9900, 295 negative triangles 109: dt=0.9900, 154 negative triangles 110: dt=0.9900, 129 negative triangles 111: dt=0.9900, 120 negative triangles 112: dt=0.9900, 106 negative triangles 113: dt=0.9900, 92 negative triangles 114: dt=0.9900, 98 negative triangles 115: dt=0.9900, 87 negative triangles 116: dt=0.9900, 81 negative triangles 117: dt=0.9900, 72 negative triangles 118: dt=0.9900, 60 negative triangles 119: dt=0.9900, 64 negative triangles 120: dt=0.9900, 54 negative triangles 121: dt=0.9900, 52 negative triangles 122: dt=0.9900, 54 negative triangles 123: dt=0.9900, 46 negative triangles 124: dt=0.9900, 33 negative triangles 125: dt=0.9900, 30 negative triangles 126: dt=0.9900, 27 negative triangles 127: dt=0.9900, 23 negative triangles 128: dt=0.9900, 22 negative triangles 129: dt=0.9900, 13 negative triangles 130: dt=0.9900, 11 negative triangles 131: dt=0.9900, 13 negative triangles 132: dt=0.9900, 12 negative triangles 133: dt=0.9900, 9 negative triangles 134: dt=0.9900, 10 negative triangles 135: dt=0.9900, 9 negative triangles 136: dt=0.9900, 10 negative triangles 137: dt=0.9900, 9 negative triangles 138: dt=0.9900, 6 negative triangles 139: dt=0.9900, 9 negative triangles 140: dt=0.9900, 7 negative triangles 141: dt=0.9900, 5 negative triangles 142: dt=0.9900, 7 negative triangles 143: dt=0.9900, 5 negative triangles 144: dt=0.9900, 5 negative triangles 145: dt=0.9900, 3 negative triangles 146: dt=0.9900, 4 negative triangles 147: dt=0.9900, 2 negative triangles 148: dt=0.9900, 3 negative triangles 149: dt=0.9900, 1 negative triangles 150: dt=0.9900, 1 negative triangles 151: dt=0.9900, 3 negative triangles 152: dt=0.9900, 1 negative triangles 153: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.0911 hours FSRUNTIME@ mris_sphere 0.0911 hours 4 threads #VMPC# mris_sphere VmPeak 777528 mris_sphere done PIDs (3119312 3119315) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Tue Oct 8 16:50:03 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Tue Oct 8 16:50:03 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 3179522 of (3179522 3179525) to complete... Waiting for PID 3179525 of (3179522 3179525) to complete... mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts cmdline mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from ../surf/lh.sphere... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.305 curvature mean = 0.035, std = 0.818 curvature mean = 0.014, std = 0.886 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (7.50, -8.50, 2.00) sse = 165408.7, elapsed since starting=0.1617 min MRISrigidBodyAlignGlobal() done 0.16 min curvature mean = 0.041, std = 0.848 curvature mean = 0.005, std = 0.959 curvature mean = 0.040, std = 0.861 curvature mean = 0.002, std = 0.984 curvature mean = 0.040, std = 0.865 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.022, std = 0.272 curvature mean = 0.045, std = 0.252 curvature mean = 0.055, std = 0.375 curvature mean = 0.038, std = 0.313 curvature mean = 0.023, std = 0.561 curvature mean = 0.036, std = 0.341 curvature mean = 0.010, std = 0.697 curvature mean = 0.036, std = 0.353 curvature mean = 0.001, std = 0.802 MRISregister() return, current seed 0 -01: dt=0.0000, 11 negative triangles VmPeak 774540 104: dt=0.9900, 11 negative triangles 105: dt=0.9900, 9 negative triangles 106: dt=0.9900, 6 negative triangles 107: dt=0.9900, 8 negative triangles 108: dt=0.9900, 6 negative triangles 109: dt=0.9900, 5 negative triangles 110: dt=0.9900, 4 negative triangles 111: dt=0.9900, 5 negative triangles 112: dt=0.9900, 2 negative triangles 113: dt=0.9900, 5 negative triangles 114: dt=0.9900, 2 negative triangles 115: dt=0.9900, 3 negative triangles 116: dt=0.9900, 4 negative triangles 117: dt=0.9900, 2 negative triangles 118: dt=0.9900, 2 negative triangles 119: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.08 hours #VMPC# mris_register VmPeak 774540 FSRUNTIME@ mris_register 0.0771 hours 4 threads mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts cmdline mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from ../surf/rh.sphere... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.308 curvature mean = 0.029, std = 0.822 curvature mean = 0.017, std = 0.878 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (8.00, -8.00, 1.50) sse = 231205.5, elapsed since starting=0.1641 min MRISrigidBodyAlignGlobal() done 0.16 min curvature mean = 0.023, std = 0.853 curvature mean = 0.007, std = 0.956 curvature mean = 0.022, std = 0.865 curvature mean = 0.003, std = 0.983 curvature mean = 0.021, std = 0.868 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.022, std = 0.268 curvature mean = 0.037, std = 0.247 curvature mean = 0.065, std = 0.373 curvature mean = 0.033, std = 0.306 curvature mean = 0.028, std = 0.569 curvature mean = 0.032, std = 0.333 curvature mean = 0.012, std = 0.706 curvature mean = 0.031, std = 0.346 curvature mean = 0.003, std = 0.811 MRISregister() return, current seed 0 -01: dt=0.0000, 15 negative triangles VmPeak 777564 099: dt=0.9900, 15 negative triangles 100: dt=0.9405, 15 negative triangles 101: dt=0.9405, 11 negative triangles 102: dt=0.9405, 9 negative triangles 103: dt=0.9405, 13 negative triangles 104: dt=0.9405, 11 negative triangles 105: dt=0.9405, 9 negative triangles 106: dt=0.9405, 5 negative triangles 107: dt=0.9405, 10 negative triangles 108: dt=0.9405, 7 negative triangles 109: dt=0.9405, 9 negative triangles 110: dt=0.9405, 11 negative triangles 111: dt=0.9405, 9 negative triangles 112: dt=0.9405, 7 negative triangles 113: dt=0.9405, 9 negative triangles 114: dt=0.9405, 4 negative triangles 115: dt=0.9405, 8 negative triangles 116: dt=0.9405, 6 negative triangles 117: dt=0.9405, 9 negative triangles 118: dt=0.9405, 8 negative triangles 119: dt=0.9405, 4 negative triangles 120: dt=0.9405, 7 negative triangles 121: dt=0.9405, 3 negative triangles 122: dt=0.9405, 7 negative triangles 123: dt=0.9405, 3 negative triangles 124: dt=0.9405, 6 negative triangles 125: dt=0.9405, 2 negative triangles 126: dt=0.9405, 4 negative triangles 127: dt=0.9405, 3 negative triangles 128: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.09 hours #VMPC# mris_register VmPeak 777564 FSRUNTIME@ mris_register 0.0949 hours 4 threads PIDs (3179522 3179525) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Tue Oct 8 16:55:45 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Tue Oct 8 16:55:45 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 3193909 of (3193909 3193913) to complete... Waiting for PID 3193913 of (3193909 3193913) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (3193909 3193913) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Tue Oct 8 16:55:47 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Tue Oct 8 16:55:47 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 3193997 of (3193997 3194000) to complete... Waiting for PID 3194000 of (3193997 3194000) to complete... mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (3193997 3194000) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Tue Oct 8 16:55:48 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Tue Oct 8 16:55:48 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 3194078 of (3194078 3194081) to complete... Waiting for PID 3194081 of (3194078 3194081) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1208 labels changed using aseg relabeling using gibbs priors... 000: 2679 changed, 115461 examined... 001: 576 changed, 11518 examined... 002: 122 changed, 3336 examined... 003: 35 changed, 774 examined... 004: 17 changed, 206 examined... 005: 5 changed, 108 examined... 006: 0 changed, 30 examined... 225 labels changed using aseg 000: 74 total segments, 28 labels (179 vertices) changed 001: 46 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1641 vertices marked for relabeling... 1641 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 12 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1340 labels changed using aseg relabeling using gibbs priors... 000: 2375 changed, 119197 examined... 001: 498 changed, 10557 examined... 002: 135 changed, 2973 examined... 003: 39 changed, 841 examined... 004: 11 changed, 238 examined... 005: 6 changed, 66 examined... 006: 3 changed, 37 examined... 007: 1 changed, 22 examined... 008: 1 changed, 7 examined... 009: 0 changed, 7 examined... 194 labels changed using aseg 000: 87 total segments, 35 labels (155 vertices) changed 001: 52 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1055 vertices marked for relabeling... 1055 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 11 seconds. PIDs (3194078 3194081) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Tue Oct 8 16:56:00 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 230918 0.34171 0.12720 0.000510 1.9386 Corner 692754 60.00000 14.93727 0.326568 179.1995 Edge 346377 0.90114 0.21162 0.018023 3.5567 Hinge 346377 11.67298 12.77634 0.000000 179.9233 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25831, wmmin=5, clip=110 MRIfindBrightNonWM(): 342 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label MRISripNotLabel() ripped 10286/115461 vertices (105175 unripped) Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 442 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57731: xyz = (-41.9392,3.3393,26.9512) oxyz = (-41.9392,3.3393,26.9512) wxzy = (-41.9392,3.3393,26.9512) pxyz = (0,0,0) CBVO Creating mask 115461 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 107.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 107.7646560; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=2 had to be increased for 282 vertices, nripped=10728 mean border=86.6, 1053 (1053) missing vertices, mean dist 0.4 [2.3 (%11.1)->0.8 (%88.9))] %26 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0506 min Finding expansion regions mean absolute distance = 0.94 +- 1.08 3445 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1134715.2, rms=6.835 001: dt: 0.5000, sse=523035.5, rms=4.169 (39.008%) 002: dt: 0.5000, sse=331689.3, rms=2.862 (31.345%) 003: dt: 0.5000, sse=277945.5, rms=2.358 (17.612%) 004: dt: 0.5000, sse=256413.9, rms=2.118 (10.196%) 005: dt: 0.5000, sse=253620.5, rms=2.056 (2.910%) 006: dt: 0.5000, sse=247351.3, rms=1.983 (3.553%) rms = 2.0095/1.9829, sse=250890.7/247351.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 007: dt: 0.2500, sse=225195.2, rms=1.679 (15.315%) 008: dt: 0.2500, sse=218270.7, rms=1.539 (8.337%) rms = 1.5110/1.5392, sse=218603.5/218270.7, time step reduction 2 of 3 to 0.125 0 1 1 009: dt: 0.2500, sse=218603.5, rms=1.511 (1.832%) rms = 1.4951/1.5110, sse=219521.2/218603.5, time step reduction 3 of 3 to 0.062 0 1 1 010: dt: 0.1250, sse=219521.2, rms=1.495 (1.053%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 107.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 107.7646560; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=1 had to be increased for 174 vertices, nripped=10728 mean border=88.6, 545 (423) missing vertices, mean dist -0.3 [0.7 (%60.5)->0.3 (%39.5))] %45 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0326 min Finding expansion regions mean absolute distance = 0.51 +- 0.86 4255 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=436749.7, rms=3.492 011: dt: 0.5000, sse=298551.9, rms=2.388 (31.615%) 012: dt: 0.5000, sse=262308.4, rms=2.018 (15.480%) 013: dt: 0.5000, sse=254184.4, rms=1.911 (5.298%) rms = 1.9105/1.9112, sse=258195.9/254184.4, time step reduction 1 of 3 to 0.250 0 1 1 014: dt: 0.5000, sse=258195.9, rms=1.910 (0.036%) 015: dt: 0.2500, sse=228183.6, rms=1.537 (19.534%) 016: dt: 0.2500, sse=223884.0, rms=1.476 (3.960%) rms = 1.4645/1.4764, sse=223716.4/223884.0, time step reduction 2 of 3 to 0.125 0 0 1 017: dt: 0.2500, sse=223716.5, rms=1.465 (0.805%) rms = 1.4497/1.4645, sse=223915.4/223716.4, time step reduction 3 of 3 to 0.062 0 1 1 018: dt: 0.1250, sse=223915.4, rms=1.450 (1.014%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 107.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 107.7646560; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 273 vertices, nripped=10728 mean border=91.3, 517 (342) missing vertices, mean dist -0.3 [0.5 (%72.9)->0.3 (%27.1))] %70 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0271 min Finding expansion regions mean absolute distance = 0.40 +- 0.51 3541 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=445768.5, rms=3.588 019: dt: 0.5000, sse=270626.5, rms=2.111 (41.172%) 020: dt: 0.5000, sse=248983.7, rms=1.853 (12.229%) rms = 1.8417/1.8527, sse=247151.3/248983.7, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=247151.3, rms=1.842 (0.594%) 022: dt: 0.2500, sse=220786.5, rms=1.436 (22.007%) 023: dt: 0.2500, sse=219664.4, rms=1.373 (4.439%) rms = 1.3720/1.3726, sse=218192.7/219664.4, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=218192.7, rms=1.372 (0.050%) rms = 1.3516/1.3720, sse=215364.5/218192.7, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=215364.5, rms=1.352 (1.485%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 107.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 107.7646560; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 360 vertices, nripped=10728 mean border=92.3, 516 (305) missing vertices, mean dist -0.1 [0.3 (%59.7)->0.2 (%40.3))] %78 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0197 min Finding expansion regions mean absolute distance = 0.28 +- 0.38 3200 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=242785.5, rms=1.818 026: dt: 0.5000, sse=221848.1, rms=1.402 (22.868%) rms = 1.5816/1.4020, sse=227822.4/221848.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=213416.0, rms=1.249 (10.877%) rms = 1.2290/1.2495, sse=207050.0/213416.0, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=207050.0, rms=1.229 (1.639%) rms = 1.2087/1.2290, sse=205383.8/207050.0, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=205383.8, rms=1.209 (1.652%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 2.84 minutes #VMPC# mris_place_surfaces VmPeak 2042172 mris_place_surface done @#@FSTIME 2024:10:08:16:56:00 mris_place_surface N 25 e 180.27 S 5.58 U 316.83 P 178% M 1617876 F 2 R 4633767 W 0 c 30272 w 2607 I 0 O 8128 L 31.17 33.86 47.17 @#@FSLOADPOST 2024:10:08:16:59:00 mris_place_surface N 25 47.85 38.33 46.40 #-------------------------------------------- #@# WhiteSurfs rh Tue Oct 8 16:59:00 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 238390 0.34091 0.13158 0.001003 2.1056 Corner 715170 60.00000 15.42864 0.433079 177.9575 Edge 357585 0.90054 0.21781 0.029036 4.5100 Hinge 357585 11.48363 12.98296 0.000000 179.9804 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25831, wmmin=5, clip=110 MRIfindBrightNonWM(): 342 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label MRISripNotLabel() ripped 10469/119197 vertices (108728 unripped) Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 351 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59599: xyz = (6.07215,5.15717,27.7914) oxyz = (6.07215,5.15717,27.7914) wxzy = (6.07215,5.15717,27.7914) pxyz = (0,0,0) CBVO Creating mask 119197 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 109.7646560; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=2 had to be increased for 290 vertices, nripped=10820 mean border=86.8, 1064 (1064) missing vertices, mean dist 0.5 [2.4 (%11.0)->0.8 (%89.0))] %31 local maxima, %59 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0428 min Finding expansion regions mean absolute distance = 1.00 +- 1.11 3624 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1258366.0, rms=7.072 001: dt: 0.5000, sse=580596.7, rms=4.369 (38.225%) 002: dt: 0.5000, sse=354119.0, rms=2.907 (33.461%) 003: dt: 0.5000, sse=288550.2, rms=2.288 (21.278%) 004: dt: 0.5000, sse=260869.5, rms=1.995 (12.815%) 005: dt: 0.5000, sse=256225.5, rms=1.906 (4.447%) 006: dt: 0.5000, sse=251313.4, rms=1.822 (4.436%) rms = 1.8359/1.8218, sse=251775.8/251313.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 007: dt: 0.2500, sse=230485.9, rms=1.526 (16.225%) 008: dt: 0.2500, sse=222038.8, rms=1.386 (9.161%) rms = 1.3541/1.3864, sse=220272.6/222038.8, time step reduction 2 of 3 to 0.125 0 0 1 009: dt: 0.2500, sse=220272.6, rms=1.354 (2.329%) rms = 1.3406/1.3541, sse=217566.0/220272.6, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=217566.0, rms=1.341 (0.998%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 109.7646560; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=1 had to be increased for 233 vertices, nripped=10820 mean border=89.0, 808 (673) missing vertices, mean dist -0.3 [0.7 (%61.9)->0.3 (%38.1))] %49 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0319 min Finding expansion regions mean absolute distance = 0.54 +- 0.87 4082 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=456631.1, rms=3.518 011: dt: 0.5000, sse=304335.4, rms=2.307 (34.418%) 012: dt: 0.5000, sse=264170.1, rms=1.851 (19.748%) 013: dt: 0.5000, sse=249995.8, rms=1.671 (9.738%) rms = 1.6353/1.6712, sse=247554.5/249995.7, time step reduction 1 of 3 to 0.250 0 0 1 014: dt: 0.5000, sse=247554.5, rms=1.635 (2.150%) 015: dt: 0.2500, sse=225577.0, rms=1.216 (25.646%) 016: dt: 0.2500, sse=217505.2, rms=1.147 (5.697%) rms = 1.1353/1.1466, sse=218384.3/217505.2, time step reduction 2 of 3 to 0.125 0 1 1 017: dt: 0.2500, sse=218384.3, rms=1.135 (0.987%) rms = 1.1231/1.1353, sse=217472.8/218384.3, time step reduction 3 of 3 to 0.062 0 0 1 018: dt: 0.1250, sse=217472.8, rms=1.123 (1.077%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 109.7646560; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 245 vertices, nripped=10820 mean border=91.7, 815 (596) missing vertices, mean dist -0.3 [0.5 (%73.5)->0.3 (%26.5))] %72 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0188 min Finding expansion regions mean absolute distance = 0.42 +- 0.53 3281 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=462533.4, rms=3.583 019: dt: 0.5000, sse=275131.8, rms=2.001 (44.153%) 020: dt: 0.5000, sse=243469.6, rms=1.575 (21.295%) rms = 1.5299/1.5748, sse=244753.9/243469.6, time step reduction 1 of 3 to 0.250 0 1 1 021: dt: 0.5000, sse=244753.9, rms=1.530 (2.851%) 022: dt: 0.2500, sse=219062.3, rms=1.073 (29.881%) rms = 1.0015/1.0728, sse=220237.9/219062.3, time step reduction 2 of 3 to 0.125 0 1 0 023: dt: 0.2500, sse=220237.9, rms=1.002 (6.639%) rms = 0.9822/1.0015, sse=212918.9/220237.9, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=212918.9, rms=0.982 (1.931%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7646560; border_low = 80.0000000; outside_low = 67.9684600; outside_hi = 109.7646560; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 303 vertices, nripped=10820 mean border=92.7, 829 (539) missing vertices, mean dist -0.1 [0.3 (%60.4)->0.2 (%39.6))] %80 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0121 min Finding expansion regions mean absolute distance = 0.29 +- 0.39 2743 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=243236.1, rms=1.600 025: dt: 0.5000, sse=218894.5, rms=1.036 (35.239%) rms = 1.2234/1.0364, sse=225996.5/218894.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=207606.5, rms=0.848 (18.152%) rms = 0.8049/0.8483, sse=204429.9/207606.5, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=204429.9, rms=0.805 (5.116%) rms = 0.7895/0.8049, sse=203118.2/204429.9, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=203118.2, rms=0.789 (1.909%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 2.38 minutes #VMPC# mris_place_surfaces VmPeak 2080460 mris_place_surface done @#@FSTIME 2024:10:08:16:59:00 mris_place_surface N 25 e 151.18 S 3.37 U 270.32 P 181% M 1657656 F 3 R 3847141 W 0 c 25114 w 1712 I 0 O 8384 L 47.85 38.33 46.40 @#@FSLOADPOST 2024:10:08:17:01:32 mris_place_surface N 25 28.21 36.08 44.48 #-------------------------------------------- #@# T1PialSurf lh Tue Oct 8 17:01:32 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 230918 0.34593 0.14372 0.001337 2.0284 Corner 692754 60.00000 16.43794 0.247267 179.1995 Edge 346377 0.90867 0.23474 0.011589 3.5567 Hinge 346377 11.81244 13.10818 0.000000 179.8281 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25831, wmmin=5, clip=110 MRIfindBrightNonWM(): 342 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 69.0704 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 8922/115461 vertices (106539 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57731: xyz = (-41.7129,2.76044,26.5245) oxyz = (-41.7129,2.76044,26.5245) wxzy = (-41.7129,2.76044,26.5245) pxyz = (-41.7129,2.76044,26.5245) CBVO Creating mask 115461 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2353440; border_hi = 67.9684600; border_low = 43.9053880; outside_low = 10.0000000; outside_hi = 61.9526940; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=2 had to be increased for 313 vertices, nripped=8922 mean border=63.0, 954 (954) missing vertices, mean dist 2.3 [1.8 (%0.2)->2.6 (%99.8))] %38 local maxima, %41 large gradients and %12 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0422 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=18961796.0, rms=29.833 001: dt: 0.5000, sse=14863241.0, rms=26.381 (11.573%) 002: dt: 0.5000, sse=11682187.0, rms=23.351 (11.486%) 003: dt: 0.5000, sse=9328080.0, rms=20.825 (10.815%) 004: dt: 0.5000, sse=7576730.5, rms=18.726 (10.081%) 005: dt: 0.5000, sse=6186606.0, rms=16.874 (9.889%) 006: dt: 0.5000, sse=4957990.5, rms=15.049 (10.818%) 007: dt: 0.5000, sse=3880605.5, rms=13.242 (12.006%) 008: dt: 0.5000, sse=2965721.5, rms=11.486 (13.261%) 009: dt: 0.5000, sse=2242643.0, rms=9.878 (13.996%) 010: dt: 0.5000, sse=1728055.4, rms=8.551 (13.438%) 011: dt: 0.5000, sse=1385315.8, rms=7.536 (11.864%) 012: dt: 0.5000, sse=1163432.5, rms=6.798 (9.794%) 013: dt: 0.5000, sse=1024937.6, rms=6.292 (7.441%) 014: dt: 0.5000, sse=930010.8, rms=5.920 (5.927%) 015: dt: 0.5000, sse=870432.9, rms=5.673 (4.173%) 016: dt: 0.5000, sse=825409.9, rms=5.478 (3.437%) 017: dt: 0.5000, sse=796053.0, rms=5.346 (2.405%) 018: dt: 0.5000, sse=768986.9, rms=5.222 (2.324%) 019: dt: 0.5000, sse=752819.2, rms=5.145 (1.461%) 020: dt: 0.5000, sse=735424.1, rms=5.062 (1.619%) rms = 5.0203/5.0620, sse=727008.5/735424.1, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=727008.6, rms=5.020 (0.823%) 022: dt: 0.2500, sse=490860.7, rms=3.718 (25.949%) 023: dt: 0.2500, sse=439254.8, rms=3.370 (9.338%) 024: dt: 0.2500, sse=427085.5, rms=3.282 (2.620%) 025: dt: 0.2500, sse=419040.4, rms=3.223 (1.788%) rms = 3.1943/3.2235, sse=415170.3/419040.4, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=415170.3, rms=3.194 (0.904%) 027: dt: 0.1250, sse=386723.8, rms=2.973 (6.931%) rms = 2.9380/2.9729, sse=382391.9/386723.8, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=382391.9, rms=2.938 (1.174%) maximum number of reductions reached, breaking from loop positioning took 1.5 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2353440; border_hi = 67.9684600; border_low = 43.9053880; outside_low = 10.0000000; outside_hi = 61.9526940; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=1 had to be increased for 2286 vertices, nripped=8922 mean border=60.0, 487 (46) missing vertices, mean dist 0.2 [0.2 (%33.5)->0.4 (%66.5))] %59 local maxima, %24 large gradients and % 8 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0122 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=836131.4, rms=5.270 029: dt: 0.5000, sse=737071.4, rms=4.802 (8.881%) rms = 4.8297/4.8022, sse=738401.6/737071.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=550142.4, rms=3.778 (21.319%) 031: dt: 0.2500, sse=483410.5, rms=3.343 (11.531%) 032: dt: 0.2500, sse=467969.5, rms=3.231 (3.329%) 033: dt: 0.2500, sse=460195.3, rms=3.176 (1.727%) rms = 3.1513/3.1756, sse=456866.3/460195.3, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=456866.3, rms=3.151 (0.768%) 035: dt: 0.1250, sse=432508.7, rms=2.961 (6.022%) rms = 2.9240/2.9615, sse=427820.6/432508.6, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=427820.6, rms=2.924 (1.265%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2353440; border_hi = 67.9684600; border_low = 43.9053880; outside_low = 10.0000000; outside_hi = 61.9526940; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 2548 vertices, nripped=8922 mean border=58.3, 636 (22) missing vertices, mean dist 0.1 [0.2 (%36.7)->0.3 (%63.3))] %69 local maxima, %14 large gradients and % 8 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0072 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=544213.4, rms=3.726 rms = 4.6189/3.7263, sse=703773.7/544213.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=463501.8, rms=3.173 (14.847%) 038: dt: 0.2500, sse=444655.1, rms=3.029 (4.536%) rms = 2.9890/3.0291, sse=439056.9/444655.1, time step reduction 2 of 3 to 0.125 0 0 1 039: dt: 0.2500, sse=439056.9, rms=2.989 (1.324%) 040: dt: 0.1250, sse=425263.8, rms=2.877 (3.761%) rms = 2.8473/2.8766, sse=421623.0/425263.7, time step reduction 3 of 3 to 0.062 0 0 1 041: dt: 0.1250, sse=421623.0, rms=2.847 (1.017%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2353440; border_hi = 67.9684600; border_low = 43.9053880; outside_low = 10.0000000; outside_hi = 61.9526940; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=115461 Gdiag_no=-1 vno start=0, stop=115461 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 2010 vertices, nripped=8922 mean border=57.6, 1269 (17) missing vertices, mean dist 0.0 [0.2 (%45.1)->0.2 (%54.9))] %71 local maxima, %12 large gradients and % 8 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0049 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=443491.0, rms=3.026 rms = 3.7162/3.0264, sse=541767.9/443491.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 042: dt: 0.2500, sse=419688.0, rms=2.834 (6.349%) 043: dt: 0.2500, sse=411820.4, rms=2.773 (2.166%) rms = 2.7528/2.7728, sse=408992.7/411820.4, time step reduction 2 of 3 to 0.125 0 0 1 044: dt: 0.2500, sse=408992.7, rms=2.753 (0.724%) 045: dt: 0.1250, sse=397256.6, rms=2.651 (3.714%) rms = 2.6252/2.6505, sse=394227.3/397256.6, time step reduction 3 of 3 to 0.062 0 0 1 046: dt: 0.1250, sse=394227.3, rms=2.625 (0.955%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 6 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 2.55 minutes #VMPC# mris_place_surfaces VmPeak 1466820 mris_place_surface done @#@FSTIME 2024:10:08:17:01:32 mris_place_surface N 28 e 160.09 S 1.94 U 320.47 P 201% M 1030404 F 2 R 1934899 W 0 c 28503 w 2265 I 0 O 8128 L 28.21 36.08 44.48 @#@FSLOADPOST 2024:10:08:17:04:12 mris_place_surface N 28 17.36 30.65 41.28 #-------------------------------------------- #@# T1PialSurf rh Tue Oct 8 17:04:12 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 238390 0.34408 0.14582 0.000532 2.9135 Corner 715170 60.00000 16.84957 0.366223 178.2345 Edge 357585 0.90648 0.23695 0.005840 3.3184 Hinge 357585 11.67533 13.42008 0.000000 179.9223 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25831, wmmin=5, clip=110 MRIfindBrightNonWM(): 342 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 70.0704 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 8993/119197 vertices (110204 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59599: xyz = (6.036,5.20373,27.773) oxyz = (6.036,5.20373,27.773) wxzy = (6.036,5.20373,27.773) pxyz = (6.036,5.20373,27.773) CBVO Creating mask 119197 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2353440; border_hi = 67.9684600; border_low = 43.9053880; outside_low = 10.0000000; outside_hi = 61.9526940; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=2 had to be increased for 349 vertices, nripped=8993 mean border=63.6, 1056 (1056) missing vertices, mean dist 2.2 [2.8 (%0.0)->2.7 (%100.0))] %35 local maxima, %40 large gradients and %16 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0389 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=19591492.0, rms=29.826 001: dt: 0.5000, sse=15436632.0, rms=26.443 (11.341%) 002: dt: 0.5000, sse=12211476.0, rms=23.483 (11.194%) 003: dt: 0.5000, sse=9817977.0, rms=21.018 (10.499%) 004: dt: 0.5000, sse=8031005.5, rms=18.968 (9.751%) 005: dt: 0.5000, sse=6596577.0, rms=17.146 (9.606%) 006: dt: 0.5000, sse=5317266.0, rms=15.339 (10.539%) 007: dt: 0.5000, sse=4177308.0, rms=13.527 (11.817%) 008: dt: 0.5000, sse=3200957.5, rms=11.753 (13.111%) 009: dt: 0.5000, sse=2416224.5, rms=10.104 (14.035%) 010: dt: 0.5000, sse=1835161.1, rms=8.681 (14.080%) 011: dt: 0.5000, sse=1460497.1, rms=7.623 (12.192%) 012: dt: 0.5000, sse=1232754.4, rms=6.898 (9.501%) 013: dt: 0.5000, sse=1092797.4, rms=6.411 (7.063%) 014: dt: 0.5000, sse=999784.0, rms=6.065 (5.402%) 015: dt: 0.5000, sse=935734.9, rms=5.813 (4.150%) 016: dt: 0.5000, sse=890086.2, rms=5.626 (3.220%) 017: dt: 0.5000, sse=853116.8, rms=5.470 (2.777%) 018: dt: 0.5000, sse=824977.3, rms=5.347 (2.244%) 019: dt: 0.5000, sse=802330.0, rms=5.246 (1.896%) 020: dt: 0.5000, sse=783851.7, rms=5.161 (1.602%) 021: dt: 0.5000, sse=770193.0, rms=5.098 (1.233%) rms = 5.0482/5.0979, sse=759666.1/770193.0, time step reduction 1 of 3 to 0.250 0 0 1 022: dt: 0.5000, sse=759666.1, rms=5.048 (0.974%) 023: dt: 0.2500, sse=534935.9, rms=3.872 (23.292%) 024: dt: 0.2500, sse=487706.5, rms=3.579 (7.564%) 025: dt: 0.2500, sse=477426.3, rms=3.511 (1.908%) rms = 3.4675/3.5112, sse=470827.8/477426.3, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=470827.8, rms=3.468 (1.243%) 027: dt: 0.1250, sse=441113.5, rms=3.262 (5.931%) rms = 3.2299/3.2618, sse=436651.8/441113.5, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=436651.8, rms=3.230 (0.980%) maximum number of reductions reached, breaking from loop positioning took 1.5 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2353440; border_hi = 67.9684600; border_low = 43.9053880; outside_low = 10.0000000; outside_hi = 61.9526940; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=1 had to be increased for 3565 vertices, nripped=8993 mean border=60.9, 1113 (303) missing vertices, mean dist 0.2 [0.1 (%35.1)->0.4 (%64.9))] %54 local maxima, %25 large gradients and %13 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0124 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=844252.9, rms=5.171 029: dt: 0.5000, sse=785522.9, rms=4.903 (5.196%) rms = 4.8825/4.9027, sse=777362.6/785522.9, time step reduction 1 of 3 to 0.250 0 0 1 030: dt: 0.5000, sse=777362.6, rms=4.883 (0.412%) 031: dt: 0.2500, sse=564137.8, rms=3.739 (23.429%) 032: dt: 0.2500, sse=523597.5, rms=3.484 (6.810%) rms = 3.4430/3.4840, sse=517669.6/523597.5, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=517669.6, rms=3.443 (1.176%) 034: dt: 0.1250, sse=485728.6, rms=3.222 (6.425%) rms = 3.1798/3.2218, sse=479868.8/485728.6, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=479868.8, rms=3.180 (1.303%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2353440; border_hi = 67.9684600; border_low = 43.9053880; outside_low = 10.0000000; outside_hi = 61.9526940; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 3927 vertices, nripped=8993 mean border=59.5, 1217 (215) missing vertices, mean dist 0.1 [0.1 (%38.4)->0.3 (%61.6))] %64 local maxima, %15 large gradients and %13 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0078 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=571709.5, rms=3.760 rms = 4.5830/3.7600, sse=723111.8/571709.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=506474.0, rms=3.339 (11.194%) 037: dt: 0.2500, sse=491644.3, rms=3.236 (3.082%) rms = 3.2059/3.2362, sse=487009.9/491644.3, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=487009.9, rms=3.206 (0.935%) 039: dt: 0.1250, sse=473664.4, rms=3.108 (3.050%) rms = 3.0840/3.1081, sse=470351.9/473664.4, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=470351.9, rms=3.084 (0.776%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2353440; border_hi = 67.9684600; border_low = 43.9053880; outside_low = 10.0000000; outside_hi = 61.9526940; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=119197 Gdiag_no=-1 vno start=0, stop=119197 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 3254 vertices, nripped=8993 mean border=58.9, 2075 (167) missing vertices, mean dist 0.1 [0.2 (%45.4)->0.2 (%54.6))] %66 local maxima, %12 large gradients and %12 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0053 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=485565.0, rms=3.197 rms = 3.7329/3.1974, sse=566275.5/485565.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 041: dt: 0.2500, sse=464231.3, rms=3.041 (4.896%) 042: dt: 0.2500, sse=457128.9, rms=2.990 (1.655%) rms = 2.9603/2.9905, sse=452621.6/457128.9, time step reduction 2 of 3 to 0.125 0 0 1 043: dt: 0.2500, sse=452621.6, rms=2.960 (1.009%) 044: dt: 0.1250, sse=441687.2, rms=2.875 (2.896%) rms = 2.8496/2.8746, sse=438380.4/441687.1, time step reduction 3 of 3 to 0.062 0 0 1 045: dt: 0.1250, sse=438380.4, rms=2.850 (0.868%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 44 intersecting 001: 31 intersecting 002: 10 intersecting step 1 with no progress (num=12, old_num=10) 003: 12 intersecting 004: 4 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.75 minutes #VMPC# mris_place_surfaces VmPeak 1482760 mris_place_surface done @#@FSTIME 2024:10:08:17:04:12 mris_place_surface N 28 e 171.43 S 1.73 U 353.09 P 206% M 1047648 F 1 R 1532157 W 0 c 31159 w 2301 I 8384 O 8384 L 17.36 30.65 41.28 @#@FSLOADPOST 2024:10:08:17:07:03 mris_place_surface N 28 11.93 22.55 36.39 #@# white curv lh Tue Oct 8 17:07:03 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2024:10:08:17:07:04 mris_place_surface N 5 e 1.57 S 0.12 U 1.85 P 125% M 159332 F 1 R 42899 W 0 c 180 w 119 I 0 O 904 L 11.93 22.55 36.39 @#@FSLOADPOST 2024:10:08:17:07:05 mris_place_surface N 5 11.93 22.37 36.26 #@# white area lh Tue Oct 8 17:07:05 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2024:10:08:17:07:05 mris_place_surface N 3 e 0.70 S 0.10 U 1.06 P 164% M 159400 F 1 R 42993 W 0 c 106 w 71 I 0 O 904 L 11.93 22.37 36.26 @#@FSLOADPOST 2024:10:08:17:07:06 mris_place_surface N 3 11.93 22.37 36.26 #@# pial curv lh Tue Oct 8 17:07:06 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2024:10:08:17:07:06 mris_place_surface N 5 e 1.47 S 0.09 U 1.73 P 123% M 159228 F 3 R 42978 W 0 c 172 w 106 I 0 O 904 L 11.93 22.37 36.26 @#@FSLOADPOST 2024:10:08:17:07:08 mris_place_surface N 5 11.93 22.37 36.26 #@# pial area lh Tue Oct 8 17:07:08 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2024:10:08:17:07:08 mris_place_surface N 3 e 0.56 S 0.11 U 0.79 P 161% M 159372 F 2 R 42980 W 0 c 85 w 114 I 0 O 904 L 11.93 22.37 36.26 @#@FSLOADPOST 2024:10:08:17:07:08 mris_place_surface N 3 11.93 22.37 36.26 #@# thickness lh Tue Oct 8 17:07:08 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 115461 vertices processed 25000 of 115461 vertices processed 50000 of 115461 vertices processed 75000 of 115461 vertices processed 100000 of 115461 vertices processed 0 of 115461 vertices processed 25000 of 115461 vertices processed 50000 of 115461 vertices processed 75000 of 115461 vertices processed 100000 of 115461 vertices processed thickness calculation complete, 177:1408 truncations. 61951 vertices at 0 distance 96221 vertices at 1 distance 50159 vertices at 2 distance 15527 vertices at 3 distance 4543 vertices at 4 distance 1457 vertices at 5 distance 501 vertices at 6 distance 202 vertices at 7 distance 96 vertices at 8 distance 73 vertices at 9 distance 44 vertices at 10 distance 19 vertices at 11 distance 21 vertices at 12 distance 19 vertices at 13 distance 24 vertices at 14 distance 13 vertices at 15 distance 12 vertices at 16 distance 8 vertices at 17 distance 6 vertices at 18 distance 12 vertices at 19 distance 14 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2024:10:08:17:07:08 mris_place_surface N 6 e 25.95 S 0.13 U 26.23 P 101% M 159660 F 1 R 153234 W 0 c 2326 w 109 I 0 O 904 L 11.93 22.37 36.26 @#@FSLOADPOST 2024:10:08:17:07:34 mris_place_surface N 6 12.12 21.59 35.63 #@# area and vertex vol lh Tue Oct 8 17:07:34 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume PIB23-310_VYr0_Bay3prisma lh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Total face volume 208392 Total vertex volume 208137 (mask=0) #@# PIB23-310_VYr0_Bay3prisma lh 208137 vertexvol Done @#@FSTIME 2024:10:08:17:07:34 vertexvol N 4 e 1.58 S 0.17 U 1.82 P 126% M 265220 F 2 R 75527 W 0 c 187 w 326 I 0 O 2712 L 12.12 21.59 35.63 @#@FSLOADPOST 2024:10:08:17:07:36 vertexvol N 4 12.76 21.56 35.54 #@# white curv rh Tue Oct 8 17:07:36 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2024:10:08:17:07:36 mris_place_surface N 5 e 1.45 S 0.10 U 1.72 P 125% M 164628 F 2 R 44346 W 0 c 159 w 97 I 0 O 936 L 12.76 21.56 35.54 @#@FSLOADPOST 2024:10:08:17:07:38 mris_place_surface N 5 12.76 21.56 35.54 #@# white area rh Tue Oct 8 17:07:38 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2024:10:08:17:07:38 mris_place_surface N 3 e 0.57 S 0.08 U 0.85 P 164% M 164704 F 0 R 44356 W 0 c 81 w 116 I 0 O 936 L 12.76 21.56 35.54 @#@FSLOADPOST 2024:10:08:17:07:38 mris_place_surface N 3 12.76 21.56 35.54 #@# pial curv rh Tue Oct 8 17:07:38 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2024:10:08:17:07:38 mris_place_surface N 5 e 1.41 S 0.10 U 1.66 P 125% M 164868 F 3 R 44343 W 0 c 159 w 121 I 8384 O 936 L 12.76 21.56 35.54 @#@FSLOADPOST 2024:10:08:17:07:40 mris_place_surface N 5 12.78 21.42 35.42 #@# pial area rh Tue Oct 8 17:07:40 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2024:10:08:17:07:40 mris_place_surface N 3 e 0.58 S 0.11 U 0.84 P 164% M 164624 F 1 R 44345 W 0 c 85 w 109 I 0 O 936 L 12.78 21.42 35.42 @#@FSLOADPOST 2024:10:08:17:07:41 mris_place_surface N 3 12.78 21.42 35.42 #@# thickness rh Tue Oct 8 17:07:41 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 119197 vertices processed 25000 of 119197 vertices processed 50000 of 119197 vertices processed 75000 of 119197 vertices processed 100000 of 119197 vertices processed 0 of 119197 vertices processed 25000 of 119197 vertices processed 50000 of 119197 vertices processed 75000 of 119197 vertices processed 100000 of 119197 vertices processed thickness calculation complete, 122:1450 truncations. 60740 vertices at 0 distance 96948 vertices at 1 distance 53856 vertices at 2 distance 17878 vertices at 3 distance 5559 vertices at 4 distance 1925 vertices at 5 distance 729 vertices at 6 distance 295 vertices at 7 distance 141 vertices at 8 distance 85 vertices at 9 distance 63 vertices at 10 distance 51 vertices at 11 distance 50 vertices at 12 distance 32 vertices at 13 distance 15 vertices at 14 distance 5 vertices at 15 distance 0 vertices at 16 distance 1 vertices at 17 distance 4 vertices at 18 distance 5 vertices at 19 distance 12 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2024:10:08:17:07:41 mris_place_surface N 6 e 26.68 S 0.19 U 26.91 P 101% M 164888 F 1 R 159145 W 0 c 2382 w 97 I 0 O 936 L 12.78 21.42 35.42 @#@FSLOADPOST 2024:10:08:17:08:07 mris_place_surface N 6 12.73 20.71 34.82 #@# area and vertex vol rh Tue Oct 8 17:08:07 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume PIB23-310_VYr0_Bay3prisma rh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Total face volume 218567 Total vertex volume 218281 (mask=0) #@# PIB23-310_VYr0_Bay3prisma rh 218281 vertexvol Done @#@FSTIME 2024:10:08:17:08:07 vertexvol N 4 e 1.47 S 0.17 U 1.73 P 129% M 273536 F 1 R 77958 W 0 c 172 w 326 I 0 O 2808 L 12.73 20.71 34.82 @#@FSLOADPOST 2024:10:08:17:08:09 vertexvol N 4 12.73 20.71 34.82 #----------------------------------------- #@# Curvature Stats lh Tue Oct 8 17:08:09 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PIB23-310_VYr0_Bay3prisma lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ PIB23-310_VYr0_Bay3prisma/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 240 ] Gb_filter = 0 @#@FSTIME 2024:10:08:17:08:09 mris_curvature_stats N 11 e 2.42 S 0.16 U 2.60 P 114% M 159616 F 2 R 73901 W 0 c 251 w 475 I 0 O 7272 L 12.73 20.71 34.82 @#@FSLOADPOST 2024:10:08:17:08:12 mris_curvature_stats N 11 12.51 20.53 34.68 #----------------------------------------- #@# Curvature Stats rh Tue Oct 8 17:08:12 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PIB23-310_VYr0_Bay3prisma rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ PIB23-310_VYr0_Bay3prisma/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 225 ] Gb_filter = 0 WARN: S lookup min: -0.035266 WARN: S explicit min: 0.000000 vertex = 52 @#@FSTIME 2024:10:08:17:08:12 mris_curvature_stats N 11 e 2.38 S 0.09 U 2.67 P 116% M 164588 F 2 R 77276 W 0 c 253 w 300 I 0 O 7528 L 12.51 20.53 34.68 @#@FSLOADPOST 2024:10:08:17:08:14 mris_curvature_stats N 11 12.51 20.53 34.68 #-------------------------------------------- #@# Cortical ribbon mask Tue Oct 8 17:08:14 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon PIB23-310_VYr0_Bay3prisma SUBJECTS_DIR is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing loading input data... Running hemis serially Processing left hemi computing distance to left white surface computing distance to left pial surface Processing right hemi computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 61 writing volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz mris_volmask took 6.88 minutes writing ribbon files @#@FSTIME 2024:10:08:17:08:14 mris_volmask N 12 e 413.06 S 1.43 U 412.92 P 100% M 912500 F 1 R 1399568 W 0 c 37162 w 275 I 0 O 816 L 12.51 20.53 34.68 @#@FSLOADPOST 2024:10:08:17:15:07 mris_volmask N 12 11.31 14.51 26.73 #----------------------------------------- #@# Cortical Parc 2 lh Tue Oct 8 17:15:07 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Tue Oct 8 17:15:07 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 3227980 of (3227980 3227984) to complete... Waiting for PID 3227984 of (3227980 3227984) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 3.0 using min determinant for regularization = 0.088 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 554 labels changed using aseg relabeling using gibbs priors... 000: 7389 changed, 115461 examined... 001: 1696 changed, 29102 examined... 002: 496 changed, 9165 examined... 003: 218 changed, 2886 examined... 004: 115 changed, 1246 examined... 005: 61 changed, 680 examined... 006: 33 changed, 349 examined... 007: 22 changed, 188 examined... 008: 10 changed, 127 examined... 009: 3 changed, 56 examined... 010: 2 changed, 15 examined... 011: 2 changed, 10 examined... 012: 1 changed, 10 examined... 013: 0 changed, 8 examined... 110 labels changed using aseg 000: 195 total segments, 109 labels (1209 vertices) changed 001: 90 total segments, 5 labels (13 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1110 vertices marked for relabeling... 1110 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 13 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.021 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 807 labels changed using aseg relabeling using gibbs priors... 000: 8020 changed, 119197 examined... 001: 1811 changed, 31305 examined... 002: 539 changed, 9691 examined... 003: 205 changed, 3102 examined... 004: 107 changed, 1205 examined... 005: 58 changed, 604 examined... 006: 37 changed, 319 examined... 007: 23 changed, 199 examined... 008: 13 changed, 132 examined... 009: 10 changed, 76 examined... 010: 6 changed, 58 examined... 011: 1 changed, 25 examined... 012: 0 changed, 7 examined... 73 labels changed using aseg 000: 229 total segments, 142 labels (1313 vertices) changed 001: 89 total segments, 2 labels (2 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 64 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 650 vertices marked for relabeling... 650 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 13 seconds. PIDs (3227980 3227984) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Tue Oct 8 17:15:21 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Tue Oct 8 17:15:21 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 3229241 of (3229241 3229245) to complete... Waiting for PID 3229245 of (3229241 3229245) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1480 labels changed using aseg relabeling using gibbs priors... 000: 1709 changed, 115461 examined... 001: 431 changed, 8198 examined... 002: 125 changed, 2421 examined... 003: 63 changed, 711 examined... 004: 52 changed, 375 examined... 005: 40 changed, 298 examined... 006: 27 changed, 214 examined... 007: 20 changed, 151 examined... 008: 18 changed, 110 examined... 009: 11 changed, 101 examined... 010: 10 changed, 64 examined... 011: 10 changed, 59 examined... 012: 13 changed, 58 examined... 013: 11 changed, 66 examined... 014: 13 changed, 58 examined... 015: 10 changed, 63 examined... 016: 10 changed, 50 examined... 017: 10 changed, 53 examined... 018: 9 changed, 49 examined... 019: 7 changed, 46 examined... 020: 6 changed, 41 examined... 021: 8 changed, 31 examined... 022: 10 changed, 37 examined... 023: 7 changed, 50 examined... 024: 9 changed, 38 examined... 025: 5 changed, 41 examined... 026: 3 changed, 26 examined... 027: 3 changed, 22 examined... 028: 4 changed, 21 examined... 029: 2 changed, 21 examined... 030: 1 changed, 9 examined... 031: 1 changed, 7 examined... 032: 1 changed, 8 examined... 033: 1 changed, 6 examined... 034: 2 changed, 8 examined... 035: 2 changed, 8 examined... 036: 3 changed, 14 examined... 037: 5 changed, 19 examined... 038: 5 changed, 23 examined... 039: 3 changed, 22 examined... 040: 2 changed, 22 examined... 041: 4 changed, 10 examined... 042: 5 changed, 21 examined... 043: 1 changed, 21 examined... 044: 1 changed, 8 examined... 045: 1 changed, 7 examined... 046: 0 changed, 6 examined... 594 labels changed using aseg 000: 48 total segments, 15 labels (69 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 8 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 582 vertices marked for relabeling... 582 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1686 labels changed using aseg relabeling using gibbs priors... 000: 1773 changed, 119197 examined... 001: 425 changed, 8366 examined... 002: 128 changed, 2460 examined... 003: 56 changed, 711 examined... 004: 34 changed, 315 examined... 005: 20 changed, 183 examined... 006: 19 changed, 114 examined... 007: 8 changed, 92 examined... 008: 10 changed, 50 examined... 009: 8 changed, 53 examined... 010: 4 changed, 47 examined... 011: 1 changed, 27 examined... 012: 1 changed, 8 examined... 013: 0 changed, 6 examined... 344 labels changed using aseg 000: 63 total segments, 30 labels (207 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 366 vertices marked for relabeling... 366 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. PIDs (3229241 3229245) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Tue Oct 8 17:15:31 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts pctsurfcon --s PIB23-310_VYr0_Bay3prisma --lh-only #----------------------------------------- #@# WM/GM Contrast rh Tue Oct 8 17:15:31 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts pctsurfcon --s PIB23-310_VYr0_Bay3prisma --rh-only Waiting for PID 3229687 of (3229687 3229691) to complete... Waiting for PID 3229691 of (3229687 3229691) to complete... pctsurfcon --s PIB23-310_VYr0_Bay3prisma --lh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/pctsurfcon.log Tue Oct 8 17:15:31 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/pctsurfcon pctsurfcon 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229687/lh.wm.mgh --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 74756 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229687/lh.wm.mgh Dim: 115461 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229687/lh.gm.mgh --projfrac 0.3 --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 88402 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229687/lh.gm.mgh Dim: 115461 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229687/lh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229687/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/lh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/lh.w-g.pct.stats --snr sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Seg base 1000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh Vertex Area is 0.691848 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s PIB23-310_VYr0_Bay3prisma --rh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/pctsurfcon.log Tue Oct 8 17:15:31 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/pctsurfcon pctsurfcon 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229691/rh.wm.mgh --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 76714 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229691/rh.wm.mgh Dim: 119197 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229691/rh.gm.mgh --projfrac 0.3 --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 91177 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229691/rh.gm.mgh Dim: 119197 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229691/rh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3229691/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/rh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/rh.w-g.pct.stats --snr sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Seg base 2000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh Vertex Area is 0.688153 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (3229687 3229691) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Tue Oct 8 17:15:36 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2734 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3036 voxels changed to hypointensity... 5369 hypointense voxels neighboring cortex changed @#@FSTIME 2024:10:08:17:15:36 mri_relabel_hypointensities N 3 e 16.70 S 0.75 U 17.73 P 110% M 453756 F 1 R 533422 W 0 c 1661 w 167 I 0 O 680 L 12.81 14.59 26.37 @#@FSLOADPOST 2024:10:08:17:15:52 mri_relabel_hypointensities N 3 11.87 14.30 26.08 #----------------------------------------- #@# APas-to-ASeg Tue Oct 8 17:15:52 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz --threads 4 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aseg.mgz 72 avail.processors, using 4 Loading aseg.presurf.hypos.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Done loading 0 128 64 192 1 193 65 2 194 66 3 195 67 196 4 68 197 5 129 69 198 6 70 199 7 200 8 71 201 9 72 202 10 203 11 73 204 12 130 205 13 74 206 14 207 75 15 208 16 209 76 17 131 210 18 211 77 19 212 20 213 21 78 214 22 132 215 23 79 216 24 217 25 80 218 26 133 219 27 220 81 28 221 29 222 30 82 134 223 31 224 32 83 225 33 226 135 34 227 35 84 228 36 229 37 136 230 85 38 231 39 232 40 86 233 137 41 234 42 235 43 236 87 44 138 237 45 238 46 239 47 88 240 48 241 139 49 242 50 243 51 89 244 52 140 245 53 246 54 90 247 55 248 141 56 249 57 250 91 58 251 59 142 252 60 253 92 61 254 62 143 255 63 93 144 94 145 95 146 96 147 97 148 98 149 99 150 151 100 152 153 101 154 102 155 156 157 103 158 159 104 160 105 161 162 106 163 107 164 108 165 109 166 110 111 167 168 112 169 113 170 114 171 172 115 173 116 174 175 117 176 177 118 178 119 179 180 120 181 182 121 183 184 122 185 186 123 187 188 189 190 124 191 125 126 127 nrelabeled = 111084 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1000576 mri_surf2volseg done @#@FSTIME 2024:10:08:17:15:53 mri_surf2volseg N 20 e 6.80 S 0.65 U 11.94 P 185% M 814720 F 1 R 443217 W 0 c 1144 w 290 I 0 O 704 L 11.87 14.30 26.08 @#@FSLOADPOST 2024:10:08:17:15:59 mri_surf2volseg N 20 11.32 14.15 25.97 mri_brainvol_stats PIB23-310_VYr0_Bay3prisma ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1607788.0 #CBVS2 BrainSegVol 1089479.0 #CBVS2 BrainSegVolNotVent 967820.0 #CBVS2 SupraTentVol 962726.0 #CBVS2 SupraTentVolNotVent 841067.0 #CBVS2 lhCtxGM 208473.5 #CBVS2 rhCtxGM 218303.9 #CBVS2 lhCerebralWM 181866.5 #CBVS2 rhCerebralWM 183021.5 #CBVS2 SubCortGMVol 50343.0 #CBVS2 CerebellumVol 126753.0 #CBVS2 CerebellumGMVol 102301.0 #CBVS2 VentChorVol 113361.0 #CBVS2 3rd4th5thCSF 8298.0 #CBVS2 AllCSF 121659.0 #CBVS2 CCVol 3871.0 @#@FSTIME 2024:10:08:17:15:59 mri_brainvol_stats N 1 e 2.88 S 0.33 U 4.88 P 180% M 214096 F 2 R 208223 W 0 c 475 w 146 I 1416 O 8 L 11.32 14.15 25.97 @#@FSLOADPOST 2024:10:08:17:16:02 mri_brainvol_stats N 1 11.37 14.11 25.89 #----------------------------------------- #@# AParc-to-ASeg aparc Tue Oct 8 17:16:02 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10286 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10469 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Done loading 0 192 64 128 1 193 2 194 3 195 4 196 5 197 6 198 7 199 8 200 9 201 65 10 202 11 203 12 204 13 205 14 206 15 207 16 208 17 209 18 210 19 211 20 21 212 22 213 66 23 214 24 215 25 216 26 217 27 218 28 219 29 220 30 221 31 222 32 223 33 224 34 225 35 226 36 227 37 38 228 67 39 229 40 230 41 231 42 232 43 233 44 234 45 235 46 236 47 237 48 238 49 239 50 51 240 52 241 53 242 54 243 55 244 56 245 57 246 58 247 59 248 60 68 249 61 250 251 252 62 253 254 255 63 129 69 70 71 72 130 73 131 74 132 75 76 133 77 134 78 135 79 136 80 137 81 138 82 139 83 84 140 85 141 142 86 143 87 144 145 88 146 89 147 90 148 149 91 150 92 151 152 93 153 94 154 95 155 96 156 157 97 158 98 159 99 160 161 100 162 101 163 102 164 103 165 104 105 166 106 167 107 168 108 169 109 170 110 171 111 112 172 173 113 174 114 175 115 176 177 116 178 117 179 180 118 181 119 182 183 120 184 185 186 187 188 189 121 190 191 122 123 124 125 126 127 nrelabeled = 425822 ndotcheck = 13307 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 984620 mri_surf2volseg done @#@FSTIME 2024:10:08:17:16:02 mri_surf2volseg N 25 e 54.29 S 1.28 U 100.23 P 186% M 799780 F 2 R 875173 W 0 c 9336 w 409 I 0 O 800 L 11.37 14.11 25.89 @#@FSLOADPOST 2024:10:08:17:16:57 mri_surf2volseg N 25 13.90 14.33 25.29 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Tue Oct 8 17:16:57 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc.a2009s+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10286 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.a2009s.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10469 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.a2009s.annot Done loading 0 192 64 128 1 193 2 194 195 3 196 4 197 5 198 6 199 200 7 201 8 202 9 203 10 204 205 11 206 12 207 65 208 13 209 14 210 211 15 212 16 213 17 214 215 18 216 19 217 218 20 219 21 220 22 221 222 23 66 223 24 224 25 225 26 226 227 27 228 28 229 230 29 231 30 232 31 233 234 32 235 33 236 34 237 35 238 239 36 240 37 241 38 242 243 67 39 244 40 245 41 246 247 42 248 43 249 44 250 251 45 252 46 253 47 254 48 255 49 50 51 52 53 54 55 56 68 57 58 59 60 61 62 63 129 69 70 71 130 72 131 73 74 132 75 133 76 134 77 135 78 136 79 137 80 138 81 82 139 83 140 84 141 142 85 143 86 144 145 87 146 88 147 89 148 149 90 150 151 91 152 153 92 154 93 155 156 94 157 158 95 159 96 160 97 161 98 162 163 99 164 100 165 101 166 102 167 168 103 169 104 170 105 171 106 172 107 173 108 174 109 175 110 176 177 111 112 178 113 179 180 114 181 115 182 183 116 184 185 186 187 188 189 117 190 191 118 119 120 121 122 123 124 125 126 127 nrelabeled = 425822 ndotcheck = 13307 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 984712 mri_surf2volseg done @#@FSTIME 2024:10:08:17:16:57 mri_surf2volseg N 25 e 59.89 S 1.05 U 107.94 P 181% M 800012 F 2 R 845703 W 0 c 9969 w 485 I 0 O 864 L 13.90 14.33 25.29 @#@FSLOADPOST 2024:10:08:17:17:57 mri_surf2volseg N 25 14.59 14.49 24.66 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Tue Oct 8 17:17:57 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc.DKTatlas+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10286 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.DKTatlas.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10469 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.DKTatlas.annot Done loading 0 192 128 64 1 193 2 194 3 195 196 4 5 197 6 198 7 199 200 8 201 9 65 10 202 11 203 12 204 205 13 206 14 207 15 208 16 209 17 210 18 211 19 212 20 213 66 21 214 22 215 23 216 24 217 25 218 26 219 27 220 28 221 29 222 30 223 31 224 32 225 33 226 34 227 35 228 36 229 67 37 230 38 231 39 232 40 233 41 234 42 235 43 236 44 237 45 238 46 239 47 240 48 241 49 242 50 243 51 244 52 245 53 246 54 247 55 248 56 249 57 250 58 251 68 59 252 60 253 61 254 255 62 63 129 69 70 71 130 72 131 73 74 132 75 133 76 134 77 135 78 136 79 137 80 138 81 139 82 140 83 141 84 142 85 143 86 144 145 87 146 88 147 148 89 149 90 150 151 91 152 153 92 154 93 155 156 94 157 95 158 159 96 160 97 161 98 162 163 99 164 100 165 101 166 102 167 103 168 104 169 105 170 106 171 172 107 173 108 174 109 175 110 176 111 177 112 178 113 179 114 180 181 115 182 116 183 184 185 186 117 187 188 189 190 191 118 119 120 121 122 123 124 125 126 127 nrelabeled = 425822 ndotcheck = 13307 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 984592 mri_surf2volseg done @#@FSTIME 2024:10:08:17:17:57 mri_surf2volseg N 25 e 62.79 S 1.08 U 112.49 P 180% M 799840 F 1 R 1231087 W 0 c 11042 w 493 I 0 O 800 L 14.59 14.49 24.66 @#@FSLOADPOST 2024:10:08:17:19:00 mri_surf2volseg N 25 27.59 18.44 25.39 #----------------------------------------- #@# WMParc Tue Oct 8 17:19:00 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot 3000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot 4000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol wmparc.mgz 72 avail.processors, using 4 Loading aparc+aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10286 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10469 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Done loading 0 192 128 64 1 65 2 193 66 3 67 194 4 5 195 68 6 196 7 197 8 198 69 9 199 10 200 11 201 12 202 13 203 14 204 70 15 205 16 206 17 207 18 208 19 209 20 210 71 21 211 22 212 23 213 129 24 214 25 215 26 216 27 217 28 218 72 29 219 30 220 31 221 32 222 33 223 34 224 35 225 36 226 37 227 38 228 39 73 40 229 41 230 42 231 43 232 44 233 45 234 46 235 47 236 48 237 49 238 50 239 130 51 240 52 241 53 54 55 56 242 57 243 58 74 244 245 59 246 60 247 61 248 249 62 250 63 251 252 253 254 255 75 131 76 132 77 78 133 79 134 80 135 81 136 82 137 83 84 138 85 139 86 140 87 88 141 89 90 142 91 143 92 93 144 94 145 95 146 96 97 147 98 148 99 149 100 150 101 151 102 152 103 153 104 154 105 155 156 106 157 107 158 159 108 160 109 161 162 110 163 111 164 165 112 166 113 167 168 114 169 115 170 116 171 172 117 173 118 174 175 119 176 120 177 178 121 179 180 122 181 182 123 183 124 184 185 186 187 188 189 190 125 191 126 127 nrelabeled = 361017 ndotcheck = 5015 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 984616 mri_surf2volseg done @#@FSTIME 2024:10:08:17:19:00 mri_surf2volseg N 25 e 24.66 S 1.05 U 45.58 P 189% M 799952 F 3 R 948508 W 0 c 4538 w 475 I 0 O 880 L 27.59 18.44 25.39 @#@FSLOADPOST 2024:10:08:17:19:25 mri_surf2volseg N 25 26.35 18.97 25.38 mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject PIB23-310_VYr0_Bay3prisma --surf-wm-vol --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 7.3.2 cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject PIB23-310_VYr0_Bay3prisma --surf-wm-vol --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/WMParcStatsLUT.txt --etiv sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2024:10:08:17:19:25 mri_segstats N 24 e 238.94 S 1.22 U 487.11 P 204% M 239960 F 0 R 1472109 W 0 c 44107 w 5609 I 0 O 24 L 26.35 18.97 25.38 @#@FSLOADPOST 2024:10:08:17:23:24 mri_segstats N 24 32.99 24.34 25.95 #----------------------------------------- #@# Parcellation Stats lh Tue Oct 8 17:23:24 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh pial #----------------------------------------- #@# Parcellation Stats rh Tue Oct 8 17:23:24 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh pial Waiting for PID 3311745 of (3311745 3311748 3311751 3311755) to complete... Waiting for PID 3311748 of (3311745 3311748 3311751 3311755) to complete... Waiting for PID 3311751 of (3311745 3311748 3311751 3311755) to complete... Waiting for PID 3311755 of (3311745 3311748 3311751 3311755) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208392 Total vertex volume 208137 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1327 887 2073 2.412 0.441 0.083 0.016 5 1.0 bankssts 796 599 2059 3.116 0.722 0.159 0.053 19 1.8 caudalanteriorcingulate 2840 2048 5828 2.534 0.483 0.120 0.033 51 3.8 caudalmiddlefrontal 1752 1171 2507 1.994 0.488 0.145 0.035 25 2.5 cuneus 556 371 1334 2.595 0.761 0.118 0.029 5 0.7 entorhinal 3829 2721 8369 2.597 0.642 0.129 0.032 48 5.0 fusiform 5203 3811 10741 2.544 0.530 0.131 0.033 66 6.9 inferiorparietal 3717 2796 9203 2.668 0.726 0.133 0.032 52 5.6 inferiortemporal 1202 773 1609 2.146 0.816 0.116 0.028 15 1.5 isthmuscingulate 5799 3900 9779 2.292 0.527 0.135 0.032 69 7.6 lateraloccipital 2998 2180 6699 2.663 0.761 0.138 0.037 39 4.5 lateralorbitofrontal 4239 2860 6387 2.055 0.588 0.128 0.033 55 5.5 lingual 2390 1745 4753 2.408 0.848 0.144 0.040 40 3.6 medialorbitofrontal 3973 2780 9032 2.687 0.614 0.117 0.026 51 4.3 middletemporal 1155 721 2097 2.433 0.655 0.081 0.020 6 0.8 parahippocampal 1927 1186 3299 2.554 0.562 0.092 0.022 12 1.6 paracentral 1927 1320 3630 2.474 0.505 0.108 0.025 17 1.9 parsopercularis 684 513 1878 2.749 0.616 0.142 0.034 9 0.9 parsorbitalis 1589 1150 3209 2.411 0.577 0.117 0.025 17 1.6 parstriangularis 2009 1333 2056 1.622 0.439 0.130 0.037 21 3.1 pericalcarine 6071 3889 8911 2.060 0.633 0.104 0.025 51 5.8 postcentral 1099 810 2335 2.706 0.609 0.141 0.036 20 1.8 posteriorcingulate 7139 4754 12575 2.480 0.538 0.113 0.030 61 8.4 precentral 4068 2997 8334 2.583 0.543 0.141 0.034 52 5.7 precuneus 1327 952 2664 2.361 1.115 0.135 0.045 23 2.6 rostralanteriorcingulate 5816 4444 13191 2.464 0.602 0.132 0.032 82 7.4 rostralmiddlefrontal 7728 5822 18345 2.609 0.638 0.128 0.036 96 11.1 superiorfrontal 6262 4423 12124 2.478 0.490 0.122 0.028 65 7.2 superiorparietal 5703 3831 11585 2.598 0.617 0.096 0.021 50 4.7 superiortemporal 5200 3618 9455 2.364 0.533 0.123 0.029 56 6.2 supramarginal 298 237 1230 3.086 0.763 0.161 0.054 7 0.6 frontalpole 579 478 2933 3.393 0.886 0.151 0.061 12 1.3 temporalpole 729 399 946 2.158 0.572 0.094 0.030 5 0.8 transversetemporal 3244 2171 6966 3.006 1.026 0.119 0.038 29 5.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208392 Total vertex volume 208137 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1327 796 2073 2.412 0.441 0.087 0.018 9 0.9 bankssts 796 771 2059 3.116 0.722 0.192 0.071 62 1.4 caudalanteriorcingulate 2840 2418 5828 2.534 0.483 0.132 0.036 33 5.4 caudalmiddlefrontal 1752 1431 2507 1.994 0.488 0.132 0.034 23 2.1 cuneus 556 692 1334 2.595 0.761 0.249 0.067 16 1.9 entorhinal 3829 3573 8369 2.597 0.642 0.155 0.035 59 5.7 fusiform 5203 4556 10741 2.544 0.530 0.141 0.031 59 6.5 inferiorparietal 3717 3736 9203 2.668 0.726 0.158 0.033 49 5.2 inferiortemporal 1202 845 1609 2.146 0.816 0.143 0.048 28 1.9 isthmuscingulate 5799 4642 9779 2.292 0.527 0.135 0.030 92 7.3 lateraloccipital 2998 2694 6699 2.663 0.761 0.159 0.045 54 4.6 lateralorbitofrontal 4239 3544 6387 2.055 0.588 0.136 0.031 52 5.4 lingual 2390 2194 4753 2.408 0.848 0.159 0.041 45 3.4 medialorbitofrontal 3973 3746 9032 2.687 0.614 0.144 0.029 50 4.7 middletemporal 1155 1034 2097 2.433 0.655 0.130 0.032 10 1.5 parahippocampal 1927 1421 3299 2.554 0.562 0.108 0.023 17 1.8 paracentral 1927 1577 3630 2.474 0.505 0.127 0.023 19 1.7 parsopercularis 684 845 1878 2.749 0.616 0.190 0.037 8 1.2 parsorbitalis 1589 1468 3209 2.411 0.577 0.142 0.026 16 1.6 parstriangularis 2009 1223 2056 1.622 0.439 0.115 0.029 21 2.3 pericalcarine 6071 4792 8911 2.060 0.633 0.110 0.020 46 4.9 postcentral 1099 973 2335 2.706 0.609 0.143 0.039 13 1.6 posteriorcingulate 7139 5304 12575 2.480 0.538 0.104 0.020 59 5.7 precentral 4068 3400 8334 2.583 0.543 0.145 0.035 70 5.8 precuneus 1327 1229 2664 2.361 1.115 0.174 0.063 36 4.5 rostralanteriorcingulate 5816 5887 13191 2.464 0.602 0.165 0.031 88 7.3 rostralmiddlefrontal 7728 7754 18345 2.609 0.638 0.156 0.034 131 10.1 superiorfrontal 6262 5271 12124 2.478 0.490 0.137 0.029 83 7.4 superiorparietal 5703 4907 11585 2.598 0.617 0.116 0.021 43 5.0 superiortemporal 5200 4291 9455 2.364 0.533 0.134 0.027 63 5.5 supramarginal 298 567 1230 3.086 0.763 0.273 0.052 4 0.7 frontalpole 579 1083 2933 3.393 0.886 0.257 0.040 8 1.1 temporalpole 729 485 946 2.158 0.572 0.085 0.013 3 0.3 transversetemporal 3244 2328 6966 3.006 1.026 0.147 0.039 56 5.3 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 218567 Total vertex volume 218281 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1203 811 2010 2.581 0.533 0.082 0.016 5 0.8 bankssts 775 541 1347 2.755 0.716 0.124 0.029 14 1.1 caudalanteriorcingulate 2885 2095 5888 2.504 0.518 0.125 0.027 29 3.2 caudalmiddlefrontal 2203 1435 3434 2.133 0.514 0.140 0.034 31 3.0 cuneus 753 514 2073 3.027 0.775 0.122 0.035 9 1.0 entorhinal 3844 2843 8803 2.606 0.666 0.129 0.028 50 4.4 fusiform 6741 4847 14042 2.584 0.528 0.127 0.031 87 8.9 inferiorparietal 3941 2911 10102 2.833 0.697 0.135 0.036 57 6.0 inferiortemporal 807 497 1164 2.210 0.697 0.113 0.028 8 1.0 isthmuscingulate 6528 4391 11057 2.321 0.616 0.129 0.030 73 8.0 lateraloccipital 2829 2068 6362 2.720 0.705 0.138 0.037 33 4.1 lateralorbitofrontal 4928 3306 7148 2.019 0.585 0.131 0.035 68 6.8 lingual 2654 1942 5492 2.390 0.763 0.137 0.040 43 4.3 medialorbitofrontal 4473 3059 10280 2.803 0.590 0.109 0.025 46 4.5 middletemporal 944 613 1921 2.685 0.726 0.105 0.026 12 0.9 parahippocampal 2083 1314 3469 2.513 0.487 0.111 0.027 18 2.2 paracentral 1519 1125 3468 2.620 0.539 0.130 0.032 17 1.9 parsopercularis 879 680 2599 2.754 0.669 0.144 0.039 15 1.2 parsorbitalis 1742 1235 3442 2.370 0.617 0.113 0.026 18 1.7 parstriangularis 2506 1519 2592 1.805 0.516 0.119 0.044 46 4.3 pericalcarine 6446 4029 9350 2.134 0.615 0.095 0.022 50 5.7 postcentral 959 664 1868 2.661 0.634 0.129 0.033 16 1.2 posteriorcingulate 6494 4253 12040 2.659 0.535 0.109 0.027 50 7.4 precentral 4702 3449 9255 2.509 0.507 0.124 0.027 53 5.3 precuneus 717 486 2049 2.956 0.951 0.121 0.035 11 1.1 rostralanteriorcingulate 5607 4458 13783 2.474 0.712 0.143 0.038 90 8.9 rostralmiddlefrontal 8028 6113 19769 2.649 0.667 0.134 0.039 108 13.3 superiorfrontal 6151 4210 11942 2.571 0.453 0.120 0.028 72 6.4 superiorparietal 5588 3530 10437 2.511 0.624 0.083 0.017 35 3.7 superiortemporal 4932 3393 9442 2.578 0.544 0.116 0.025 47 5.2 supramarginal 387 334 1562 3.016 0.708 0.182 0.053 10 1.0 frontalpole 623 485 2499 3.285 0.865 0.144 0.046 9 1.0 temporalpole 653 338 892 2.304 0.456 0.109 0.032 7 0.8 transversetemporal 3204 2175 6700 2.921 0.931 0.115 0.035 34 3.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 218567 Total vertex volume 218281 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1203 715 2010 2.581 0.533 0.084 0.017 7 0.8 bankssts 775 505 1347 2.755 0.716 0.161 0.033 345 0.6 caudalanteriorcingulate 2885 2513 5888 2.504 0.518 0.130 0.024 29 2.5 caudalmiddlefrontal 2203 1853 3434 2.133 0.514 0.137 0.032 31 2.8 cuneus 753 871 2073 3.027 0.775 0.267 0.067 51 2.5 entorhinal 3844 3699 8803 2.606 0.666 0.158 0.036 79 5.7 fusiform 6741 5840 14042 2.584 0.528 0.139 0.030 94 8.8 inferiorparietal 3941 4003 10102 2.833 0.697 0.169 0.039 251 6.0 inferiortemporal 807 597 1164 2.210 0.697 0.133 0.037 11 1.0 isthmuscingulate 6528 5149 11057 2.321 0.616 0.134 0.031 187 8.6 lateraloccipital 2829 2607 6362 2.720 0.705 0.170 0.043 53 5.2 lateralorbitofrontal 4928 3955 7148 2.019 0.585 0.138 0.036 87 6.5 lingual 2654 2591 5492 2.390 0.763 0.167 0.055 64 4.5 medialorbitofrontal 4473 4126 10280 2.803 0.590 0.136 0.025 59 4.6 middletemporal 944 820 1921 2.685 0.726 0.148 0.035 13 1.4 parahippocampal 2083 1470 3469 2.513 0.487 0.146 0.100 29615 2.0 paracentral 1519 1468 3468 2.620 0.539 0.153 0.028 15 1.8 parsopercularis 879 1162 2599 2.754 0.669 0.203 0.042 19 1.6 parsorbitalis 1742 1606 3442 2.370 0.617 0.150 0.030 24 2.1 parstriangularis 2506 1360 2592 1.805 0.516 0.126 0.054 78 4.7 pericalcarine 6446 4855 9350 2.134 0.615 0.097 0.019 38 4.6 postcentral 959 821 1868 2.661 0.634 0.174 0.064 33 2.1 posteriorcingulate 6494 4702 12040 2.659 0.535 0.104 0.021 67 5.8 precentral 4702 3886 9255 2.509 0.507 0.139 0.032 77 5.5 precuneus 717 816 2049 2.956 0.951 0.197 0.037 9 1.1 rostralanteriorcingulate 5607 6226 13783 2.474 0.712 0.188 0.035 86 8.7 rostralmiddlefrontal 8028 8258 19769 2.649 0.667 0.160 0.034 176 10.9 superiorfrontal 6151 5070 11942 2.571 0.453 0.137 0.036 105 7.7 superiorparietal 5588 4586 10437 2.511 0.624 0.104 0.017 32 4.2 superiortemporal 4932 3860 9442 2.578 0.544 0.124 0.025 50 4.8 supramarginal 387 710 1562 3.016 0.708 0.306 0.050 8 0.9 frontalpole 623 1036 2499 3.285 0.865 0.246 0.048 8 1.3 temporalpole 653 437 892 2.304 0.456 0.094 0.017 3 0.4 transversetemporal 3204 2263 6700 2.921 0.931 0.135 0.035 48 4.9 insula PIDs (3311745 3311748 3311751 3311755) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Oct 8 17:23:37 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 2 rh Tue Oct 8 17:23:37 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma rh white Waiting for PID 3316153 of (3316153 3316156) to complete... Waiting for PID 3316156 of (3316153 3316156) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208392 Total vertex volume 208137 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 807 607 2005 2.656 0.749 0.129 0.033 10 1.0 G_and_S_frontomargin 1190 815 2548 2.566 0.504 0.137 0.030 16 1.4 G_and_S_occipital_inf 1563 971 2837 2.377 0.615 0.107 0.028 16 1.6 G_and_S_paracentral 1143 776 2668 2.860 0.521 0.130 0.038 13 1.5 G_and_S_subcentral 549 441 1879 2.837 0.679 0.168 0.055 13 1.3 G_and_S_transv_frontopol 2014 1533 4331 2.633 0.754 0.141 0.037 32 3.2 G_and_S_cingul-Ant 1103 757 2166 2.754 0.747 0.128 0.041 18 1.7 G_and_S_cingul-Mid-Ant 1157 815 2091 2.597 0.610 0.127 0.035 17 1.6 G_and_S_cingul-Mid-Post 508 338 902 2.610 0.537 0.157 0.034 11 0.9 G_cingul-Post-dorsal 291 189 430 2.063 0.630 0.128 0.040 5 0.4 G_cingul-Post-ventral 1753 1136 2662 2.014 0.492 0.146 0.037 26 2.6 G_cuneus 1112 768 2640 2.624 0.486 0.126 0.034 15 1.5 G_front_inf-Opercular 273 211 782 2.731 0.484 0.154 0.031 4 0.3 G_front_inf-Orbital 909 686 2476 2.723 0.539 0.144 0.035 16 1.2 G_front_inf-Triangul 3166 2589 9234 2.629 0.588 0.151 0.044 87 5.1 G_front_middle 5148 3966 14355 2.749 0.692 0.140 0.042 81 8.9 G_front_sup 659 443 1813 3.338 0.888 0.133 0.047 8 1.1 G_Ins_lg_and_S_cent_ins 634 427 2105 3.895 0.792 0.141 0.047 7 1.3 G_insular_short 1648 1095 3955 2.638 0.503 0.141 0.037 28 2.4 G_occipital_middle 1094 730 2177 2.472 0.706 0.138 0.034 14 1.5 G_occipital_sup 1511 1042 3624 2.675 0.491 0.134 0.032 25 2.1 G_oc-temp_lat-fusifor 2905 1892 4765 2.111 0.566 0.137 0.039 48 4.2 G_oc-temp_med-Lingual 1424 882 3210 2.690 0.731 0.107 0.031 13 1.6 G_oc-temp_med-Parahip 1775 1337 5164 2.831 0.773 0.145 0.041 33 2.8 G_orbital 2176 1672 5440 2.608 0.499 0.150 0.037 39 3.1 G_pariet_inf-Angular 2405 1679 5251 2.532 0.542 0.131 0.032 32 3.1 G_pariet_inf-Supramar 2260 1701 5453 2.567 0.482 0.137 0.034 34 3.1 G_parietal_sup 2337 1379 3616 2.092 0.579 0.103 0.028 25 2.3 G_postcentral 2586 1625 5514 2.664 0.467 0.118 0.034 29 3.2 G_precentral 2173 1670 5501 2.636 0.549 0.163 0.043 41 3.9 G_precuneus 773 583 2285 2.727 0.906 0.157 0.053 15 1.3 G_rectus 696 437 657 1.646 0.899 0.106 0.038 8 1.1 G_subcallosal 557 279 820 2.277 0.560 0.087 0.031 5 0.6 G_temp_sup-G_T_transv 1915 1320 5547 2.988 0.546 0.129 0.032 33 2.2 G_temp_sup-Lateral 740 516 1572 2.659 0.627 0.067 0.014 2 0.4 G_temp_sup-Plan_polar 920 631 1676 2.395 0.562 0.097 0.023 7 0.8 G_temp_sup-Plan_tempo 1877 1474 5955 2.888 0.775 0.145 0.040 35 3.4 G_temporal_inf 2280 1606 5937 2.826 0.600 0.125 0.031 35 2.8 G_temporal_middle 210 146 226 1.679 0.313 0.096 0.018 1 0.2 Lat_Fis-ant-Horizont 357 247 492 2.262 0.314 0.081 0.013 1 0.2 Lat_Fis-ant-Vertical 1062 716 1351 2.217 0.525 0.111 0.028 6 1.2 Lat_Fis-post 1803 1176 2385 1.891 0.489 0.132 0.034 22 2.3 Pole_occipital 1325 1108 5772 3.184 0.843 0.164 0.054 29 2.7 Pole_temporal 2346 1612 2416 1.648 0.548 0.120 0.029 20 3.0 S_calcarine 3545 2491 4248 1.967 0.570 0.109 0.025 22 3.9 S_central 910 635 1269 2.341 0.326 0.100 0.014 4 0.7 S_cingul-Marginalis 417 283 684 2.822 0.640 0.101 0.034 2 0.7 S_circular_insula_ant 1608 1051 2333 2.498 0.913 0.079 0.016 5 1.2 S_circular_insula_inf 1521 1015 2066 2.381 0.550 0.097 0.024 6 1.6 S_circular_insula_sup 870 597 1612 2.534 0.754 0.106 0.024 7 0.9 S_collat_transv_ant 350 264 499 2.165 0.360 0.142 0.030 3 0.6 S_collat_transv_post 2107 1456 3199 2.239 0.436 0.102 0.020 12 1.8 S_front_inf 1004 731 1617 2.247 0.482 0.129 0.027 10 1.3 S_front_middle 1936 1350 3252 2.495 0.409 0.097 0.021 9 1.5 S_front_sup 264 188 402 2.321 0.442 0.113 0.023 1 0.3 S_interm_prim-Jensen 2508 1697 3561 2.360 0.448 0.110 0.026 17 3.0 S_intrapariet_and_P_trans 835 612 1164 2.270 0.352 0.130 0.027 6 1.0 S_oc_middle_and_Lunatus 1118 782 1686 2.524 0.429 0.121 0.026 8 1.3 S_oc_sup_and_transversal 642 456 977 2.451 0.396 0.117 0.025 5 0.8 S_occipital_ant 803 545 1171 2.401 0.394 0.100 0.018 3 0.6 S_oc-temp_lat 2083 1478 3006 2.225 0.534 0.106 0.021 12 1.8 S_oc-temp_med_and_Lingual 268 205 405 2.252 0.414 0.130 0.028 2 0.4 S_orbital_lateral 531 381 717 2.094 0.692 0.133 0.027 5 0.7 S_orbital_med-olfact 1088 794 2249 2.685 0.715 0.142 0.037 12 1.7 S_orbital-H_Shaped 1390 964 2203 2.515 0.537 0.120 0.026 11 1.5 S_parieto_occipital 773 487 771 1.899 0.983 0.105 0.035 7 1.3 S_pericallosal 2836 1911 3790 2.077 0.412 0.098 0.019 16 2.5 S_postcentral 1488 1001 2176 2.414 0.450 0.096 0.020 7 1.3 S_precentral-inf-part 1245 830 1878 2.469 0.482 0.090 0.020 5 1.1 S_precentral-sup-part 827 611 1572 2.522 0.765 0.148 0.032 13 1.2 S_suborbital 671 474 1169 2.599 0.487 0.119 0.030 6 0.7 S_subparietal 1048 764 1525 2.307 0.557 0.131 0.023 10 1.3 S_temporal_inf 5057 3405 7890 2.418 0.477 0.092 0.019 27 4.0 S_temporal_sup 298 209 361 1.911 0.506 0.107 0.019 2 0.3 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 218567 Total vertex volume 218281 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 697 546 1744 2.472 0.691 0.158 0.046 17 1.5 G_and_S_frontomargin 1204 856 2760 2.714 0.644 0.139 0.032 15 1.5 G_and_S_occipital_inf 1513 914 2544 2.348 0.522 0.118 0.030 18 1.8 G_and_S_paracentral 1142 767 2493 2.818 0.462 0.118 0.026 11 1.2 G_and_S_subcentral 930 751 3045 2.808 0.799 0.140 0.043 16 1.6 G_and_S_transv_frontopol 2407 1695 5281 2.667 0.731 0.119 0.030 31 3.0 G_and_S_cingul-Ant 1181 809 2039 2.504 0.534 0.122 0.031 14 1.4 G_and_S_cingul-Mid-Ant 1120 790 1928 2.586 0.538 0.123 0.029 13 1.2 G_and_S_cingul-Mid-Post 289 185 430 2.294 0.742 0.141 0.036 5 0.5 G_cingul-Post-dorsal 296 180 448 2.367 0.650 0.136 0.043 4 0.5 G_cingul-Post-ventral 2069 1346 3300 2.086 0.531 0.140 0.038 31 3.0 G_cuneus 1041 807 3004 2.839 0.565 0.151 0.041 17 1.6 G_front_inf-Opercular 269 191 772 2.800 0.445 0.127 0.031 3 0.3 G_front_inf-Orbital 759 563 1974 2.622 0.538 0.122 0.028 10 0.9 G_front_inf-Triangul 2778 2330 8576 2.699 0.637 0.164 0.042 57 4.6 G_front_middle 5027 3937 14754 2.790 0.707 0.151 0.048 88 10.6 G_front_sup 807 554 1916 2.980 0.812 0.145 0.052 17 1.3 G_Ins_lg_and_S_cent_ins 669 479 2223 3.930 0.859 0.146 0.051 10 1.3 G_insular_short 1950 1373 4663 2.721 0.517 0.134 0.031 32 2.5 G_occipital_middle 1266 831 2524 2.420 0.541 0.116 0.025 15 1.3 G_occipital_sup 1691 1174 4286 2.806 0.595 0.131 0.030 28 1.9 G_oc-temp_lat-fusifor 3102 2039 5063 2.145 0.548 0.132 0.037 46 4.4 G_oc-temp_med-Lingual 1457 941 3788 2.974 0.763 0.122 0.035 23 1.8 G_oc-temp_med-Parahip 2030 1552 6374 2.987 0.722 0.143 0.042 33 3.1 G_orbital 2513 1824 6676 2.792 0.472 0.146 0.039 46 4.1 G_pariet_inf-Angular 2301 1580 5294 2.696 0.589 0.125 0.029 29 2.6 G_pariet_inf-Supramar 1863 1319 4460 2.636 0.537 0.139 0.041 36 2.4 G_parietal_sup 2293 1297 3423 2.138 0.566 0.096 0.026 24 2.0 G_postcentral 2390 1430 5490 2.886 0.461 0.112 0.032 25 2.8 G_precentral 2048 1613 5319 2.636 0.523 0.153 0.037 39 3.1 G_precuneus 777 621 2224 2.557 0.728 0.165 0.060 21 1.7 G_rectus 462 287 636 2.216 0.942 0.125 0.042 6 0.9 G_subcallosal 541 252 812 2.468 0.416 0.103 0.029 6 0.6 G_temp_sup-G_T_transv 1886 1121 4695 2.905 0.562 0.104 0.026 23 1.7 G_temp_sup-Lateral 728 499 1472 2.681 0.767 0.069 0.017 2 0.4 G_temp_sup-Plan_polar 822 526 1561 2.699 0.597 0.082 0.016 4 0.5 G_temp_sup-Plan_tempo 1959 1500 6566 3.024 0.789 0.151 0.049 39 3.8 G_temporal_inf 2545 1725 7013 2.953 0.578 0.123 0.031 38 3.2 G_temporal_middle 271 184 317 1.970 0.484 0.089 0.013 1 0.2 Lat_Fis-ant-Horizont 164 119 210 1.864 0.432 0.106 0.018 1 0.1 Lat_Fis-ant-Vertical 1406 946 1850 2.318 0.487 0.101 0.023 7 1.4 Lat_Fis-post 3323 2109 4179 1.888 0.480 0.134 0.035 43 4.8 Pole_occipital 1604 1290 6026 3.088 0.753 0.155 0.042 26 2.8 Pole_temporal 2773 1720 2720 1.755 0.605 0.117 0.038 48 4.5 S_calcarine 3218 2256 3878 2.008 0.599 0.101 0.022 17 3.4 S_central 1128 785 1725 2.446 0.346 0.095 0.014 6 0.7 S_cingul-Marginalis 444 297 708 2.825 0.640 0.112 0.042 4 0.6 S_circular_insula_ant 1445 945 1745 2.116 0.583 0.074 0.012 4 0.8 S_circular_insula_inf 1162 743 1700 2.632 0.497 0.087 0.019 4 0.9 S_circular_insula_sup 1140 826 1809 2.199 0.536 0.108 0.024 11 1.1 S_collat_transv_ant 359 265 481 2.123 0.401 0.125 0.021 2 0.3 S_collat_transv_post 1588 1126 2375 2.158 0.516 0.106 0.023 9 1.7 S_front_inf 1498 1153 3136 2.346 0.687 0.130 0.034 20 2.0 S_front_middle 2121 1493 3644 2.490 0.469 0.105 0.021 13 2.0 S_front_sup 304 225 504 2.330 0.481 0.124 0.026 2 0.4 S_interm_prim-Jensen 2377 1673 4049 2.603 0.418 0.113 0.021 16 2.1 S_intrapariet_and_P_trans 671 501 1058 2.605 0.375 0.137 0.029 6 0.8 S_oc_middle_and_Lunatus 1040 696 1509 2.582 0.302 0.098 0.020 5 0.8 S_oc_sup_and_transversal 531 377 779 2.377 0.484 0.103 0.024 3 0.5 S_occipital_ant 806 585 1345 2.549 0.479 0.102 0.015 4 0.5 S_oc-temp_lat 1603 1219 2679 2.342 0.534 0.114 0.022 12 1.4 S_oc-temp_med_and_Lingual 357 265 590 2.210 0.617 0.145 0.027 4 0.5 S_orbital_lateral 597 417 903 2.167 0.688 0.122 0.022 4 0.6 S_orbital_med-olfact 1086 818 1962 2.353 0.593 0.142 0.037 12 1.7 S_orbital-H_Shaped 1941 1336 2958 2.423 0.459 0.107 0.022 13 1.9 S_parieto_occipital 488 314 590 2.573 1.017 0.107 0.027 6 0.7 S_pericallosal 2916 1893 3856 2.345 0.446 0.089 0.016 13 2.0 S_postcentral 1351 926 2003 2.451 0.447 0.112 0.023 8 1.5 S_precentral-inf-part 1295 877 2003 2.538 0.448 0.100 0.020 7 1.2 S_precentral-sup-part 307 220 467 2.245 0.634 0.113 0.016 2 0.2 S_suborbital 990 681 1808 2.507 0.526 0.110 0.022 6 0.9 S_subparietal 1275 890 1928 2.638 0.437 0.119 0.024 8 1.4 S_temporal_inf 6108 4137 8973 2.362 0.480 0.091 0.018 31 4.8 S_temporal_sup 219 150 248 1.860 0.263 0.119 0.022 1 0.3 S_temporal_transverse PIDs (3316153 3316156) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Oct 8 17:23:50 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 3 rh Tue Oct 8 17:23:50 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma rh white Waiting for PID 3318882 of (3318882 3318886) to complete... Waiting for PID 3318886 of (3318882 3318886) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208392 Total vertex volume 208137 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1225 872 2594 2.903 0.729 0.143 0.045 23 2.2 caudalanteriorcingulate 3056 2199 6306 2.545 0.480 0.119 0.032 53 4.0 caudalmiddlefrontal 2391 1598 3646 2.130 0.540 0.137 0.032 30 3.2 cuneus 511 328 1194 2.640 0.817 0.120 0.032 5 0.7 entorhinal 3510 2479 7077 2.543 0.587 0.126 0.029 42 4.4 fusiform 5315 3903 11026 2.542 0.534 0.133 0.033 67 7.1 inferiorparietal 3776 2855 10057 2.724 0.745 0.136 0.035 56 6.0 inferiortemporal 1202 772 1606 2.147 0.818 0.116 0.028 15 1.5 isthmuscingulate 5841 3930 9986 2.324 0.547 0.136 0.032 70 7.7 lateraloccipital 3252 2391 7728 2.706 0.831 0.142 0.040 49 5.2 lateralorbitofrontal 4301 2905 6469 2.046 0.581 0.128 0.033 55 5.6 lingual 1956 1432 4215 2.467 0.867 0.148 0.043 35 3.3 medialorbitofrontal 5220 3632 11167 2.627 0.606 0.113 0.025 60 5.5 middletemporal 1222 767 2223 2.428 0.667 0.082 0.021 6 0.9 parahippocampal 2198 1356 3855 2.585 0.572 0.092 0.022 15 1.8 paracentral 1784 1214 3367 2.507 0.467 0.106 0.026 16 1.8 parsopercularis 750 563 1632 2.466 0.574 0.134 0.034 9 1.0 parsorbitalis 1947 1403 3919 2.424 0.556 0.117 0.025 21 2.0 parstriangularis 1955 1296 1973 1.613 0.439 0.132 0.037 21 3.1 pericalcarine 6786 4390 10152 2.088 0.633 0.105 0.025 57 6.6 postcentral 1214 879 2408 2.629 0.591 0.138 0.036 21 1.9 posteriorcingulate 7071 4713 12433 2.482 0.537 0.114 0.030 61 8.4 precentral 4015 2983 8400 2.564 0.552 0.143 0.035 54 5.8 precuneus 1745 1275 3492 2.407 1.032 0.137 0.041 29 3.2 rostralanteriorcingulate 4360 3309 9841 2.461 0.599 0.128 0.031 56 5.2 rostralmiddlefrontal 8229 6311 20288 2.591 0.659 0.134 0.037 113 12.6 superiorfrontal 5003 3536 9609 2.467 0.450 0.120 0.028 52 5.9 superiorparietal 7206 4919 16001 2.645 0.668 0.101 0.024 66 6.8 superiortemporal 4690 3263 8359 2.351 0.529 0.123 0.029 50 5.7 supramarginal 739 405 949 2.143 0.573 0.094 0.029 6 0.8 transversetemporal 2705 1809 6166 3.114 1.019 0.111 0.034 21 3.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 218567 Total vertex volume 218281 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 888 615 1548 2.718 0.692 0.127 0.031 16 1.2 caudalanteriorcingulate 2957 2144 6038 2.514 0.514 0.125 0.027 30 3.4 caudalmiddlefrontal 2621 1717 4081 2.171 0.484 0.132 0.030 31 3.3 cuneus 678 462 1915 3.019 0.809 0.124 0.035 9 0.9 entorhinal 3407 2486 7250 2.567 0.624 0.124 0.026 42 3.5 fusiform 6635 4785 13688 2.574 0.526 0.128 0.031 86 8.9 inferiorparietal 4452 3319 11831 2.838 0.710 0.138 0.037 67 7.0 inferiortemporal 859 527 1258 2.230 0.700 0.116 0.027 9 1.0 isthmuscingulate 6596 4423 11142 2.317 0.624 0.129 0.030 74 8.1 lateraloccipital 3290 2451 7722 2.683 0.743 0.145 0.040 45 5.3 lateralorbitofrontal 4871 3258 7024 2.013 0.585 0.131 0.037 84 7.5 lingual 1812 1372 4170 2.454 0.770 0.143 0.043 32 2.9 medialorbitofrontal 5401 3675 11921 2.784 0.585 0.104 0.024 50 5.1 middletemporal 1012 660 2084 2.708 0.716 0.105 0.026 13 0.9 parahippocampal 2162 1360 3665 2.533 0.504 0.112 0.027 19 2.4 paracentral 1712 1253 3746 2.559 0.570 0.128 0.031 19 2.1 parsopercularis 831 602 2011 2.576 0.680 0.134 0.038 10 1.1 parsorbitalis 1666 1182 3293 2.370 0.616 0.107 0.024 15 1.6 parstriangularis 2441 1484 2536 1.811 0.515 0.119 0.041 30 3.5 pericalcarine 7120 4477 10477 2.155 0.604 0.097 0.022 57 6.3 postcentral 1034 722 2024 2.650 0.618 0.128 0.033 17 1.3 posteriorcingulate 6257 4106 11646 2.661 0.536 0.111 0.028 49 7.2 precentral 4780 3513 9557 2.508 0.521 0.124 0.028 55 5.5 precuneus 1022 678 2551 2.732 1.003 0.118 0.034 15 1.5 rostralanteriorcingulate 4030 3267 9980 2.476 0.701 0.149 0.039 72 6.7 rostralmiddlefrontal 10012 7632 24945 2.646 0.675 0.133 0.038 134 16.3 superiorfrontal 4857 3336 9534 2.600 0.448 0.121 0.029 59 5.0 superiorparietal 7095 4602 14455 2.589 0.674 0.091 0.020 50 5.6 superiortemporal 4668 3242 9064 2.586 0.542 0.115 0.025 43 4.9 supramarginal 618 314 854 2.329 0.463 0.106 0.032 7 0.7 transversetemporal 2944 1998 6269 2.931 0.940 0.113 0.034 31 3.5 insula PIDs (3318882 3318886) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Tue Oct 8 17:24:02 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/ASegStatsLUT.txt --subject PIB23-310_VYr0_Bay3prisma setting seed for random number genererator to 1234 7.3.2 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/ASegStatsLUT.txt --subject PIB23-310_VYr0_Bay3prisma sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) Computing euler number orig.nofix lheno = -76, rheno = -72 orig.nofix lhholes = 39, rhholes = 37 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2024:10:08:17:24:02 mri_segstats N 32 e 74.55 S 0.84 U 278.88 P 375% M 282912 F 2 R 970778 W 0 c 25622 w 221 I 0 O 24 L 34.30 26.07 26.48 @#@FSLOADPOST 2024:10:08:17:25:17 mri_segstats N 32 39.88 29.86 27.77 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label #-------------------------------------------- #@# BA_exvivo Labels lh Tue Oct 8 17:25:17 CDT 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 3340526 of (3340526 3340530 3340604 3340607 3340611) to complete... Waiting for PID 3340530 of (3340526 3340530 3340604 3340607 3340611) to complete... Waiting for PID 3340604 of (3340526 3340530 3340604 3340607 3340611) to complete... Waiting for PID 3340607 of (3340526 3340530 3340604 3340607 3340611) to complete... Waiting for PID 3340611 of (3340526 3340530 3340604 3340607 3340611) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4277 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 167 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4175 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 190 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6173 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5911 mri_label2label: Done PIDs (3340526 3340530 3340604 3340607 3340611) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 3341889 of (3341889 3341892 3341895 3341898) to complete... Waiting for PID 3341892 of (3341889 3341892 3341895 3341898) to complete... Waiting for PID 3341895 of (3341889 3341892 3341895 3341898) to complete... Waiting for PID 3341898 of (3341889 3341892 3341895 3341898) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 299 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13888 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4234 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 172 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3594 mri_label2label: Done PIDs (3341889 3341892 3341895 3341898) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 3345306 of (3345306 3345309 3345313 3345316 3345319) to complete... Waiting for PID 3345309 of (3345306 3345309 3345313 3345316 3345319) to complete... Waiting for PID 3345313 of (3345306 3345309 3345313 3345316 3345319) to complete... Waiting for PID 3345316 of (3345306 3345309 3345313 3345316 3345319) to complete... Waiting for PID 3345319 of (3345306 3345309 3345313 3345316 3345319) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 739 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5380 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 1197 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9311 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1254 mri_label2label: Done PIDs (3345306 3345309 3345313 3345316 3345319) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 3346129 of (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) to complete... Waiting for PID 3346132 of (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) to complete... Waiting for PID 3346135 of (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) to complete... Waiting for PID 3346138 of (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) to complete... Waiting for PID 3346142 of (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) to complete... Waiting for PID 3346145 of (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) to complete... Waiting for PID 3346148 of (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) to complete... Waiting for PID 3346151 of (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 414 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 475 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 703 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 782 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1873 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1969 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2101 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2163 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3877 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 626 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4503 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2919 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 427 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3346 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1286 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 254 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1540 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1006 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1217 mri_label2label: Done PIDs (3346129 3346132 3346135 3346138 3346142 3346145 3346148 3346151) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt Number of ctab entries 9 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 102017 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.mpm.vpnl.annot @#@FSTIME 2024:10:08:17:25:43 mris_label2annot N 26 e 0.63 S 0.08 U 0.70 P 123% M 135348 F 1 R 36883 W 0 c 74 w 179 I 0 O 1808 L 33.87 29.23 27.62 @#@FSLOADPOST 2024:10:08:17:25:44 mris_label2annot N 26 33.87 29.23 27.62 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3347718 of (3347718 3347721 3347724 3347727 3347730) to complete... Waiting for PID 3347721 of (3347718 3347721 3347724 3347727 3347730) to complete... Waiting for PID 3347724 of (3347718 3347721 3347724 3347727 3347730) to complete... Waiting for PID 3347727 of (3347718 3347721 3347724 3347727 3347730) to complete... Waiting for PID 3347730 of (3347718 3347721 3347724 3347727 3347730) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1084 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2147 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1521 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2068 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2375 mri_label2label: Done PIDs (3347718 3347721 3347724 3347727 3347730) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3350671 of (3350671 3350674 3350677 3350680) to complete... Waiting for PID 3350674 of (3350671 3350674 3350677 3350680) to complete... Waiting for PID 3350677 of (3350671 3350674 3350677 3350680) to complete... Waiting for PID 3350680 of (3350671 3350674 3350677 3350680) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1625 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7144 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1929 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1205 mri_label2label: Done PIDs (3350671 3350674 3350677 3350680) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3351480 of (3351480 3351484 3351487 3351490 3351494) to complete... Waiting for PID 3351484 of (3351480 3351484 3351487 3351490 3351494) to complete... Waiting for PID 3351487 of (3351480 3351484 3351487 3351490 3351494) to complete... Waiting for PID 3351490 of (3351480 3351484 3351487 3351490 3351494) to complete... Waiting for PID 3351494 of (3351480 3351484 3351487 3351490 3351494) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 573 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3978 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 522 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 3856 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 40 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 553 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 115461 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 474 mri_label2label: Done PIDs (3351480 3351484 3351487 3351490 3351494) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 79059 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.BA_exvivo.annot @#@FSTIME 2024:10:08:17:26:01 mris_label2annot N 38 e 0.73 S 0.09 U 0.80 P 122% M 135728 F 2 R 36931 W 0 c 85 w 205 I 0 O 1808 L 35.57 29.96 27.90 @#@FSLOADPOST 2024:10:08:17:26:01 mris_label2annot N 38 35.57 29.96 27.90 mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 93401 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2024:10:08:17:26:02 mris_label2annot N 38 e 0.71 S 0.09 U 0.83 P 129% M 135512 F 3 R 36930 W 0 c 109 w 266 I 0 O 1808 L 35.57 29.96 27.90 @#@FSLOADPOST 2024:10:08:17:26:02 mris_label2annot N 38 35.57 29.96 27.90 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 208392 Total vertex volume 208137 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1145 642 2036 2.316 0.636 0.119 0.036 17 1.2 BA1_exvivo 3690 2454 5828 2.189 0.517 0.103 0.023 28 3.6 BA2_exvivo 1114 818 1094 1.690 0.291 0.132 0.029 8 1.4 BA3a_exvivo 2308 1523 3171 1.885 0.649 0.100 0.024 18 2.3 BA3b_exvivo 1562 938 3017 2.761 0.502 0.098 0.028 15 1.5 BA4a_exvivo 1483 970 2317 2.510 0.463 0.111 0.032 11 2.0 BA4p_exvivo 7747 5490 17507 2.629 0.576 0.125 0.037 116 11.5 BA6_exvivo 1894 1290 3665 2.528 0.468 0.109 0.027 17 2.0 BA44_exvivo 2398 1745 4917 2.416 0.526 0.116 0.025 27 2.3 BA45_exvivo 3333 2211 3730 1.644 0.472 0.128 0.038 37 4.9 V1_exvivo 6740 4496 10496 2.124 0.552 0.139 0.034 89 9.2 V2_exvivo 1614 1103 3177 2.549 0.452 0.127 0.029 19 1.9 MT_exvivo 707 495 1802 2.788 0.798 0.132 0.040 8 1.2 perirhinal_exvivo 667 428 1324 2.366 1.002 0.123 0.040 10 1.1 entorhinal_exvivo @#@FSTIME 2024:10:08:17:26:02 mris_anatomical_stats N 12 e 3.78 S 0.29 U 5.06 P 141% M 408852 F 1 R 195926 W 0 c 519 w 286 I 0 O 136 L 35.57 29.96 27.90 @#@FSLOADPOST 2024:10:08:17:26:06 mris_anatomical_stats N 12 34.16 29.76 27.85 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 208392 Total vertex volume 208137 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 797 402 1351 2.307 0.628 0.120 0.040 12 1.0 BA1_exvivo 1580 1019 2173 2.009 0.450 0.082 0.015 8 1.0 BA2_exvivo 924 676 887 1.688 0.296 0.136 0.031 7 1.2 BA3a_exvivo 1482 1001 1564 1.570 0.314 0.087 0.016 7 1.2 BA3b_exvivo 1557 978 2937 2.705 0.505 0.101 0.029 13 1.6 BA4a_exvivo 1251 811 1918 2.484 0.483 0.112 0.033 10 1.7 BA4p_exvivo 4251 2876 9525 2.676 0.567 0.117 0.032 44 5.5 BA6_exvivo 1196 815 2422 2.575 0.490 0.117 0.030 13 1.5 BA44_exvivo 929 695 2282 2.619 0.540 0.119 0.025 11 0.9 BA45_exvivo 3568 2351 4076 1.661 0.475 0.127 0.038 41 5.1 V1_exvivo 3379 2238 4690 1.970 0.487 0.141 0.036 44 4.9 V2_exvivo 450 310 827 2.468 0.443 0.122 0.026 4 0.7 MT_exvivo 304 198 741 3.011 0.768 0.134 0.048 4 0.6 perirhinal_exvivo 392 257 802 2.535 0.784 0.101 0.023 2 0.4 entorhinal_exvivo @#@FSTIME 2024:10:08:17:26:06 mris_anatomical_stats N 12 e 4.14 S 0.30 U 5.39 P 137% M 408784 F 2 R 201643 W 0 c 595 w 276 I 0 O 136 L 34.16 29.76 27.85 @#@FSLOADPOST 2024:10:08:17:26:10 mris_anatomical_stats N 12 33.43 29.68 27.83 #-------------------------------------------- #@# BA_exvivo Labels rh Tue Oct 8 17:26:10 CDT 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 3355604 of (3355604 3355607 3355611 3355614 3355617) to complete... Waiting for PID 3355607 of (3355604 3355607 3355611 3355614 3355617) to complete... Waiting for PID 3355611 of (3355604 3355607 3355611 3355614 3355617) to complete... Waiting for PID 3355614 of (3355604 3355607 3355611 3355614 3355617) to complete... Waiting for PID 3355617 of (3355604 3355607 3355611 3355614 3355617) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 218 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4180 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6934 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4100 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4704 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5886 mri_label2label: Done PIDs (3355604 3355607 3355611 3355614 3355617) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 3357448 of (3357448 3357452 3357455 3357458) to complete... Waiting for PID 3357452 of (3357448 3357452 3357455 3357458) to complete... Waiting for PID 3357455 of (3357448 3357452 3357455 3357458) to complete... Waiting for PID 3357458 of (3357448 3357452 3357455 3357458) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4611 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 218 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12474 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 6980 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5494 mri_label2label: Done PIDs (3357448 3357452 3357455 3357458) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 3358395 of (3358395 3358398 3358401 3358404 3358407) to complete... Waiting for PID 3358398 of (3358395 3358398 3358401 3358404 3358407) to complete... Waiting for PID 3358401 of (3358395 3358398 3358401 3358404 3358407) to complete... Waiting for PID 3358404 of (3358395 3358398 3358401 3358404 3358407) to complete... Waiting for PID 3358407 of (3358395 3358398 3358401 3358404 3358407) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 1531 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6258 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 2101 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10117 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2155 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 89 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1127 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 824 mri_label2label: Done PIDs (3358395 3358398 3358401 3358404 3358407) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 3359985 of (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) to complete... Waiting for PID 3359988 of (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) to complete... Waiting for PID 3359991 of (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) to complete... Waiting for PID 3359994 of (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) to complete... Waiting for PID 3359998 of (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) to complete... Waiting for PID 3360001 of (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) to complete... Waiting for PID 3360004 of (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) to complete... Waiting for PID 3360007 of (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 541 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 676 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 721 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 836 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1523 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1575 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1586 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1704 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3667 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 1227 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4894 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2719 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 743 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3462 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1228 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 478 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1706 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1025 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 340 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1365 mri_label2label: Done PIDs (3359985 3359988 3359991 3359994 3359998 3360001 3360004 3360007) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt Number of ctab entries 9 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 104540 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.mpm.vpnl.annot @#@FSTIME 2024:10:08:17:26:37 mris_label2annot N 26 e 0.79 S 0.08 U 1.00 P 136% M 139348 F 2 R 37961 W 0 c 125 w 166 I 0 O 1864 L 39.32 31.35 28.43 @#@FSLOADPOST 2024:10:08:17:26:38 mris_label2annot N 26 39.32 31.35 28.43 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3363633 of (3363633 3363636 3363639 3363642 3363646) to complete... Waiting for PID 3363636 of (3363633 3363636 3363639 3363642 3363646) to complete... Waiting for PID 3363639 of (3363633 3363636 3363639 3363642 3363646) to complete... Waiting for PID 3363642 of (3363633 3363636 3363639 3363642 3363646) to complete... Waiting for PID 3363646 of (3363633 3363636 3363639 3363642 3363646) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 945 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 91 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2779 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1712 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2251 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 19 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1407 mri_label2label: Done PIDs (3363633 3363636 3363639 3363642 3363646) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3364529 of (3364529 3364532 3364535 3364539) to complete... Waiting for PID 3364532 of (3364529 3364532 3364535 3364539) to complete... Waiting for PID 3364535 of (3364529 3364532 3364535 3364539) to complete... Waiting for PID 3364539 of (3364529 3364532 3364535 3364539) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1595 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7021 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1033 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1196 mri_label2label: Done PIDs (3364529 3364532 3364535 3364539) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3365898 of (3365898 3365901 3365905 3365908 3365912) to complete... Waiting for PID 3365901 of (3365898 3365901 3365905 3365908 3365912) to complete... Waiting for PID 3365905 of (3365898 3365901 3365905 3365908 3365912) to complete... Waiting for PID 3365908 of (3365898 3365901 3365905 3365908 3365912) to complete... Waiting for PID 3365912 of (3365898 3365901 3365905 3365908 3365912) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 1104 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 1068 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4505 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 326 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 755 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 119197 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 330 mri_label2label: Done PIDs (3365898 3365901 3365905 3365908 3365912) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 81581 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.BA_exvivo.annot @#@FSTIME 2024:10:08:17:26:55 mris_label2annot N 38 e 0.71 S 0.10 U 0.83 P 129% M 139764 F 2 R 38064 W 0 c 93 w 282 I 0 O 1864 L 41.58 32.15 28.74 @#@FSLOADPOST 2024:10:08:17:26:56 mris_label2annot N 38 39.94 31.97 28.69 mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 96695 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2024:10:08:17:26:56 mris_label2annot N 38 e 0.68 S 0.08 U 0.87 P 139% M 139680 F 1 R 38002 W 0 c 93 w 165 I 0 O 1864 L 39.94 31.97 28.69 @#@FSLOADPOST 2024:10:08:17:26:57 mris_label2annot N 38 39.94 31.97 28.69 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 218567 Total vertex volume 218281 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1047 529 1772 2.405 0.582 0.116 0.038 16 1.2 BA1_exvivo 3413 2188 4888 2.277 0.452 0.084 0.016 18 2.2 BA2_exvivo 1136 811 1211 1.861 0.404 0.112 0.022 6 1.1 BA3a_exvivo 2092 1354 2538 1.750 0.461 0.094 0.020 15 1.9 BA3b_exvivo 1436 845 2589 2.671 0.508 0.106 0.032 12 1.8 BA4a_exvivo 1329 865 2151 2.653 0.516 0.107 0.031 10 1.7 BA4p_exvivo 6566 4625 14736 2.701 0.565 0.126 0.036 79 10.7 BA6_exvivo 2748 1935 5446 2.579 0.532 0.124 0.030 27 3.5 BA44_exvivo 3077 2266 6649 2.403 0.632 0.122 0.027 33 3.5 BA45_exvivo 4236 2600 4981 1.826 0.540 0.126 0.042 70 7.1 V1_exvivo 7635 5060 11323 2.069 0.554 0.134 0.033 101 10.2 V2_exvivo 1829 1267 3324 2.552 0.513 0.124 0.027 19 2.0 MT_exvivo 416 305 941 3.066 0.552 0.121 0.030 3 0.4 perirhinal_exvivo 656 448 1891 2.994 0.828 0.091 0.025 3 0.6 entorhinal_exvivo @#@FSTIME 2024:10:08:17:26:57 mris_anatomical_stats N 12 e 4.28 S 0.32 U 5.79 P 142% M 420896 F 1 R 237463 W 0 c 619 w 357 I 0 O 136 L 39.94 31.97 28.69 @#@FSLOADPOST 2024:10:08:17:27:01 mris_anatomical_stats N 12 44.51 33.05 29.06 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 218567 Total vertex volume 218281 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 742 361 1068 2.141 0.560 0.109 0.036 12 0.8 BA1_exvivo 2037 1280 2965 2.220 0.497 0.076 0.014 9 1.3 BA2_exvivo 1020 738 1046 1.839 0.378 0.116 0.021 6 1.1 BA3a_exvivo 1660 1090 1773 1.634 0.348 0.089 0.018 11 1.4 BA3b_exvivo 877 487 1588 2.670 0.536 0.110 0.036 8 1.2 BA4a_exvivo 1166 756 1928 2.730 0.517 0.108 0.034 9 1.6 BA4p_exvivo 4218 2877 9137 2.737 0.513 0.116 0.031 42 5.9 BA6_exvivo 687 529 1878 2.724 0.576 0.152 0.044 11 1.2 BA44_exvivo 786 629 2012 2.461 0.584 0.135 0.030 11 0.9 BA45_exvivo 4106 2491 4705 1.814 0.548 0.125 0.044 70 7.1 V1_exvivo 4225 2744 5899 1.973 0.538 0.138 0.035 59 6.0 V2_exvivo 292 190 509 2.197 0.537 0.126 0.032 4 0.4 MT_exvivo 38 28 85 3.233 0.331 0.102 0.021 0 0.0 perirhinal_exvivo 648 447 1530 2.880 0.688 0.102 0.025 4 0.6 entorhinal_exvivo @#@FSTIME 2024:10:08:17:27:01 mris_anatomical_stats N 12 e 3.87 S 0.32 U 5.42 P 148% M 421200 F 1 R 204546 W 0 c 531 w 351 I 0 O 136 L 44.51 33.05 29.06 @#@FSLOADPOST 2024:10:08:17:27:05 mris_anatomical_stats N 12 44.51 33.05 29.06 Started at Tue Oct 8 12:29:19 CDT 2024 Ended at Tue Oct 8 17:27:05 CDT 2024 #@#%# recon-all-run-time-hours 4.963 recon-all -s PIB23-310_VYr0_Bay3prisma finished without error at Tue Oct 8 17:27:05 CDT 2024 #New# invocation of recon-all Wed Oct 9 15:50:41 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/recon-all -3T -parallel -s PIB23-310_VYr0_Bay3prisma -autorecon2 -autorecon3 subjid PIB23-310_VYr0_Bay3prisma setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Actual FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 build-stamp.txt: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 1029556 maxlocks unlimited maxsignal 1029556 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 251Gi 196Gi 22Gi 28Mi 32Gi 52Gi Swap: 111Gi 220Mi 111Gi ######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275) 7.3.2 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:41-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:42-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/09-20:50:43-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Wed Oct 9 15:50:43 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (56, 76, 44) --> (193, 210, 212) finding center of left hemi white matter using (102, 121, 128) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (85,105,107) --> (118, 137,148) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 6.0 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.361 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.236524 @ (-10.526, -10.526, -10.526) max log p = -4.131704 @ (15.789, -5.263, -5.263) max log p = -4.014275 @ (-7.895, 7.895, -2.632) max log p = -3.929690 @ (3.947, -3.947, -1.316) max log p = -3.917706 @ (-0.658, 0.658, -0.658) max log p = -3.917706 @ (0.000, 0.000, 0.000) max log p = -3.917706 @ (0.000, 0.000, 0.000) max log p = -3.917706 @ (0.000, 0.000, 0.000) Found translation: (0.7, -11.2, -20.4): log p = -3.918 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.916, old_max_log_p =-3.918 (thresh=-3.9) 1.07500 0.00000 0.00000 -8.80294; 0.00000 1.03837 0.27823 -51.19630; 0.00000 -0.25882 0.96593 25.16160; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.841, old_max_log_p =-3.916 (thresh=-3.9) 1.01529 0.00000 0.00000 -3.14550; 0.00000 1.05307 0.21446 -47.45707; 0.00000 -0.18665 0.96295 15.95796; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.841, old_max_log_p =-3.841 (thresh=-3.8) 1.01529 0.00000 0.00000 -3.14550; 0.00000 1.05307 0.21446 -47.45707; 0.00000 -0.18665 0.96295 15.95796; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 19 seconds. **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.812, old_max_log_p =-3.841 (thresh=-3.8) 1.01590 0.03295 0.01520 -8.98766; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 18 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.808, old_max_log_p =-3.812 (thresh=-3.8) 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 18 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.808, old_max_log_p =-3.808 (thresh=-3.8) 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.808 (old=-4.361) transform before final EM align: 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 798460 FSRUNTIME@ mri_em_register 0.0418 hours 4 threads registration took 2 minutes and 31 seconds. @#@FSTIME 2024:10:09:15:50:43 mri_em_register N 7 e 150.64 S 1.19 U 507.88 P 337% M 616620 F 0 R 984379 W 0 c 44091 w 326 I 0 O 32 L 16.80 35.55 35.52 @#@FSLOADPOST 2024:10:09:15:53:14 mri_em_register N 7 7.97 24.35 31.29 #-------------------------------------- #@# CA Normalize Wed Oct 9 15:53:14 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (56, 76, 43) --> (193, 210, 212) finding center of left hemi white matter using (102, 121, 128) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (85,105,107) --> (118, 137,148) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 104 +- 6.0 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 246437 sample points... INFO: compute sample coordinates transform 1.01708 0.03299 0.01521 -9.14642; -0.03326 1.05500 0.21471 -43.02065; -0.00859 -0.18744 0.96628 16.29087; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 71, 42) --> (192, 179, 210) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 124.0 1 of 165 (0.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (63, 72, 40) --> (129, 177, 210) Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 256 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 153, 70) --> (175, 198, 124) Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0 0 of 24 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (82, 153, 66) --> (127, 194, 125) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (110, 144, 106) --> (144, 209, 136) Brain_Stem: limiting intensities to 92.0 --> 132.0 0 of 66 (0.0%) samples deleted using 527 total control points for intensity normalization... bias field = 0.889 +- 0.088 0 of 526 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 71, 42) --> (192, 179, 210) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 354 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (63, 72, 40) --> (129, 177, 210) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 440 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 153, 70) --> (175, 198, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 96 (7.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (82, 153, 66) --> (127, 194, 125) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 73 (19.2%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (110, 144, 106) --> (144, 209, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 39 of 145 (26.9%) samples deleted using 1108 total control points for intensity normalization... bias field = 1.005 +- 0.064 1 of 1023 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 71, 42) --> (192, 179, 210) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 11 of 399 (2.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (63, 72, 40) --> (129, 177, 210) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 12 of 503 (2.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 153, 70) --> (175, 198, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 37 of 142 (26.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (82, 153, 66) --> (127, 194, 125) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 30 of 81 (37.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (110, 144, 106) --> (144, 209, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 174 of 232 (75.0%) samples deleted using 1357 total control points for intensity normalization... bias field = 1.007 +- 0.046 0 of 1076 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 0 seconds. @#@FSTIME 2024:10:09:15:53:14 mri_ca_normalize N 8 e 59.74 S 0.83 U 60.94 P 103% M 681496 F 0 R 718916 W 0 c 5343 w 362 I 0 O 3608 L 7.97 24.35 31.29 @#@FSLOADPOST 2024:10:09:15:54:14 mri_ca_normalize N 8 6.03 20.81 29.64 #-------------------------------------- #@# SubCort Seg Wed Oct 9 15:54:14 CDT 2024 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz sysname Linux hostname chopin machine x86_64 user grossens Seg1 aseg.auto.mgz Seg2 aseg.presurf.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname chopin machine x86_64 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.35 Atlas used for the 3D morph was /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.14186 (25) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (24807 voxels, overlap=0.859) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (24807 voxels, peak = 22), gca=22.5 gca peak = 0.20380 (13) mri peak = 0.18857 (24) Right_Lateral_Ventricle (43): linear fit = 1.51 x + 0.0 (22176 voxels, overlap=0.317) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (22176 voxels, peak = 20), gca=19.5 gca peak = 0.26283 (96) mri peak = 0.11350 (105) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (602 voxels, overlap=0.033) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (602 voxels, peak = 105), gca=105.1 gca peak = 0.15814 (97) mri peak = 0.12299 (103) Left_Pallidum (13): linear fit = 1.11 x + 0.0 (491 voxels, overlap=0.218) Left_Pallidum (13): linear fit = 1.11 x + 0.0 (491 voxels, peak = 107), gca=107.2 gca peak = 0.27624 (56) mri peak = 0.10565 (73) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (968 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (968 voxels, peak = 70), gca=69.7 gca peak = 0.28723 (59) mri peak = 0.08791 (74) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (815 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (815 voxels, peak = 76), gca=76.4 gca peak = 0.07623 (103) mri peak = 0.10196 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (18560 voxels, overlap=0.713) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (18560 voxels, peak = 105), gca=104.5 gca peak = 0.07837 (105) mri peak = 0.10659 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (20637 voxels, overlap=0.572) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (20637 voxels, peak = 108), gca=107.6 gca peak = 0.10165 (58) mri peak = 0.05397 (80) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (23719 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (23719 voxels, peak = 78), gca=78.0 gca peak = 0.11113 (58) mri peak = 0.05539 (80) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (24978 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (24978 voxels, peak = 78), gca=78.0 gca peak = 0.27796 (67) mri peak = 0.12539 (91) Right_Caudate (50): linear fit = 1.33 x + 0.0 (1289 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.33 x + 0.0 (1289 voxels, peak = 89), gca=88.8 gca peak = 0.14473 (69) mri peak = 0.11555 (89) Left_Caudate (11): linear fit = 1.18 x + 0.0 (1032 voxels, overlap=0.017) Left_Caudate (11): linear fit = 1.18 x + 0.0 (1032 voxels, peak = 82), gca=81.8 gca peak = 0.14301 (56) mri peak = 0.06211 (71) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (17990 voxels, overlap=0.041) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (17990 voxels, peak = 70), gca=69.7 gca peak = 0.14610 (55) mri peak = 0.06619 (72) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (21480 voxels, overlap=0.018) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (21480 voxels, peak = 70), gca=69.6 gca peak = 0.16309 (85) mri peak = 0.14536 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5530 voxels, overlap=0.426) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5530 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.16345 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4965 voxels, overlap=0.588) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4965 voxels, peak = 88), gca=87.8 gca peak = 0.30461 (58) mri peak = 0.10476 (75) Left_Amygdala (18): linear fit = 1.34 x + 0.0 (406 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.34 x + 0.0 (406 voxels, peak = 77), gca=77.4 gca peak = 0.32293 (57) mri peak = 0.09318 (77) Right_Amygdala (54): linear fit = 1.34 x + 0.0 (450 voxels, overlap=0.047) Right_Amygdala (54): linear fit = 1.34 x + 0.0 (450 voxels, peak = 76), gca=76.1 gca peak = 0.11083 (90) mri peak = 0.08469 (94) Left_Thalamus (10): linear fit = 1.09 x + 0.0 (3738 voxels, overlap=0.631) Left_Thalamus (10): linear fit = 1.09 x + 0.0 (3738 voxels, peak = 98), gca=97.7 gca peak = 0.11393 (83) mri peak = 0.07245 (91) Right_Thalamus (49): linear fit = 1.09 x + 0.0 (3521 voxels, overlap=0.660) Right_Thalamus (49): linear fit = 1.09 x + 0.0 (3521 voxels, peak = 90), gca=90.1 gca peak = 0.08575 (81) mri peak = 0.11830 (96) Left_Putamen (12): linear fit = 1.17 x + 0.0 (990 voxels, overlap=0.011) Left_Putamen (12): linear fit = 1.17 x + 0.0 (990 voxels, peak = 95), gca=95.2 gca peak = 0.08618 (78) mri peak = 0.13225 (95) Right_Putamen (51): linear fit = 1.17 x + 0.0 (1172 voxels, overlap=0.013) Right_Putamen (51): linear fit = 1.17 x + 0.0 (1172 voxels, peak = 92), gca=91.6 gca peak = 0.08005 (78) mri peak = 0.08537 (85) Brain_Stem (16): linear fit = 1.07 x + 0.0 (13543 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.07 x + 0.0 (13543 voxels, peak = 83), gca=83.1 gca peak = 0.12854 (88) mri peak = 0.09636 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1130 voxels, overlap=0.213) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1130 voxels, peak = 98), gca=98.1 gca peak = 0.15703 (87) mri peak = 0.08291 (100) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1028 voxels, overlap=0.246) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1028 voxels, peak = 99), gca=98.7 gca peak = 0.17522 (25) mri peak = 0.19615 (27) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (534 voxels, overlap=0.936) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (534 voxels, peak = 25), gca=24.6 gca peak = 0.17113 (14) mri peak = 0.18790 (22) Fourth_Ventricle (15): linear fit = 1.40 x + 0.0 (770 voxels, overlap=0.484) Fourth_Ventricle (15): linear fit = 1.40 x + 0.0 (770 voxels, peak = 20), gca=19.7 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.32 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.25 x + 0.0 Left_Putamen too bright - rescaling by 1.003 (from 1.175) to 95.5 (was 95.2) Left_Pallidum too bright - rescaling by 0.960 (from 1.105) to 102.9 (was 107.2) Right_Pallidum too bright - rescaling by 0.979 (from 1.095) to 102.9 (was 105.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15076 (21) mri peak = 0.14186 (25) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (24807 voxels, overlap=0.883) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (24807 voxels, peak = 21), gca=20.7 gca peak = 0.16341 (19) mri peak = 0.18857 (24) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (22176 voxels, overlap=0.613) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (22176 voxels, peak = 21), gca=21.4 gca peak = 0.27514 (102) mri peak = 0.11350 (105) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, overlap=0.836) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak = 105), gca=104.5 gca peak = 0.14336 (103) mri peak = 0.12299 (103) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (491 voxels, overlap=0.929) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (491 voxels, peak = 107), gca=106.6 gca peak = 0.22626 (69) mri peak = 0.10565 (73) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (968 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (968 voxels, peak = 69), gca=69.0 gca peak = 0.28992 (73) mri peak = 0.08791 (74) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (815 voxels, overlap=1.002) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (815 voxels, peak = 69), gca=69.0 gca peak = 0.07897 (105) mri peak = 0.10196 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (18560 voxels, overlap=0.768) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (18560 voxels, peak = 105), gca=105.0 gca peak = 0.07733 (107) mri peak = 0.10659 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (20637 voxels, overlap=0.683) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (20637 voxels, peak = 107), gca=107.0 gca peak = 0.07336 (78) mri peak = 0.05397 (80) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (23719 voxels, overlap=0.936) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (23719 voxels, peak = 78), gca=78.0 gca peak = 0.08476 (78) mri peak = 0.05539 (80) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (24978 voxels, overlap=0.947) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (24978 voxels, peak = 77), gca=76.8 gca peak = 0.19749 (88) mri peak = 0.12539 (91) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1289 voxels, overlap=0.994) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1289 voxels, peak = 87), gca=86.7 gca peak = 0.14698 (92) mri peak = 0.11555 (89) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1032 voxels, overlap=0.715) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1032 voxels, peak = 93), gca=93.4 gca peak = 0.11231 (69) mri peak = 0.06211 (71) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (17990 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (17990 voxels, peak = 69), gca=69.0 gca peak = 0.12794 (70) mri peak = 0.06619 (72) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21480 voxels, overlap=0.978) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21480 voxels, peak = 70), gca=70.0 gca peak = 0.15236 (90) mri peak = 0.14536 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5530 voxels, overlap=0.880) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5530 voxels, peak = 90), gca=89.6 gca peak = 0.15236 (88) mri peak = 0.16345 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4965 voxels, overlap=0.857) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4965 voxels, peak = 88), gca=88.0 gca peak = 0.28025 (76) mri peak = 0.10476 (75) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (406 voxels, overlap=1.013) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (406 voxels, peak = 76), gca=76.0 gca peak = 0.30626 (76) mri peak = 0.09318 (77) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (450 voxels, overlap=1.002) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (450 voxels, peak = 76), gca=76.0 gca peak = 0.10254 (96) mri peak = 0.08469 (94) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3738 voxels, overlap=0.932) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3738 voxels, peak = 96), gca=96.5 gca peak = 0.10556 (90) mri peak = 0.07245 (91) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3521 voxels, overlap=0.905) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3521 voxels, peak = 90), gca=89.6 gca peak = 0.07769 (89) mri peak = 0.11830 (96) Left_Putamen (12): linear fit = 1.01 x + 0.0 (990 voxels, overlap=0.729) Left_Putamen (12): linear fit = 1.01 x + 0.0 (990 voxels, peak = 90), gca=90.3 gca peak = 0.07679 (89) mri peak = 0.13225 (95) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1172 voxels, overlap=0.800) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1172 voxels, peak = 90), gca=90.3 gca peak = 0.07351 (86) mri peak = 0.08537 (85) Brain_Stem (16): linear fit = 0.99 x + 0.0 (13543 voxels, overlap=0.735) Brain_Stem (16): linear fit = 0.99 x + 0.0 (13543 voxels, peak = 85), gca=84.7 gca peak = 0.12037 (98) mri peak = 0.09636 (99) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1130 voxels, overlap=0.800) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1130 voxels, peak = 98), gca=98.0 gca peak = 0.14511 (97) mri peak = 0.08291 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1028 voxels, overlap=0.878) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1028 voxels, peak = 97), gca=96.5 gca peak = 0.20053 (26) mri peak = 0.19615 (27) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (534 voxels, overlap=0.890) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (534 voxels, peak = 26), gca=25.6 gca peak = 0.15172 (20) mri peak = 0.18790 (22) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (770 voxels, overlap=0.628) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (770 voxels, peak = 19), gca=18.7 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.14276 (36) gca peak CSF = 0.20004 (45) gca peak Left_Accumbens_area = 0.66571 (74) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.63642 (53) gca peak Left_choroid_plexus = 0.10623 (35) gca peak Right_Inf_Lat_Vent = 0.24874 (29) gca peak Right_Accumbens_area = 0.28369 (87) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13305 (38) gca peak Fifth_Ventricle = 0.77755 (40) gca peak WM_hypointensities = 0.11570 (78) gca peak non_WM_hypointensities = 0.08220 (42) gca peak Optic_Chiasm = 0.60862 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 Left_Pallidum too bright - rescaling by 0.964 (from 1.035) to 102.8 (was 106.6) Right_Pallidum too bright - rescaling by 0.983 (from 1.025) to 102.8 (was 104.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 51747 voxels changed in iteration 0 of unlikely voxel relabeling 91 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 56760 gm and wm labels changed (%37 to gray, %63 to white out of all changed labels) 360 hippocampal voxels changed. 1 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 70925 changed. image ll: -2.114, PF=0.500 pass 2: 16150 changed. image ll: -2.112, PF=0.500 pass 3: 4843 changed. 39846 voxels changed in iteration 0 of unlikely voxel relabeling 161 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5216 voxels changed in iteration 0 of unlikely voxel relabeling 83 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5182 voxels changed in iteration 0 of unlikely voxel relabeling 47 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4688 voxels changed in iteration 0 of unlikely voxel relabeling 27 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 1 with volume 55367 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 2178 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 51555 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 1687 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2480.972152 mri_ca_label stimesec 7.777680 mri_ca_label ru_maxrss 2073024 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 8347099 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 66376 mri_ca_label ru_oublock 696 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 465 mri_ca_label ru_nivcsw 218267 auto-labeling took 40 minutes and 37 seconds. @#@FSTIME 2024:10:09:15:54:18 mri_ca_label N 10 e 2437.16 S 7.90 U 2480.97 P 102% M 2073024 F 0 R 8347116 W 0 c 218280 w 466 I 66376 O 696 L 5.95 20.55 29.50 @#@FSLOADPOST 2024:10:09:16:34:55 mri_ca_label N 10 6.62 6.99 8.89 #-------------------------------------- #@# CC Seg Wed Oct 9 16:34:55 CDT 2024 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/cc_up.lta PIB23-310_VYr0_Bay3prisma will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/transforms/cc_up.lta reading aseg from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.auto_noCCseg.mgz reading norm from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/norm.mgz 35795 voxels in left wm, 41599 in right wm, xrange [121, 132] searching rotation angles z=[-8 6], y=[-10 4] searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 global minimum found at slice 125.6, rotations (-3.11, -0.59) final transformation (x=125.6, yr=-3.112, zr=-0.590): 0.99847 0.01030 -0.05428 7.01482; -0.01028 0.99995 0.00056 13.23949; 0.05428 0.00000 0.99853 18.33560; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 130] in xformed coordinates best xformed slice 127 min_x_fornix = 131 min_x_fornix = 132 min_x_fornix = 132 min_x_fornix = 138 min_x_fornix = 134 cc center is found at 127 116 103 eigenvectors: -0.00039 -0.00778 0.99997; -0.03117 -0.99948 -0.00779; 0.99951 -0.03117 0.00015; writing aseg with callosum to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #VMPC# mri_cc VmPeak 461576 mri_cc done @#@FSTIME 2024:10:09:16:34:55 mri_cc N 7 e 36.72 S 0.45 U 37.22 P 102% M 344884 F 0 R 451954 W 0 c 3437 w 94 I 0 O 680 L 6.62 6.99 8.89 @#@FSLOADPOST 2024:10:09:16:35:32 mri_cc N 7 7.77 7.23 8.88 #-------------------------------------- #@# Merge ASeg Wed Oct 9 16:35:32 CDT 2024 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Oct 9 16:35:32 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 1040 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 82 (82), valley at 58 (58) csf peak at 23, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 83 (83), valley at 57 (57) csf peak at 24, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 25 seconds. @#@FSTIME 2024:10:09:16:35:32 mri_normalize N 9 e 146.37 S 1.57 U 158.19 P 109% M 1211096 F 0 R 1096215 W 0 c 14459 w 173 I 0 O 2744 L 7.77 7.23 8.88 @#@FSLOADPOST 2024:10:09:16:37:59 mri_normalize N 9 8.96 8.06 8.97 #-------------------------------------------- #@# Mask BFS Wed Oct 9 16:37:59 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1592378 voxels in mask (pct= 9.49) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:10:09:16:37:59 mri_mask N 5 e 1.08 S 0.06 U 1.42 P 136% M 74408 F 0 R 17271 W 0 c 137 w 145 I 0 O 2728 L 8.96 8.06 8.97 @#@FSLOADPOST 2024:10:09:16:38:00 mri_mask N 5 8.96 8.06 8.97 #-------------------------------------------- #@# WM Segmentation Wed Oct 9 16:38:00 CDT 2024 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname chopin machine x86_64 user grossens input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Writing output to wm255.mgz Count: -1 -1.000000 16777216 -0.000006 mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname chopin machine x86_64 user grossens input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Writing output to wm1.mgz Count: -1 -1.000000 16777216 -0.000006 mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: -1 deletes, -1 fills cp wm.mgz wm.seg.mgz AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2024:10:09:16:38:03 AntsDenoiseImageFs N 4 e 47.33 S 0.21 U 47.25 P 100% M 351308 F 0 R 238379 W 0 c 4057 w 116 I 0 O 2696 L 9.13 8.11 8.98 @#@FSLOADPOST 2024:10:09:16:38:51 AntsDenoiseImageFs N 4 9.49 8.37 9.02 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz preserving editing changes in output volume... wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (101.0): 101.4 +- 5.8 [79.0 --> 125.0] CCS GM (77.0) : 74.3 +- 14.0 [30.0 --> 95.0] white_mean 101.435 white_sigma 5.82245 gray_mean 74.2619 gray_sigma 14.0277 setting bottom of white matter range wm_low to 88.3 setting top of gray matter range gray_hi to 100.4 wm_low 88.2897 wm_hi 125 gray_low 30 gray_hi 100.435 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 88.2897 wm_hi 125 gray_low 30 gray_hi 100.435 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 100.435, wm_low = 88.2897 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=100.435, wmlow=88.2897 164708 voxels processed (0.98%) 83388 voxels white (0.50%) 81320 voxels non-white (0.48%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=83.2897, gray_hi=100.435, wsize=13 328045 voxels tested (1.96%) 55391 voxels changed (0.33%) 48267 multi-scale searches (0.29%) Recovering bright white MRIrecoverBrightWhite() wm_low 88.2897 wm_hi 125 slack 5.82245 pct_thresh 0.33 intensity_thresh 130.822 nvox_thresh 8.58 47 voxels tested (0.00%) 23 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=83.2897, hithr=100.435 smoothing input volume with sigma = 0.250 154462 voxels tested (0.92%) 17518 voxels changed (0.10%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 2834 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 2813 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 4511 filled MRIfindBrightNonWM(): 225 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.4 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:10:09:16:38:51 mri_segment N 6 e 83.55 S 0.38 U 84.45 P 101% M 147448 F 0 R 340861 W 0 c 7539 w 88 I 0 O 776 L 9.49 8.37 9.02 @#@FSLOADPOST 2024:10:09:16:40:14 mri_segment N 6 8.78 8.31 8.94 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.55 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 8442 additional wm voxels added 0 additional wm voxels added SEG EDIT: 176613 voxels turned on, 33028 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:10:09:16:40:14 mri_edit_wm_with_aseg N 5 e 32.86 S 0.45 U 34.55 P 106% M 463920 F 0 R 461048 W 0 c 3116 w 143 I 0 O 728 L 8.78 8.31 8.94 @#@FSLOADPOST 2024:10:09:16:40:47 mri_edit_wm_with_aseg N 5 9.58 8.56 9.00 mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 48 found - 48 modified | TOTAL: 48 pass 2 (xy+): 0 found - 48 modified | TOTAL: 48 pass 1 (xy-): 32 found - 32 modified | TOTAL: 80 pass 2 (xy-): 0 found - 32 modified | TOTAL: 80 pass 1 (yz+): 52 found - 52 modified | TOTAL: 132 pass 2 (yz+): 0 found - 52 modified | TOTAL: 132 pass 1 (yz-): 50 found - 50 modified | TOTAL: 182 pass 2 (yz-): 0 found - 50 modified | TOTAL: 182 pass 1 (xz+): 24 found - 24 modified | TOTAL: 206 pass 2 (xz+): 0 found - 24 modified | TOTAL: 206 pass 1 (xz-): 45 found - 45 modified | TOTAL: 251 pass 2 (xz-): 0 found - 45 modified | TOTAL: 251 Iteration Number : 1 pass 1 (+++): 14 found - 14 modified | TOTAL: 14 pass 2 (+++): 0 found - 14 modified | TOTAL: 14 pass 1 (+++): 14 found - 14 modified | TOTAL: 28 pass 2 (+++): 0 found - 14 modified | TOTAL: 28 pass 1 (+++): 16 found - 16 modified | TOTAL: 44 pass 2 (+++): 0 found - 16 modified | TOTAL: 44 pass 1 (+++): 9 found - 9 modified | TOTAL: 53 pass 2 (+++): 0 found - 9 modified | TOTAL: 53 Iteration Number : 1 pass 1 (++): 78 found - 78 modified | TOTAL: 78 pass 2 (++): 0 found - 78 modified | TOTAL: 78 pass 1 (+-): 100 found - 100 modified | TOTAL: 178 pass 2 (+-): 1 found - 101 modified | TOTAL: 179 pass 3 (+-): 0 found - 101 modified | TOTAL: 179 pass 1 (--): 129 found - 129 modified | TOTAL: 308 pass 2 (--): 0 found - 129 modified | TOTAL: 308 pass 1 (-+): 93 found - 93 modified | TOTAL: 401 pass 2 (-+): 0 found - 93 modified | TOTAL: 401 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 7 found - 7 modified | TOTAL: 12 pass 2 (xy-): 0 found - 7 modified | TOTAL: 12 pass 1 (yz+): 7 found - 7 modified | TOTAL: 19 pass 2 (yz+): 0 found - 7 modified | TOTAL: 19 pass 1 (yz-): 5 found - 5 modified | TOTAL: 24 pass 2 (yz-): 0 found - 5 modified | TOTAL: 24 pass 1 (xz+): 5 found - 5 modified | TOTAL: 29 pass 2 (xz+): 0 found - 5 modified | TOTAL: 29 pass 1 (xz-): 7 found - 7 modified | TOTAL: 36 pass 2 (xz-): 0 found - 7 modified | TOTAL: 36 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 0 found - 0 modified | TOTAL: 10 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 2 found - 2 modified | TOTAL: 7 pass 2 (+-): 0 found - 2 modified | TOTAL: 7 pass 1 (--): 1 found - 1 modified | TOTAL: 8 pass 2 (--): 0 found - 1 modified | TOTAL: 8 pass 1 (-+): 3 found - 3 modified | TOTAL: 11 pass 2 (-+): 0 found - 3 modified | TOTAL: 11 Iteration Number : 3 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 766 (out of 535614: 0.143013) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done @#@FSTIME 2024:10:09:16:40:47 mri_pretess N 5 e 4.78 S 0.07 U 5.61 P 118% M 57364 F 0 R 29943 W 0 c 530 w 79 I 0 O 728 L 9.53 8.56 9.00 @#@FSLOADPOST 2024:10:09:16:40:52 mri_pretess N 5 9.53 8.56 9.00 #-------------------------------------------- #@# Fill Wed Oct 9 16:40:52 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/SubCorticalMassLUT.txt -auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01708 0.03299 0.01521 -9.14641; -0.03326 1.05500 0.21471 -43.02063; -0.00859 -0.18744 0.96628 16.29088; 0.00000 0.00000 0.00000 1.00000; Using auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt ndiff 0 voxel to talairach voxel transform 1.01708 0.03299 0.01521 -9.14641; -0.03326 1.05500 0.21471 -43.02063; -0.00859 -0.18744 0.96628 16.29088; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 2127 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) need search nearby using seed (128, 119, 157), TAL = (0.0, 29.0, 9.0) talairach voxel to voxel transform 0.98208 -0.03219 -0.00831 7.73326; 0.02807 0.91094 -0.20286 42.75090; 0.01417 0.17642 0.99548 -8.49771; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (128, 119, 157) --> (0.0, 29.0, 9.0) done. filling took 1.1 minutes talairach cc position changed to (0.00, 29.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(18.00, 29.00, 9.00) SRC: (110.63, 122.39, 170.35) search lh wm seed point around talairach space (-18.00, 29.00, 9.00), SRC: (145.98, 123.40, 170.86) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... DoAutoMan 1 No edits to apply Writing edits to ../tmp/filled.edits.txt Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2024:10:09:16:40:52 mri_fill N 14 e 63.60 S 1.40 U 63.52 P 102% M 988740 F 0 R 1019004 W 0 c 5867 w 98 I 232 O 240 L 9.53 8.56 9.00 @#@FSLOADPOST 2024:10:09:16:41:56 mri_fill N 14 9.30 8.73 9.03 #-------------------------------------------- #@# Tessellate lh Wed Oct 9 16:41:56 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 9 found - 9 modified | TOTAL: 12 pass 2 (xy-): 0 found - 9 modified | TOTAL: 12 pass 1 (yz+): 3 found - 3 modified | TOTAL: 15 pass 2 (yz+): 0 found - 3 modified | TOTAL: 15 pass 1 (yz-): 3 found - 3 modified | TOTAL: 18 pass 2 (yz-): 0 found - 3 modified | TOTAL: 18 pass 1 (xz+): 3 found - 3 modified | TOTAL: 21 pass 2 (xz+): 0 found - 3 modified | TOTAL: 21 pass 1 (xz-): 2 found - 2 modified | TOTAL: 23 pass 2 (xz-): 0 found - 2 modified | TOTAL: 23 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 2 found - 2 modified | TOTAL: 6 pass 2 (--): 0 found - 2 modified | TOTAL: 6 pass 1 (-+): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 32 (out of 258981: 0.012356) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:10:09:16:41:56 mri_pretess N 4 e 2.46 S 0.02 U 2.75 P 112% M 40624 F 0 R 13162 W 0 c 255 w 45 I 0 O 232 L 9.30 8.73 9.03 @#@FSLOADPOST 2024:10:09:16:41:58 mri_pretess N 4 9.28 8.74 9.03 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.3.2 7.3.2 slice 50: 1196 vertices, 1304 faces slice 60: 6650 vertices, 6898 faces slice 70: 14888 vertices, 15188 faces slice 80: 23536 vertices, 23851 faces slice 90: 32114 vertices, 32425 faces slice 100: 40379 vertices, 40753 faces slice 110: 49776 vertices, 50184 faces slice 120: 59219 vertices, 59604 faces slice 130: 68069 vertices, 68441 faces slice 140: 76700 vertices, 77089 faces slice 150: 85484 vertices, 85874 faces slice 160: 92710 vertices, 93017 faces slice 170: 99141 vertices, 99434 faces slice 180: 104793 vertices, 105038 faces slice 190: 109172 vertices, 109393 faces slice 200: 111696 vertices, 111844 faces slice 210: 112096 vertices, 112178 faces slice 220: 112096 vertices, 112178 faces slice 230: 112096 vertices, 112178 faces slice 240: 112096 vertices, 112178 faces slice 250: 112096 vertices, 112178 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:10:09:16:41:59 mri_tessellate N 3 e 1.70 S 0.03 U 1.89 P 113% M 35544 F 0 R 7895 W 0 c 174 w 180 I 0 O 5264 L 9.28 8.74 9.03 @#@FSLOADPOST 2024:10:09:16:42:00 mri_tessellate N 3 9.28 8.74 9.03 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 112096 voxel in cpt #1: X=-82 [v=112096,e=336534,f=224356] located at (-25.393547, -11.052508, 1.404751) For the whole surface: X=-82 [v=112096,e=336534,f=224356] One single component has been found nothing to do done @#@FSTIME 2024:10:09:16:42:00 mris_extract_main_component N 2 e 0.65 S 0.14 U 0.66 P 122% M 223640 F 1 R 59106 W 0 c 79 w 271 I 0 O 7888 L 9.28 8.74 9.03 @#@FSLOADPOST 2024:10:09:16:42:01 mris_extract_main_component N 2 9.28 8.74 9.03 #-------------------------------------------- #@# Tessellate rh Wed Oct 9 16:42:01 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 7 found - 7 modified | TOTAL: 9 pass 2 (yz+): 0 found - 7 modified | TOTAL: 9 pass 1 (yz-): 1 found - 1 modified | TOTAL: 10 pass 2 (yz-): 0 found - 1 modified | TOTAL: 10 pass 1 (xz+): 3 found - 3 modified | TOTAL: 13 pass 2 (xz+): 0 found - 3 modified | TOTAL: 13 pass 1 (xz-): 0 found - 0 modified | TOTAL: 13 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 14 (out of 258693: 0.005412) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:10:09:16:42:01 mri_pretess N 4 e 1.75 S 0.05 U 1.96 P 114% M 40548 F 0 R 8835 W 0 c 191 w 41 I 0 O 232 L 9.28 8.74 9.03 @#@FSLOADPOST 2024:10:09:16:42:03 mri_pretess N 4 9.02 8.69 9.01 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 50: 777 vertices, 862 faces slice 60: 6157 vertices, 6374 faces slice 70: 13497 vertices, 13760 faces slice 80: 22842 vertices, 23203 faces slice 90: 31691 vertices, 31971 faces slice 100: 40272 vertices, 40596 faces slice 110: 49468 vertices, 49819 faces slice 120: 58788 vertices, 59158 faces slice 130: 67795 vertices, 68166 faces slice 140: 76554 vertices, 76925 faces slice 150: 85356 vertices, 85712 faces slice 160: 93563 vertices, 93902 faces slice 170: 100554 vertices, 100827 faces slice 180: 106631 vertices, 106869 faces slice 190: 111015 vertices, 111224 faces slice 200: 114673 vertices, 114834 faces slice 210: 115982 vertices, 116048 faces slice 220: 115982 vertices, 116048 faces slice 230: 115982 vertices, 116048 faces slice 240: 115982 vertices, 116048 faces slice 250: 115982 vertices, 116048 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:10:09:16:42:03 mri_tessellate N 3 e 1.75 S 0.02 U 1.97 P 113% M 35876 F 0 R 7975 W 0 c 182 w 232 I 0 O 5448 L 9.02 8.69 9.01 @#@FSLOADPOST 2024:10:09:16:42:05 mri_tessellate N 3 9.02 8.69 9.01 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 115982 voxel in cpt #1: X=-66 [v=115982,e=348144,f=232096] located at (29.053844, -8.443707, 2.983325) For the whole surface: X=-66 [v=115982,e=348144,f=232096] One single component has been found nothing to do done @#@FSTIME 2024:10:09:16:42:05 mris_extract_main_component N 2 e 0.69 S 0.13 U 0.73 P 124% M 231576 F 1 R 61117 W 0 c 82 w 353 I 0 O 8160 L 9.02 8.69 9.01 @#@FSLOADPOST 2024:10:09:16:42:05 mris_extract_main_component N 2 9.02 8.69 9.01 #-------------------------------------------- #@# Smooth1 lh Wed Oct 9 16:42:05 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Wed Oct 9 16:42:06 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 834177 of (834177 834180) to complete... Waiting for PID 834180 of (834177 834180) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (834177 834180) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Wed Oct 9 16:42:08 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Wed Oct 9 16:42:08 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 834262 of (834262 834265) to complete... Waiting for PID 834265 of (834262 834265) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.8 mm, total surface area = 60325 mm^2 step 000: RMS=0.155 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.064 (target=0.015) step 030: RMS=0.058 (target=0.015) step 035: RMS=0.056 (target=0.015) step 040: RMS=0.053 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.051 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.051 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 22.734086 mris_inflate stimesec 1.044463 mris_inflate ru_maxrss 179316 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 590914 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7904 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2245 mris_inflate ru_nivcsw 2062 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.2 mm, total surface area = 62761 mm^2 step 000: RMS=0.153 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.070 (target=0.015) step 025: RMS=0.063 (target=0.015) step 030: RMS=0.058 (target=0.015) step 035: RMS=0.054 (target=0.015) step 040: RMS=0.051 (target=0.015) step 045: RMS=0.050 (target=0.015) step 050: RMS=0.049 (target=0.015) step 055: RMS=0.049 (target=0.015) step 060: RMS=0.049 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 23.717912 mris_inflate stimesec 1.071905 mris_inflate ru_maxrss 185504 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 624481 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8176 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2799 mris_inflate ru_nivcsw 2123 PIDs (834262 834265) completed and logs appended. #-------------------------------------------- #@# QSphere lh Wed Oct 9 16:42:20 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Wed Oct 9 16:42:20 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 834384 of (834384 834387) to complete... Waiting for PID 834387 of (834384 834387) to complete... mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 scaling brain by 0.343... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.09 +- 0.62 (0.00-->6.26) (max @ vno 45700 --> 46582) face area 0.03 +- 0.04 (-0.13-->0.71) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.169, avgs=0 005/300: dt: 0.9000, rms radial error=175.911, avgs=0 010/300: dt: 0.9000, rms radial error=175.358, avgs=0 015/300: dt: 0.9000, rms radial error=174.632, avgs=0 020/300: dt: 0.9000, rms radial error=173.805, avgs=0 025/300: dt: 0.9000, rms radial error=172.920, avgs=0 030/300: dt: 0.9000, rms radial error=172.003, avgs=0 035/300: dt: 0.9000, rms radial error=171.068, avgs=0 040/300: dt: 0.9000, rms radial error=170.126, avgs=0 045/300: dt: 0.9000, rms radial error=169.182, avgs=0 050/300: dt: 0.9000, rms radial error=168.238, avgs=0 055/300: dt: 0.9000, rms radial error=167.296, avgs=0 060/300: dt: 0.9000, rms radial error=166.358, avgs=0 065/300: dt: 0.9000, rms radial error=165.423, avgs=0 070/300: dt: 0.9000, rms radial error=164.492, avgs=0 075/300: dt: 0.9000, rms radial error=163.570, avgs=0 080/300: dt: 0.9000, rms radial error=162.653, avgs=0 085/300: dt: 0.9000, rms radial error=161.741, avgs=0 090/300: dt: 0.9000, rms radial error=160.833, avgs=0 095/300: dt: 0.9000, rms radial error=159.931, avgs=0 100/300: dt: 0.9000, rms radial error=159.034, avgs=0 105/300: dt: 0.9000, rms radial error=158.142, avgs=0 110/300: dt: 0.9000, rms radial error=157.255, avgs=0 115/300: dt: 0.9000, rms radial error=156.372, avgs=0 120/300: dt: 0.9000, rms radial error=155.495, avgs=0 125/300: dt: 0.9000, rms radial error=154.622, avgs=0 130/300: dt: 0.9000, rms radial error=153.753, avgs=0 135/300: dt: 0.9000, rms radial error=152.890, avgs=0 140/300: dt: 0.9000, rms radial error=152.031, avgs=0 145/300: dt: 0.9000, rms radial error=151.176, avgs=0 150/300: dt: 0.9000, rms radial error=150.327, avgs=0 155/300: dt: 0.9000, rms radial error=149.481, avgs=0 160/300: dt: 0.9000, rms radial error=148.641, avgs=0 165/300: dt: 0.9000, rms radial error=147.805, avgs=0 170/300: dt: 0.9000, rms radial error=146.973, avgs=0 175/300: dt: 0.9000, rms radial error=146.146, avgs=0 180/300: dt: 0.9000, rms radial error=145.324, avgs=0 185/300: dt: 0.9000, rms radial error=144.506, avgs=0 190/300: dt: 0.9000, rms radial error=143.693, avgs=0 195/300: dt: 0.9000, rms radial error=142.884, avgs=0 200/300: dt: 0.9000, rms radial error=142.080, avgs=0 205/300: dt: 0.9000, rms radial error=141.280, avgs=0 210/300: dt: 0.9000, rms radial error=140.485, avgs=0 215/300: dt: 0.9000, rms radial error=139.694, avgs=0 220/300: dt: 0.9000, rms radial error=138.907, avgs=0 225/300: dt: 0.9000, rms radial error=138.125, avgs=0 230/300: dt: 0.9000, rms radial error=137.347, avgs=0 235/300: dt: 0.9000, rms radial error=136.574, avgs=0 240/300: dt: 0.9000, rms radial error=135.805, avgs=0 245/300: dt: 0.9000, rms radial error=135.040, avgs=0 250/300: dt: 0.9000, rms radial error=134.279, avgs=0 255/300: dt: 0.9000, rms radial error=133.523, avgs=0 260/300: dt: 0.9000, rms radial error=132.771, avgs=0 265/300: dt: 0.9000, rms radial error=132.023, avgs=0 270/300: dt: 0.9000, rms radial error=131.279, avgs=0 275/300: dt: 0.9000, rms radial error=130.539, avgs=0 280/300: dt: 0.9000, rms radial error=129.804, avgs=0 285/300: dt: 0.9000, rms radial error=129.073, avgs=0 290/300: dt: 0.9000, rms radial error=128.345, avgs=0 295/300: dt: 0.9000, rms radial error=127.622, avgs=0 300/300: dt: 0.9000, rms radial error=126.903, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12609.82 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00038 epoch 2 (K=40.0), pass 1, starting sse = 1898.96 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00106 epoch 3 (K=160.0), pass 1, starting sse = 152.95 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/15 = 0.00829 epoch 4 (K=640.0), pass 1, starting sse = 9.50 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/16 = 0.00262 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0203 hours FSRUNTIME@ mris_sphere 0.0203 hours 4 threads #VMPC# mris_sphere VmPeak 772004 mris_sphere done mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 scaling brain by 0.331... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.06 +- 0.61 (0.00-->8.68) (max @ vno 53711 --> 54661) face area 0.03 +- 0.04 (-0.10-->1.19) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.536, avgs=0 005/300: dt: 0.9000, rms radial error=176.279, avgs=0 010/300: dt: 0.9000, rms radial error=175.726, avgs=0 015/300: dt: 0.9000, rms radial error=174.999, avgs=0 020/300: dt: 0.9000, rms radial error=174.174, avgs=0 025/300: dt: 0.9000, rms radial error=173.292, avgs=0 030/300: dt: 0.9000, rms radial error=172.379, avgs=0 035/300: dt: 0.9000, rms radial error=171.448, avgs=0 040/300: dt: 0.9000, rms radial error=170.509, avgs=0 045/300: dt: 0.9000, rms radial error=169.567, avgs=0 050/300: dt: 0.9000, rms radial error=168.625, avgs=0 055/300: dt: 0.9000, rms radial error=167.686, avgs=0 060/300: dt: 0.9000, rms radial error=166.750, avgs=0 065/300: dt: 0.9000, rms radial error=165.818, avgs=0 070/300: dt: 0.9000, rms radial error=164.890, avgs=0 075/300: dt: 0.9000, rms radial error=163.967, avgs=0 080/300: dt: 0.9000, rms radial error=163.049, avgs=0 085/300: dt: 0.9000, rms radial error=162.135, avgs=0 090/300: dt: 0.9000, rms radial error=161.227, avgs=0 095/300: dt: 0.9000, rms radial error=160.324, avgs=0 100/300: dt: 0.9000, rms radial error=159.425, avgs=0 105/300: dt: 0.9000, rms radial error=158.531, avgs=0 110/300: dt: 0.9000, rms radial error=157.642, avgs=0 115/300: dt: 0.9000, rms radial error=156.757, avgs=0 120/300: dt: 0.9000, rms radial error=155.878, avgs=0 125/300: dt: 0.9000, rms radial error=155.003, avgs=0 130/300: dt: 0.9000, rms radial error=154.132, avgs=0 135/300: dt: 0.9000, rms radial error=153.267, avgs=0 140/300: dt: 0.9000, rms radial error=152.406, avgs=0 145/300: dt: 0.9000, rms radial error=151.549, avgs=0 150/300: dt: 0.9000, rms radial error=150.698, avgs=0 155/300: dt: 0.9000, rms radial error=149.851, avgs=0 160/300: dt: 0.9000, rms radial error=149.009, avgs=0 165/300: dt: 0.9000, rms radial error=148.171, avgs=0 170/300: dt: 0.9000, rms radial error=147.338, avgs=0 175/300: dt: 0.9000, rms radial error=146.509, avgs=0 180/300: dt: 0.9000, rms radial error=145.685, avgs=0 185/300: dt: 0.9000, rms radial error=144.865, avgs=0 190/300: dt: 0.9000, rms radial error=144.050, avgs=0 195/300: dt: 0.9000, rms radial error=143.240, avgs=0 200/300: dt: 0.9000, rms radial error=142.434, avgs=0 205/300: dt: 0.9000, rms radial error=141.632, avgs=0 210/300: dt: 0.9000, rms radial error=140.835, avgs=0 215/300: dt: 0.9000, rms radial error=140.042, avgs=0 220/300: dt: 0.9000, rms radial error=139.254, avgs=0 225/300: dt: 0.9000, rms radial error=138.470, avgs=0 230/300: dt: 0.9000, rms radial error=137.691, avgs=0 235/300: dt: 0.9000, rms radial error=136.915, avgs=0 240/300: dt: 0.9000, rms radial error=136.145, avgs=0 245/300: dt: 0.9000, rms radial error=135.378, avgs=0 250/300: dt: 0.9000, rms radial error=134.616, avgs=0 255/300: dt: 0.9000, rms radial error=133.857, avgs=0 260/300: dt: 0.9000, rms radial error=133.103, avgs=0 265/300: dt: 0.9000, rms radial error=132.353, avgs=0 270/300: dt: 0.9000, rms radial error=131.608, avgs=0 275/300: dt: 0.9000, rms radial error=130.866, avgs=0 280/300: dt: 0.9000, rms radial error=130.129, avgs=0 285/300: dt: 0.9000, rms radial error=129.396, avgs=0 290/300: dt: 0.9000, rms radial error=128.667, avgs=0 295/300: dt: 0.9000, rms radial error=127.942, avgs=0 300/300: dt: 0.9000, rms radial error=127.221, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13224.27 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00028 epoch 2 (K=40.0), pass 1, starting sse = 2053.66 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00086 epoch 3 (K=160.0), pass 1, starting sse = 181.24 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/14 = 0.00957 epoch 4 (K=640.0), pass 1, starting sse = 10.92 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/17 = 0.00337 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0224 hours FSRUNTIME@ mris_sphere 0.0224 hours 4 threads #VMPC# mris_sphere VmPeak 775144 mris_sphere done PIDs (834384 834387) completed and logs appended. #@# Fix Topology lh Wed Oct 9 16:43:41 CDT 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma lh #@# Fix Topology rh Wed Oct 9 16:43:41 CDT 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma rh Waiting for PID 835165 of (835165 835168) to complete... Waiting for PID 835168 of (835165 835168) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-82 (nv=112096, nf=224356, ne=336534, g=42) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 4996 ambiguous faces found in tessellation segmenting defects... 58 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 58 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7970 (-4.3985) -vertex loglikelihood: -6.3047 (-3.1524) -normal dot loglikelihood: -3.5493 (-3.5493) -quad curv loglikelihood: -5.9853 (-2.9927) Total Loglikelihood : -24.6363 CORRECTING DEFECT 0 (vertices=19, convex hull=23, v0=3624) After retessellation of defect 0 (v0=3624), euler #=-55 (109024,325805,216726) : difference with theory (-55) = 0 CORRECTING DEFECT 1 (vertices=10, convex hull=16, v0=6246) After retessellation of defect 1 (v0=6246), euler #=-54 (109025,325814,216735) : difference with theory (-54) = 0 CORRECTING DEFECT 2 (vertices=513, convex hull=158, v0=6966) After retessellation of defect 2 (v0=6966), euler #=-53 (109109,326144,216982) : difference with theory (-53) = 0 CORRECTING DEFECT 3 (vertices=72, convex hull=106, v0=9076) After retessellation of defect 3 (v0=9076), euler #=-52 (109145,326298,217101) : difference with theory (-52) = 0 CORRECTING DEFECT 4 (vertices=44, convex hull=82, v0=10146) After retessellation of defect 4 (v0=10146), euler #=-51 (109174,326417,217192) : difference with theory (-51) = 0 CORRECTING DEFECT 5 (vertices=34, convex hull=69, v0=12407) After retessellation of defect 5 (v0=12407), euler #=-50 (109197,326512,217265) : difference with theory (-50) = 0 CORRECTING DEFECT 6 (vertices=44, convex hull=57, v0=14718) After retessellation of defect 6 (v0=14718), euler #=-49 (109209,326571,217313) : difference with theory (-49) = 0 CORRECTING DEFECT 7 (vertices=45, convex hull=73, v0=14954) After retessellation of defect 7 (v0=14954), euler #=-48 (109236,326683,217399) : difference with theory (-48) = 0 CORRECTING DEFECT 8 (vertices=65, convex hull=35, v0=18501) After retessellation of defect 8 (v0=18501), euler #=-47 (109243,326714,217424) : difference with theory (-47) = 0 CORRECTING DEFECT 9 (vertices=6, convex hull=14, v0=19813) After retessellation of defect 9 (v0=19813), euler #=-46 (109244,326721,217431) : difference with theory (-46) = 0 CORRECTING DEFECT 10 (vertices=59, convex hull=43, v0=21564) After retessellation of defect 10 (v0=21564), euler #=-45 (109249,326748,217454) : difference with theory (-45) = 0 CORRECTING DEFECT 11 (vertices=56, convex hull=97, v0=22647) After retessellation of defect 11 (v0=22647), euler #=-44 (109283,326890,217563) : difference with theory (-44) = 0 CORRECTING DEFECT 12 (vertices=58, convex hull=90, v0=22769) After retessellation of defect 12 (v0=22769), euler #=-43 (109321,327039,217675) : difference with theory (-43) = 0 CORRECTING DEFECT 13 (vertices=195, convex hull=143, v0=22938) After retessellation of defect 13 (v0=22938), euler #=-42 (109388,327302,217872) : difference with theory (-42) = 0 CORRECTING DEFECT 14 (vertices=24, convex hull=54, v0=25461) After retessellation of defect 14 (v0=25461), euler #=-41 (109403,327368,217924) : difference with theory (-41) = 0 CORRECTING DEFECT 15 (vertices=8, convex hull=21, v0=28936) After retessellation of defect 15 (v0=28936), euler #=-40 (109404,327378,217934) : difference with theory (-40) = 0 CORRECTING DEFECT 16 (vertices=24, convex hull=57, v0=30754) After retessellation of defect 16 (v0=30754), euler #=-39 (109418,327441,217984) : difference with theory (-39) = 0 CORRECTING DEFECT 17 (vertices=28, convex hull=76, v0=31481) After retessellation of defect 17 (v0=31481), euler #=-38 (109434,327518,218046) : difference with theory (-38) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=38, v0=31763) After retessellation of defect 18 (v0=31763), euler #=-37 (109442,327555,218076) : difference with theory (-37) = 0 CORRECTING DEFECT 19 (vertices=26, convex hull=71, v0=32822) After retessellation of defect 19 (v0=32822), euler #=-36 (109450,327603,218117) : difference with theory (-36) = 0 CORRECTING DEFECT 20 (vertices=46, convex hull=76, v0=35843) After retessellation of defect 20 (v0=35843), euler #=-35 (109483,327734,218216) : difference with theory (-35) = 0 CORRECTING DEFECT 21 (vertices=17, convex hull=57, v0=39889) After retessellation of defect 21 (v0=39889), euler #=-34 (109491,327781,218256) : difference with theory (-34) = 0 CORRECTING DEFECT 22 (vertices=18, convex hull=22, v0=43025) After retessellation of defect 22 (v0=43025), euler #=-33 (109496,327804,218275) : difference with theory (-33) = 0 CORRECTING DEFECT 23 (vertices=49, convex hull=76, v0=44877) After retessellation of defect 23 (v0=44877), euler #=-32 (109504,327860,218324) : difference with theory (-32) = 0 CORRECTING DEFECT 24 (vertices=185, convex hull=80, v0=46094) After retessellation of defect 24 (v0=46094), euler #=-31 (109518,327934,218385) : difference with theory (-31) = 0 CORRECTING DEFECT 25 (vertices=7, convex hull=29, v0=48647) After retessellation of defect 25 (v0=48647), euler #=-30 (109521,327952,218401) : difference with theory (-30) = 0 CORRECTING DEFECT 26 (vertices=75, convex hull=135, v0=49121) After retessellation of defect 26 (v0=49121), euler #=-29 (109560,328125,218536) : difference with theory (-29) = 0 CORRECTING DEFECT 27 (vertices=18, convex hull=26, v0=49262) After retessellation of defect 27 (v0=49262), euler #=-28 (109564,328148,218556) : difference with theory (-28) = 0 CORRECTING DEFECT 28 (vertices=45, convex hull=59, v0=54571) After retessellation of defect 28 (v0=54571), euler #=-27 (109582,328225,218616) : difference with theory (-27) = 0 CORRECTING DEFECT 29 (vertices=20, convex hull=24, v0=56682) After retessellation of defect 29 (v0=56682), euler #=-26 (109583,328239,218630) : difference with theory (-26) = 0 CORRECTING DEFECT 30 (vertices=52, convex hull=55, v0=57428) After retessellation of defect 30 (v0=57428), euler #=-25 (109597,328305,218683) : difference with theory (-25) = 0 CORRECTING DEFECT 31 (vertices=10, convex hull=25, v0=63098) After retessellation of defect 31 (v0=63098), euler #=-24 (109599,328320,218697) : difference with theory (-24) = 0 CORRECTING DEFECT 32 (vertices=36, convex hull=81, v0=63980) After retessellation of defect 32 (v0=63980), euler #=-23 (109618,328410,218769) : difference with theory (-23) = 0 CORRECTING DEFECT 33 (vertices=17, convex hull=16, v0=66352) After retessellation of defect 33 (v0=66352), euler #=-22 (109620,328421,218779) : difference with theory (-22) = 0 CORRECTING DEFECT 34 (vertices=22, convex hull=19, v0=67296) After retessellation of defect 34 (v0=67296), euler #=-21 (109623,328435,218791) : difference with theory (-21) = 0 CORRECTING DEFECT 35 (vertices=7, convex hull=14, v0=69051) After retessellation of defect 35 (v0=69051), euler #=-20 (109624,328442,218798) : difference with theory (-20) = 0 CORRECTING DEFECT 36 (vertices=41, convex hull=50, v0=72521) After retessellation of defect 36 (v0=72521), euler #=-19 (109639,328510,218852) : difference with theory (-19) = 0 CORRECTING DEFECT 37 (vertices=16, convex hull=23, v0=73785) After retessellation of defect 37 (v0=73785), euler #=-18 (109642,328524,218864) : difference with theory (-18) = 0 CORRECTING DEFECT 38 (vertices=48, convex hull=53, v0=76313) After retessellation of defect 38 (v0=76313), euler #=-17 (109651,328572,218904) : difference with theory (-17) = 0 CORRECTING DEFECT 39 (vertices=34, convex hull=28, v0=76903) After retessellation of defect 39 (v0=76903), euler #=-16 (109659,328605,218930) : difference with theory (-16) = 0 CORRECTING DEFECT 40 (vertices=10, convex hull=28, v0=77448) After retessellation of defect 40 (v0=77448), euler #=-15 (109663,328628,218950) : difference with theory (-15) = 0 CORRECTING DEFECT 41 (vertices=54, convex hull=81, v0=80404) After retessellation of defect 41 (v0=80404), euler #=-14 (109679,328714,219021) : difference with theory (-14) = 0 CORRECTING DEFECT 42 (vertices=12, convex hull=27, v0=82470) After retessellation of defect 42 (v0=82470), euler #=-13 (109682,328732,219037) : difference with theory (-13) = 0 CORRECTING DEFECT 43 (vertices=105, convex hull=94, v0=82852) After retessellation of defect 43 (v0=82852), euler #=-12 (109711,328859,219136) : difference with theory (-12) = 0 CORRECTING DEFECT 44 (vertices=26, convex hull=28, v0=83257) After retessellation of defect 44 (v0=83257), euler #=-11 (109714,328877,219152) : difference with theory (-11) = 0 CORRECTING DEFECT 45 (vertices=49, convex hull=29, v0=83896) After retessellation of defect 45 (v0=83896), euler #=-10 (109721,328909,219178) : difference with theory (-10) = 0 CORRECTING DEFECT 46 (vertices=52, convex hull=65, v0=84426) After retessellation of defect 46 (v0=84426), euler #=-9 (109741,328997,219247) : difference with theory (-9) = 0 CORRECTING DEFECT 47 (vertices=56, convex hull=88, v0=86609) After retessellation of defect 47 (v0=86609), euler #=-8 (109773,329129,219348) : difference with theory (-8) = 0 CORRECTING DEFECT 48 (vertices=26, convex hull=28, v0=87179) After retessellation of defect 48 (v0=87179), euler #=-7 (109777,329150,219366) : difference with theory (-7) = 0 CORRECTING DEFECT 49 (vertices=59, convex hull=35, v0=88898) After retessellation of defect 49 (v0=88898), euler #=-6 (109786,329191,219399) : difference with theory (-6) = 0 CORRECTING DEFECT 50 (vertices=20, convex hull=29, v0=89872) After retessellation of defect 50 (v0=89872), euler #=-5 (109790,329210,219415) : difference with theory (-5) = 0 CORRECTING DEFECT 51 (vertices=17, convex hull=20, v0=90832) After retessellation of defect 51 (v0=90832), euler #=-4 (109793,329225,219428) : difference with theory (-4) = 0 CORRECTING DEFECT 52 (vertices=28, convex hull=33, v0=92107) After retessellation of defect 52 (v0=92107), euler #=-3 (109798,329251,219450) : difference with theory (-3) = 0 CORRECTING DEFECT 53 (vertices=107, convex hull=102, v0=93938) After retessellation of defect 53 (v0=93938), euler #=-2 (109843,329433,219588) : difference with theory (-2) = 0 CORRECTING DEFECT 54 (vertices=35, convex hull=74, v0=94890) After retessellation of defect 54 (v0=94890), euler #=-1 (109855,329497,219641) : difference with theory (-1) = 0 CORRECTING DEFECT 55 (vertices=154, convex hull=48, v0=100170) After retessellation of defect 55 (v0=100170), euler #=0 (109866,329547,219681) : difference with theory (0) = 0 CORRECTING DEFECT 56 (vertices=125, convex hull=72, v0=108402) After retessellation of defect 56 (v0=108402), euler #=1 (109897,329672,219776) : difference with theory (1) = 0 CORRECTING DEFECT 57 (vertices=21, convex hull=40, v0=111138) After retessellation of defect 57 (v0=111138), euler #=2 (109911,329727,219818) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.05-->7.84) (max @ vno 50554 --> 50589) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.05-->7.84) (max @ vno 50554 --> 50589) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 186 mutations (34.3%), 357 crossovers (65.7%), 107 vertices were eliminated building final representation... 2185 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=109911, nf=219818, ne=329727, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 291 intersecting 001: 31 intersecting terminating search with 0 intersecting topology fixing took 1.8 minutes FSRUNTIME@ mris_fix_topology lh 0.0297 hours 4 threads #VMPC# mris_fix_topology VmPeak 949336 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-66 (nv=115982, nf=232096, ne=348144, g=34) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 4449 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 2 -merging segment 10 into 9 -merging segment 21 into 16 48 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7780 (-4.3890) -vertex loglikelihood: -6.2308 (-3.1154) -normal dot loglikelihood: -3.5777 (-3.5777) -quad curv loglikelihood: -6.1691 (-3.0846) Total Loglikelihood : -24.7556 CORRECTING DEFECT 0 (vertices=28, convex hull=31, v0=5809) After retessellation of defect 0 (v0=5809), euler #=-48 (113206,338477,225223) : difference with theory (-45) = 3 CORRECTING DEFECT 1 (vertices=36, convex hull=32, v0=8240) After retessellation of defect 1 (v0=8240), euler #=-47 (113214,338510,225249) : difference with theory (-44) = 3 CORRECTING DEFECT 2 (vertices=721, convex hull=233, v0=8536) After retessellation of defect 2 (v0=8536), euler #=-45 (113224,338663,225394) : difference with theory (-43) = 2 CORRECTING DEFECT 3 (vertices=59, convex hull=88, v0=12814) After retessellation of defect 3 (v0=12814), euler #=-44 (113255,338788,225489) : difference with theory (-42) = 2 CORRECTING DEFECT 4 (vertices=106, convex hull=67, v0=15004) After retessellation of defect 4 (v0=15004), euler #=-43 (113278,338888,225567) : difference with theory (-41) = 2 CORRECTING DEFECT 5 (vertices=12, convex hull=17, v0=17448) After retessellation of defect 5 (v0=17448), euler #=-42 (113278,338895,225575) : difference with theory (-40) = 2 CORRECTING DEFECT 6 (vertices=21, convex hull=28, v0=19016) After retessellation of defect 6 (v0=19016), euler #=-41 (113280,338911,225590) : difference with theory (-39) = 2 CORRECTING DEFECT 7 (vertices=24, convex hull=63, v0=32909) After retessellation of defect 7 (v0=32909), euler #=-40 (113289,338965,225636) : difference with theory (-38) = 2 CORRECTING DEFECT 8 (vertices=27, convex hull=56, v0=33790) After retessellation of defect 8 (v0=33790), euler #=-38 (113292,338998,225668) : difference with theory (-37) = 1 CORRECTING DEFECT 9 (vertices=95, convex hull=37, v0=39721) After retessellation of defect 9 (v0=39721), euler #=-37 (113301,339035,225697) : difference with theory (-36) = 1 CORRECTING DEFECT 10 (vertices=185, convex hull=55, v0=42353) After retessellation of defect 10 (v0=42353), euler #=-36 (113318,339106,225752) : difference with theory (-35) = 1 CORRECTING DEFECT 11 (vertices=45, convex hull=88, v0=46384) After retessellation of defect 11 (v0=46384), euler #=-35 (113328,339169,225806) : difference with theory (-34) = 1 CORRECTING DEFECT 12 (vertices=18, convex hull=32, v0=50443) After retessellation of defect 12 (v0=50443), euler #=-34 (113330,339187,225823) : difference with theory (-33) = 1 CORRECTING DEFECT 13 (vertices=9, convex hull=26, v0=52767) After retessellation of defect 13 (v0=52767), euler #=-33 (113333,339202,225836) : difference with theory (-32) = 1 CORRECTING DEFECT 14 (vertices=51, convex hull=95, v0=53022) After retessellation of defect 14 (v0=53022), euler #=-31 (113366,339350,225953) : difference with theory (-31) = 0 CORRECTING DEFECT 15 (vertices=10, convex hull=25, v0=53663) After retessellation of defect 15 (v0=53663), euler #=-30 (113372,339373,225971) : difference with theory (-30) = 0 CORRECTING DEFECT 16 (vertices=54, convex hull=34, v0=54002) After retessellation of defect 16 (v0=54002), euler #=-29 (113380,339409,226000) : difference with theory (-29) = 0 CORRECTING DEFECT 17 (vertices=29, convex hull=64, v0=55319) After retessellation of defect 17 (v0=55319), euler #=-28 (113391,339466,226047) : difference with theory (-28) = 0 CORRECTING DEFECT 18 (vertices=29, convex hull=74, v0=56568) After retessellation of defect 18 (v0=56568), euler #=-27 (113408,339553,226118) : difference with theory (-27) = 0 CORRECTING DEFECT 19 (vertices=44, convex hull=40, v0=57854) After retessellation of defect 19 (v0=57854), euler #=-26 (113416,339593,226151) : difference with theory (-26) = 0 CORRECTING DEFECT 20 (vertices=30, convex hull=53, v0=61694) After retessellation of defect 20 (v0=61694), euler #=-25 (113429,339655,226201) : difference with theory (-25) = 0 CORRECTING DEFECT 21 (vertices=23, convex hull=48, v0=63703) After retessellation of defect 21 (v0=63703), euler #=-24 (113436,339694,226234) : difference with theory (-24) = 0 CORRECTING DEFECT 22 (vertices=10, convex hull=16, v0=65479) After retessellation of defect 22 (v0=65479), euler #=-23 (113436,339699,226240) : difference with theory (-23) = 0 CORRECTING DEFECT 23 (vertices=9, convex hull=32, v0=70890) After retessellation of defect 23 (v0=70890), euler #=-22 (113437,339709,226250) : difference with theory (-22) = 0 CORRECTING DEFECT 24 (vertices=61, convex hull=82, v0=72547) After retessellation of defect 24 (v0=72547), euler #=-21 (113466,339831,226344) : difference with theory (-21) = 0 CORRECTING DEFECT 25 (vertices=135, convex hull=126, v0=76652) After retessellation of defect 25 (v0=76652), euler #=-20 (113497,339987,226470) : difference with theory (-20) = 0 CORRECTING DEFECT 26 (vertices=12, convex hull=17, v0=80240) After retessellation of defect 26 (v0=80240), euler #=-19 (113498,339994,226477) : difference with theory (-19) = 0 CORRECTING DEFECT 27 (vertices=9, convex hull=13, v0=80749) After retessellation of defect 27 (v0=80749), euler #=-18 (113499,340002,226485) : difference with theory (-18) = 0 CORRECTING DEFECT 28 (vertices=32, convex hull=23, v0=85129) After retessellation of defect 28 (v0=85129), euler #=-17 (113505,340026,226504) : difference with theory (-17) = 0 CORRECTING DEFECT 29 (vertices=33, convex hull=60, v0=88721) After retessellation of defect 29 (v0=88721), euler #=-16 (113529,340121,226576) : difference with theory (-16) = 0 CORRECTING DEFECT 30 (vertices=53, convex hull=94, v0=90734) After retessellation of defect 30 (v0=90734), euler #=-15 (113542,340202,226645) : difference with theory (-15) = 0 CORRECTING DEFECT 31 (vertices=36, convex hull=36, v0=91376) After retessellation of defect 31 (v0=91376), euler #=-14 (113548,340233,226671) : difference with theory (-14) = 0 CORRECTING DEFECT 32 (vertices=166, convex hull=187, v0=91771) After retessellation of defect 32 (v0=91771), euler #=-13 (113608,340501,226880) : difference with theory (-13) = 0 CORRECTING DEFECT 33 (vertices=51, convex hull=41, v0=92032) After retessellation of defect 33 (v0=92032), euler #=-12 (113617,340546,226917) : difference with theory (-12) = 0 CORRECTING DEFECT 34 (vertices=30, convex hull=28, v0=93667) After retessellation of defect 34 (v0=93667), euler #=-11 (113621,340569,226937) : difference with theory (-11) = 0 CORRECTING DEFECT 35 (vertices=58, convex hull=60, v0=93992) After retessellation of defect 35 (v0=93992), euler #=-10 (113655,340696,227031) : difference with theory (-10) = 0 CORRECTING DEFECT 36 (vertices=77, convex hull=92, v0=95141) After retessellation of defect 36 (v0=95141), euler #=-9 (113691,340844,227144) : difference with theory (-9) = 0 CORRECTING DEFECT 37 (vertices=10, convex hull=21, v0=95638) After retessellation of defect 37 (v0=95638), euler #=-8 (113693,340856,227155) : difference with theory (-8) = 0 CORRECTING DEFECT 38 (vertices=127, convex hull=139, v0=98423) After retessellation of defect 38 (v0=98423), euler #=-7 (113760,341125,227358) : difference with theory (-7) = 0 CORRECTING DEFECT 39 (vertices=35, convex hull=45, v0=100422) After retessellation of defect 39 (v0=100422), euler #=-6 (113778,341196,227412) : difference with theory (-6) = 0 CORRECTING DEFECT 40 (vertices=33, convex hull=68, v0=102222) After retessellation of defect 40 (v0=102222), euler #=-5 (113800,341287,227482) : difference with theory (-5) = 0 CORRECTING DEFECT 41 (vertices=6, convex hull=24, v0=104668) After retessellation of defect 41 (v0=104668), euler #=-4 (113801,341295,227490) : difference with theory (-4) = 0 CORRECTING DEFECT 42 (vertices=10, convex hull=26, v0=104906) After retessellation of defect 42 (v0=104906), euler #=-3 (113804,341313,227506) : difference with theory (-3) = 0 CORRECTING DEFECT 43 (vertices=15, convex hull=28, v0=108981) After retessellation of defect 43 (v0=108981), euler #=-2 (113805,341327,227520) : difference with theory (-2) = 0 CORRECTING DEFECT 44 (vertices=29, convex hull=59, v0=110133) After retessellation of defect 44 (v0=110133), euler #=-1 (113814,341379,227564) : difference with theory (-1) = 0 CORRECTING DEFECT 45 (vertices=25, convex hull=47, v0=114573) After retessellation of defect 45 (v0=114573), euler #=0 (113830,341444,227614) : difference with theory (0) = 0 CORRECTING DEFECT 46 (vertices=24, convex hull=41, v0=114916) After retessellation of defect 46 (v0=114916), euler #=1 (113833,341470,227638) : difference with theory (1) = 0 CORRECTING DEFECT 47 (vertices=35, convex hull=63, v0=115734) After retessellation of defect 47 (v0=115734), euler #=2 (113853,341553,227702) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.08-->16.21) (max @ vno 9259 --> 21626) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.08-->16.21) (max @ vno 9259 --> 21626) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 173 mutations (37.8%), 285 crossovers (62.2%), 251 vertices were eliminated building final representation... 2129 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=113853, nf=227702, ne=341553, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 342 intersecting 001: 15 intersecting terminating search with 0 intersecting topology fixing took 2.5 minutes FSRUNTIME@ mris_fix_topology rh 0.0414 hours 4 threads #VMPC# mris_fix_topology VmPeak 953336 PIDs (835165 835168) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 109911 - 329727 + 219818 = 2 --> 0 holes F =2V-4: 219818 = 219822-4 (0) 2E=3F: 659454 = 659454 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 113853 - 341553 + 227702 = 2 --> 0 holes F =2V-4: 227702 = 227706-4 (0) 2E=3F: 683106 = 683106 (0) total defect index = 0 Wed Oct 9 16:46:11 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/defect2seg --s PIB23-310_VYr0_Bay3prisma --cortex freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 defect2seg 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 836303 mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 27 non-cortical segments detected only using segment with 9160 vertices erasing segment 0 (vno[0] = 7036) erasing segment 1 (vno[0] = 10355) erasing segment 2 (vno[0] = 11251) erasing segment 3 (vno[0] = 14532) erasing segment 4 (vno[0] = 15381) erasing segment 5 (vno[0] = 17117) erasing segment 6 (vno[0] = 18008) erasing segment 7 (vno[0] = 18914) erasing segment 8 (vno[0] = 19813) erasing segment 9 (vno[0] = 21443) erasing segment 10 (vno[0] = 22423) erasing segment 12 (vno[0] = 52371) erasing segment 13 (vno[0] = 63095) erasing segment 14 (vno[0] = 77833) erasing segment 15 (vno[0] = 81774) erasing segment 16 (vno[0] = 82599) erasing segment 17 (vno[0] = 83618) erasing segment 18 (vno[0] = 84275) erasing segment 19 (vno[0] = 84286) erasing segment 20 (vno[0] = 85878) erasing segment 21 (vno[0] = 85891) erasing segment 22 (vno[0] = 86716) erasing segment 23 (vno[0] = 86725) erasing segment 24 (vno[0] = 88360) erasing segment 25 (vno[0] = 90545) erasing segment 26 (vno[0] = 91829) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz 1000 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 527388 mris_defects_pointset done mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 43 non-cortical segments detected only using segment with 9026 vertices erasing segment 0 (vno[0] = 6534) erasing segment 1 (vno[0] = 7884) erasing segment 2 (vno[0] = 7886) erasing segment 3 (vno[0] = 10131) erasing segment 4 (vno[0] = 10921) erasing segment 5 (vno[0] = 12400) erasing segment 6 (vno[0] = 13131) erasing segment 7 (vno[0] = 13256) erasing segment 8 (vno[0] = 14765) erasing segment 9 (vno[0] = 15696) erasing segment 10 (vno[0] = 16621) erasing segment 11 (vno[0] = 16654) erasing segment 12 (vno[0] = 16680) erasing segment 13 (vno[0] = 17775) erasing segment 14 (vno[0] = 18609) erasing segment 15 (vno[0] = 18647) erasing segment 16 (vno[0] = 19512) erasing segment 17 (vno[0] = 21610) erasing segment 18 (vno[0] = 26401) erasing segment 19 (vno[0] = 27287) erasing segment 20 (vno[0] = 27991) erasing segment 21 (vno[0] = 29706) erasing segment 22 (vno[0] = 29715) erasing segment 23 (vno[0] = 29749) erasing segment 24 (vno[0] = 30602) erasing segment 25 (vno[0] = 31444) erasing segment 26 (vno[0] = 31458) erasing segment 27 (vno[0] = 32259) erasing segment 29 (vno[0] = 51100) erasing segment 30 (vno[0] = 58497) erasing segment 31 (vno[0] = 65834) erasing segment 32 (vno[0] = 70294) erasing segment 33 (vno[0] = 84225) erasing segment 34 (vno[0] = 86599) erasing segment 35 (vno[0] = 89172) erasing segment 36 (vno[0] = 90990) erasing segment 37 (vno[0] = 92394) erasing segment 38 (vno[0] = 92406) erasing segment 39 (vno[0] = 94806) erasing segment 40 (vno[0] = 98338) erasing segment 41 (vno[0] = 99655) erasing segment 42 (vno[0] = 100330) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz 2000 1 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 530528 mris_defects_pointset done Started at Wed Oct 9 16:46:11 CDT 2024 Ended at Wed Oct 9 16:46:47 CDT 2024 Defect2seg-Run-Time-Sec 36 Defect2seg-Run-Time-Min 0.72 Defect2seg-Run-Time-Hours 0.01 tkmeditfv PIB23-310_VYr0_Bay3prisma brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2024:10:09:16:46:11 defect2seg N 3 e 36.78 S 0.97 U 39.01 P 108% M 451800 F 17 R 568206 W 0 c 3522 w 1408 I 11904 O 18648 L 11.19 10.51 9.71 @#@FSLOADPOST 2024:10:09:16:46:47 defect2seg N 3 9.30 10.11 9.60 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.709935 remeshing to edge length 0.709935 with 3 iterations avg qual before : 0.890729 after: 0.970772 Removing intersections Remeshed surface quality stats nv0 = 109911 nv = 114660 1.04321 Area 229316 0.30164 0.03376 0.076852 0.4665 Corner 687948 60.00000 8.86013 15.887606 146.9837 Edge 343974 0.84271 0.08286 0.401458 1.2903 Hinge 343974 9.78343 10.69054 0.000000 126.1343 mris_remesh done @#@FSTIME 2024:10:09:16:46:47 mris_remesh N 7 e 28.76 S 0.79 U 29.31 P 104% M 645660 F 2 R 773727 W 0 c 2727 w 550 I 0 O 8064 L 9.30 10.11 9.60 @#@FSLOADPOST 2024:10:09:16:47:16 mris_remesh N 7 8.96 9.98 9.57 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.711324 remeshing to edge length 0.711324 with 3 iterations avg qual before : 0.891293 after: 0.970932 Removing intersections Remeshed surface quality stats nv0 = 113853 nv = 118918 1.04449 Area 237832 0.30272 0.03391 0.070412 0.4627 Corner 713496 60.00000 8.83522 15.482169 148.8724 Edge 356748 0.84416 0.08288 0.435371 1.2495 Hinge 356748 9.70488 10.65088 0.000000 169.5836 mris_remesh done @#@FSTIME 2024:10:09:16:47:16 mris_remesh N 7 e 30.97 S 0.94 U 31.62 P 105% M 670460 F 2 R 844469 W 0 c 2960 w 625 I 0 O 8368 L 8.96 9.98 9.57 @#@FSLOADPOST 2024:10:09:16:47:47 mris_remesh N 7 8.56 9.79 9.52 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2024:10:09:16:47:47 mris_remove_intersection N 2 e 2.14 S 0.19 U 2.15 P 109% M 300128 F 2 R 139950 W 0 c 214 w 374 I 0 O 8064 L 8.56 9.79 9.52 @#@FSLOADPOST 2024:10:09:16:47:49 mris_remove_intersection N 2 8.52 9.76 9.52 rm -f ../surf/lh.inflated /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2024:10:09:16:47:50 mris_remove_intersection N 2 e 2.24 S 0.18 U 2.26 P 109% M 307236 F 2 R 144758 W 0 c 223 w 433 I 8368 O 8368 L 8.52 9.76 9.52 @#@FSLOADPOST 2024:10:09:16:47:52 mris_remove_intersection N 2 8.52 9.76 9.52 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Wed Oct 9 16:47:52 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 227628 voxels (1.36%) border gray 232862 voxels (1.39%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=25585, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 100.3 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 80.8 +- 11.9 [30.0 --> 110.0] white_mean = 100.333 +/- 6.75214, gray_mean = 80.8497 +/- 11.9323 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=212 nbins=213 intensity peaks found at WM=102+-6.1, GM=80+-7.8 white_mode = 102, gray_mode = 80 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 68.1 (was 70.000000) setting MAX_BORDER_WHITE to 108.8 (was 105.000000) setting MIN_BORDER_WHITE to 80.0 (was 85.000000) setting MAX_CSF to 56.1 (was 40.000000) setting MAX_GRAY to 95.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 44.2 (was 40.000000) When placing the white surface white_border_hi = 108.752; white_border_low = 80; white_outside_low = 68.0677; white_inside_hi = 120; white_outside_hi = 108.752; When placing the pial surface pial_border_hi = 68.0677; pial_border_low = 44.203; pial_outside_low = 10; pial_inside_hi = 95.2479; pial_outside_hi = 62.1015; #VMPC# mris_autodet_gwstats VmPeak 564648 mris_autodet_gwstats done @#@FSTIME 2024:10:09:16:47:52 mris_autodet_gwstats N 8 e 4.03 S 0.14 U 4.67 P 119% M 206540 F 3 R 102388 W 0 c 430 w 86 I 0 O 8 L 8.52 9.76 9.52 @#@FSLOADPOST 2024:10:09:16:47:56 mris_autodet_gwstats N 8 8.16 9.66 9.49 #-------------------------------------------- #@# AutoDetGWStats rh Wed Oct 9 16:47:56 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 227628 voxels (1.36%) border gray 232862 voxels (1.39%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=25585, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 100.3 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 80.8 +- 11.9 [30.0 --> 110.0] white_mean = 100.333 +/- 6.75214, gray_mean = 80.8497 +/- 11.9323 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=212 nbins=213 intensity peaks found at WM=103+-5.2, GM=80+-7.8 white_mode = 103, gray_mode = 80 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 68.1 (was 70.000000) setting MAX_BORDER_WHITE to 109.8 (was 105.000000) setting MIN_BORDER_WHITE to 80.0 (was 85.000000) setting MAX_CSF to 56.1 (was 40.000000) setting MAX_GRAY to 96.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 44.2 (was 40.000000) When placing the white surface white_border_hi = 109.752; white_border_low = 80; white_outside_low = 68.0677; white_inside_hi = 120; white_outside_hi = 109.752; When placing the pial surface pial_border_hi = 68.0677; pial_border_low = 44.203; pial_outside_low = 10; pial_inside_hi = 96.2479; pial_outside_hi = 62.1015; #VMPC# mris_autodet_gwstats VmPeak 567960 mris_autodet_gwstats done @#@FSTIME 2024:10:09:16:47:56 mris_autodet_gwstats N 8 e 4.10 S 0.18 U 4.78 P 120% M 211912 F 2 R 102135 W 0 c 437 w 115 I 0 O 8 L 8.16 9.66 9.49 @#@FSLOADPOST 2024:10:09:16:48:00 mris_autodet_gwstats N 8 8.06 9.62 9.47 #-------------------------------------------- #@# WhitePreAparc lh Wed Oct 9 16:48:00 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface before ripping with 5 iterations Area 229316 0.26692 0.06543 0.001471 0.6139 Corner 687948 60.00000 9.64205 7.007220 152.1663 Edge 343974 0.78838 0.11870 0.030392 1.4139 Hinge 343974 6.28624 6.77709 0.000000 144.2289 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25585, wmmin=5, clip=110 MRIfindBrightNonWM(): 372 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8083, nmarked2=6, nripped=8083 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57330: xyz = (-52.5737,2.1962,7.12427) oxyz = (-52.5737,2.1962,7.12427) wxzy = (-52.5737,2.1962,7.12427) pxyz = (0,0,0) CBVO Creating mask 114660 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8083 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8083, nmarked2=6, nripped=8083 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 108.7521360; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=2 had to be increased for 252 vertices, nripped=8083 mean border=86.8, 595 (594) missing vertices, mean dist 0.3 [1.1 (%31.0)->1.0 (%69.0))] %28 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0398 min Finding expansion regions mean absolute distance = 1.01 +- 1.18 4002 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1802447.1, rms=8.896 001: dt: 0.5000, sse=1004423.4, rms=6.458 (27.399%) 002: dt: 0.5000, sse=614334.6, rms=4.826 (25.278%) 003: dt: 0.5000, sse=430672.8, rms=3.791 (21.452%) 004: dt: 0.5000, sse=340745.8, rms=3.167 (16.450%) 005: dt: 0.5000, sse=302133.9, rms=2.769 (12.567%) 006: dt: 0.5000, sse=275481.8, rms=2.526 (8.784%) 007: dt: 0.5000, sse=270914.8, rms=2.362 (6.500%) 008: dt: 0.5000, sse=248871.7, rms=2.276 (3.633%) rms = 2.2090/2.2758, sse=250419.4/248871.7, time step reduction 1 of 3 to 0.250 0 1 0 009: dt: 0.5000, sse=250419.4, rms=2.209 (2.936%) 010: dt: 0.2500, sse=214476.7, rms=1.668 (24.511%) 011: dt: 0.2500, sse=203173.6, rms=1.583 (5.072%) rms = 1.5650/1.5830, sse=201501.0/203173.6, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=201501.0, rms=1.565 (1.132%) rms = 1.5436/1.5650, sse=204374.7/201501.0, time step reduction 3 of 3 to 0.062 0 1 1 013: dt: 0.1250, sse=204374.7, rms=1.544 (1.372%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8083 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8463, nmarked2=36, nripped=8463 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 108.7521360; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=1 had to be increased for 262 vertices, nripped=8463 mean border=88.9, 433 (162) missing vertices, mean dist -0.3 [0.7 (%63.3)->0.3 (%36.7))] %47 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0283 min Finding expansion regions mean absolute distance = 0.53 +- 0.87 4483 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=486314.1, rms=3.705 014: dt: 0.5000, sse=330257.2, rms=2.452 (33.835%) 015: dt: 0.5000, sse=286921.0, rms=2.033 (17.074%) 016: dt: 0.5000, sse=264756.3, rms=1.882 (7.438%) rms = 1.8470/1.8818, sse=273772.4/264756.3, time step reduction 1 of 3 to 0.250 0 1 1 017: dt: 0.5000, sse=273772.4, rms=1.847 (1.848%) 018: dt: 0.2500, sse=236466.2, rms=1.375 (25.569%) 019: dt: 0.2500, sse=226189.0, rms=1.287 (6.359%) rms = 1.2703/1.2873, sse=227888.7/226189.0, time step reduction 2 of 3 to 0.125 0 1 1 020: dt: 0.2500, sse=227888.7, rms=1.270 (1.317%) rms = 1.2428/1.2703, sse=225609.6/227888.7, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=225609.6, rms=1.243 (2.165%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8463 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8560, nmarked2=35, nripped=8560 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 108.7521360; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 386 vertices, nripped=8560 mean border=91.4, 387 (107) missing vertices, mean dist -0.2 [0.4 (%72.1)->0.3 (%27.9))] %71 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0161 min Finding expansion regions mean absolute distance = 0.39 +- 0.50 3417 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=435896.0, rms=3.402 022: dt: 0.5000, sse=283713.3, rms=1.917 (43.645%) 023: dt: 0.5000, sse=245441.3, rms=1.697 (11.497%) rms = 1.7162/1.6968, sse=261766.4/245441.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=222972.0, rms=1.359 (19.930%) rms = 1.1856/1.3587, sse=230567.1/222972.0, time step reduction 2 of 3 to 0.125 0 1 0 025: dt: 0.2500, sse=230567.1, rms=1.186 (12.734%) rms = 1.1383/1.1856, sse=225719.0/230567.1, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=225719.0, rms=1.138 (3.990%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8560 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8600, nmarked2=35, nripped=8600 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 108.7521360; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 428 vertices, nripped=8600 mean border=92.3, 398 (94) missing vertices, mean dist -0.1 [0.3 (%59.8)->0.2 (%40.2))] %79 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0107 min Finding expansion regions mean absolute distance = 0.29 +- 0.40 2916 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=254406.2, rms=1.666 027: dt: 0.5000, sse=221538.7, rms=1.218 (26.916%) rms = 1.4216/1.2179, sse=243521.9/221538.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=207226.8, rms=0.992 (18.553%) rms = 0.9472/0.9919, sse=210406.0/207226.7, time step reduction 2 of 3 to 0.125 0 1 1 029: dt: 0.2500, sse=210406.0, rms=0.947 (4.509%) rms = 0.8987/0.9472, sse=203388.4/210406.0, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=203388.4, rms=0.899 (5.117%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 1.96 minutes #VMPC# mris_place_surfaces VmPeak 2052096 mris_place_surface done @#@FSTIME 2024:10:09:16:48:00 mris_place_surface N 18 e 123.09 S 1.70 U 231.80 P 189% M 1615116 F 2 R 1940578 W 0 c 20891 w 1559 I 0 O 8064 L 8.06 9.62 9.47 @#@FSLOADPOST 2024:10:09:16:50:04 mris_place_surface N 18 7.08 8.86 9.22 #-------------------------------------------- #@# WhitePreAparc rh Wed Oct 9 16:50:04 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface before ripping with 5 iterations Area 237832 0.26796 0.06546 0.000647 0.6023 Corner 713496 60.00000 9.63850 3.254976 158.4042 Edge 356748 0.78994 0.11870 0.029290 1.2824 Hinge 356748 6.28615 6.76677 0.000000 146.3566 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25585, wmmin=5, clip=110 MRIfindBrightNonWM(): 372 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8850, nmarked2=0, nripped=8850 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59459: xyz = (43.2355,5.21234,27.6348) oxyz = (43.2355,5.21234,27.6348) wxzy = (43.2355,5.21234,27.6348) pxyz = (0,0,0) CBVO Creating mask 118918 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8850 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8850, nmarked2=0, nripped=8850 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 109.7521360; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=2 had to be increased for 157 vertices, nripped=8850 mean border=87.0, 499 (499) missing vertices, mean dist 0.4 [1.2 (%29.2)->1.0 (%70.8))] %33 local maxima, %59 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0440 min Finding expansion regions mean absolute distance = 1.04 +- 1.21 4296 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1892442.2, rms=8.971 001: dt: 0.5000, sse=1076297.0, rms=6.589 (26.551%) 002: dt: 0.5000, sse=671591.0, rms=4.995 (24.199%) 003: dt: 0.5000, sse=470010.2, rms=3.952 (20.881%) 004: dt: 0.5000, sse=367374.2, rms=3.266 (17.345%) 005: dt: 0.5000, sse=327263.4, rms=2.804 (14.155%) 006: dt: 0.5000, sse=278503.2, rms=2.507 (10.599%) 007: dt: 0.5000, sse=269733.4, rms=2.324 (7.290%) 008: dt: 0.5000, sse=246675.5, rms=2.208 (4.995%) 009: dt: 0.5000, sse=246536.8, rms=2.145 (2.870%) 010: dt: 0.5000, sse=240298.1, rms=2.093 (2.426%) rms = 2.0718/2.0927, sse=237908.6/240298.1, time step reduction 1 of 3 to 0.250 0 0 1 011: dt: 0.5000, sse=237908.6, rms=2.072 (0.995%) 012: dt: 0.2500, sse=196747.8, rms=1.558 (24.819%) rms = 1.4897/1.5576, sse=199127.4/196747.8, time step reduction 2 of 3 to 0.125 0 1 0 013: dt: 0.2500, sse=199127.4, rms=1.490 (4.362%) rms = 1.4665/1.4897, sse=190767.1/199127.4, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=190767.1, rms=1.467 (1.554%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8850 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=9101, nmarked2=0, nripped=9101 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 109.7521360; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=1 had to be increased for 283 vertices, nripped=9101 mean border=89.2, 460 (276) missing vertices, mean dist -0.3 [0.7 (%64.6)->0.3 (%35.4))] %51 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0312 min Finding expansion regions mean absolute distance = 0.54 +- 0.86 4012 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=517352.6, rms=3.873 015: dt: 0.5000, sse=349530.4, rms=2.585 (33.258%) 016: dt: 0.5000, sse=290076.2, rms=2.122 (17.907%) 017: dt: 0.5000, sse=280483.6, rms=1.924 (9.321%) 018: dt: 0.5000, sse=268103.0, rms=1.855 (3.616%) rms = 1.8414/1.8548, sse=266085.1/268103.0, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=266085.1, rms=1.841 (0.719%) 020: dt: 0.2500, sse=233659.8, rms=1.367 (25.756%) 021: dt: 0.2500, sse=230638.5, rms=1.292 (5.528%) rms = 1.2811/1.2916, sse=227518.9/230638.5, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=227518.9, rms=1.281 (0.812%) rms = 1.2638/1.2811, sse=250791.5/227518.9, time step reduction 3 of 3 to 0.062 0 1 1 023: dt: 0.1250, sse=250791.5, rms=1.264 (1.350%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=9101 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=9157, nmarked2=0, nripped=9157 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 109.7521360; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 359 vertices, nripped=9157 mean border=91.9, 434 (250) missing vertices, mean dist -0.3 [0.5 (%73.4)->0.3 (%26.6))] %73 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0179 min Finding expansion regions mean absolute distance = 0.41 +- 0.51 3571 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=493149.1, rms=3.585 024: dt: 0.5000, sse=287657.7, rms=2.048 (42.863%) 025: dt: 0.5000, sse=260132.4, rms=1.676 (18.153%) rms = 1.6472/1.6763, sse=252901.5/260132.4, time step reduction 1 of 3 to 0.250 0 0 1 026: dt: 0.5000, sse=252901.5, rms=1.647 (1.736%) 027: dt: 0.2500, sse=221625.7, rms=1.216 (26.176%) rms = 1.1508/1.2161, sse=238332.2/221625.7, time step reduction 2 of 3 to 0.125 0 1 0 028: dt: 0.2500, sse=238332.2, rms=1.151 (5.366%) rms = 1.1265/1.1508, sse=216113.6/238332.2, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=216113.6, rms=1.126 (2.114%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=9157 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=9207, nmarked2=0, nripped=9207 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 109.7521360; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 406 vertices, nripped=9207 mean border=92.9, 502 (238) missing vertices, mean dist -0.1 [0.3 (%60.6)->0.2 (%39.4))] %81 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0119 min Finding expansion regions mean absolute distance = 0.29 +- 0.39 2776 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=245528.9, rms=1.670 030: dt: 0.5000, sse=223531.4, rms=1.165 (30.269%) rms = 1.3457/1.1648, sse=223638.1/223531.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=207384.2, rms=0.981 (15.780%) rms = 0.9383/0.9810, sse=207564.2/207384.2, time step reduction 2 of 3 to 0.125 0 1 1 032: dt: 0.2500, sse=207564.2, rms=0.938 (4.351%) rms = 0.9167/0.9383, sse=206086.1/207564.2, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=206086.1, rms=0.917 (2.300%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.21 minutes #VMPC# mris_place_surfaces VmPeak 2129844 mris_place_surface done @#@FSTIME 2024:10:09:16:50:04 mris_place_surface N 18 e 138.31 S 1.87 U 256.43 P 186% M 1694440 F 3 R 2462948 W 0 c 22665 w 1486 I 8368 O 8368 L 7.08 8.86 9.22 @#@FSLOADPOST 2024:10:09:16:52:22 mris_place_surface N 18 9.88 9.40 9.37 #-------------------------------------------- #@# CortexLabel lh Wed Oct 9 16:52:22 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 9 non-cortical segments detected only using segment with 10199 vertices erasing segment 0 (vno[0] = 8558) erasing segment 2 (vno[0] = 53302) erasing segment 3 (vno[0] = 64701) erasing segment 4 (vno[0] = 66273) erasing segment 5 (vno[0] = 69191) erasing segment 6 (vno[0] = 70119) erasing segment 7 (vno[0] = 75111) erasing segment 8 (vno[0] = 79251) @#@FSTIME 2024:10:09:16:52:22 mri_label2label N 5 e 16.73 S 0.20 U 17.48 P 105% M 307516 F 4 R 167922 W 0 c 1548 w 336 I 0 O 9064 L 9.88 9.40 9.37 @#@FSLOADPOST 2024:10:09:16:52:39 mri_label2label N 5 9.65 9.38 9.36 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Wed Oct 9 16:52:39 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 11 non-cortical segments detected only using segment with 8753 vertices erasing segment 0 (vno[0] = 8558) erasing segment 2 (vno[0] = 38384) erasing segment 3 (vno[0] = 39122) erasing segment 4 (vno[0] = 64392) erasing segment 5 (vno[0] = 64701) erasing segment 6 (vno[0] = 66273) erasing segment 7 (vno[0] = 69191) erasing segment 8 (vno[0] = 70119) erasing segment 9 (vno[0] = 75111) erasing segment 10 (vno[0] = 79251) @#@FSTIME 2024:10:09:16:52:39 mri_label2label N 5 e 16.79 S 0.22 U 17.48 P 105% M 315700 F 2 R 169525 W 0 c 1546 w 377 I 0 O 9192 L 9.65 9.38 9.36 @#@FSLOADPOST 2024:10:09:16:52:56 mri_label2label N 5 9.63 9.40 9.37 #-------------------------------------------- #@# CortexLabel rh Wed Oct 9 16:52:56 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 16 non-cortical segments detected only using segment with 10116 vertices erasing segment 0 (vno[0] = 7753) erasing segment 1 (vno[0] = 8436) erasing segment 2 (vno[0] = 15171) erasing segment 3 (vno[0] = 18324) erasing segment 4 (vno[0] = 20626) erasing segment 5 (vno[0] = 20674) erasing segment 6 (vno[0] = 23590) erasing segment 7 (vno[0] = 24314) erasing segment 8 (vno[0] = 25093) erasing segment 9 (vno[0] = 29519) erasing segment 11 (vno[0] = 37744) erasing segment 12 (vno[0] = 55426) erasing segment 13 (vno[0] = 74533) erasing segment 14 (vno[0] = 97047) erasing segment 15 (vno[0] = 118634) @#@FSTIME 2024:10:09:16:52:56 mri_label2label N 5 e 15.67 S 0.22 U 16.22 P 104% M 342924 F 1 R 171237 W 0 c 1459 w 471 I 8368 O 9240 L 9.63 9.40 9.37 @#@FSLOADPOST 2024:10:09:16:53:12 mri_label2label N 5 9.48 9.38 9.36 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Wed Oct 9 16:53:12 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 17 non-cortical segments detected only using segment with 8522 vertices erasing segment 0 (vno[0] = 7753) erasing segment 1 (vno[0] = 8436) erasing segment 2 (vno[0] = 15171) erasing segment 3 (vno[0] = 18324) erasing segment 4 (vno[0] = 20626) erasing segment 5 (vno[0] = 20674) erasing segment 6 (vno[0] = 23590) erasing segment 7 (vno[0] = 24314) erasing segment 8 (vno[0] = 25093) erasing segment 9 (vno[0] = 29519) erasing segment 11 (vno[0] = 37744) erasing segment 12 (vno[0] = 46126) erasing segment 13 (vno[0] = 49331) erasing segment 14 (vno[0] = 74533) erasing segment 15 (vno[0] = 74603) erasing segment 16 (vno[0] = 118634) @#@FSTIME 2024:10:09:16:53:12 mri_label2label N 5 e 15.48 S 0.23 U 16.08 P 105% M 347392 F 2 R 168491 W 0 c 1433 w 412 I 0 O 9360 L 9.48 9.38 9.36 @#@FSLOADPOST 2024:10:09:16:53:27 mri_label2label N 5 9.00 9.28 9.33 #-------------------------------------------- #@# Smooth2 lh Wed Oct 9 16:53:27 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Wed Oct 9 16:53:27 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 840544 of (840544 840548) to complete... Waiting for PID 840548 of (840544 840548) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (840544 840548) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Wed Oct 9 16:53:30 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Wed Oct 9 16:53:30 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 840638 of (840638 840641) to complete... Waiting for PID 840641 of (840638 840641) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.7 mm, total surface area = 71022 mm^2 step 000: RMS=0.170 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 29.561601 mris_inflate stimesec 0.260436 mris_inflate ru_maxrss 178676 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 229742 mris_inflate ru_majflt 4 mris_inflate ru_nswap 0 mris_inflate ru_inblock 96 mris_inflate ru_oublock 8984 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3363 mris_inflate ru_nivcsw 2512 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 47.1 mm, total surface area = 73639 mm^2 step 000: RMS=0.168 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 33.363114 mris_inflate stimesec 0.283720 mris_inflate ru_maxrss 185140 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 232417 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8464 mris_inflate ru_oublock 9320 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 4050 mris_inflate ru_nivcsw 2885 PIDs (840638 840641) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Wed Oct 9 16:53:46 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature -w -seed 1234 lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Wed Oct 9 16:53:46 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf reconbatchjobs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 840812 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840815 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840818 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840821 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840824 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840828 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840831 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840834 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840838 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840841 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840845 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... Waiting for PID 840848 of (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 23.839*4pi (299.574) --> -23 handles ICI = 155.5, FI = 1325.5, variation=21585.920 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 132 vertices thresholded to be in k1 ~ [-2.45 0.63], k2 ~ [-0.59 0.10] total integrated curvature = 0.514*4pi (6.465) --> 0 handles ICI = 1.4, FI = 8.5, variation=148.761 116 vertices thresholded to be in [-0.05 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 87 vertices thresholded to be in [-0.70 0.26] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.019, std = 0.027 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 19.705*4pi (247.626) --> -19 handles ICI = 152.4, FI = 1375.8, variation=22168.847 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 161 vertices thresholded to be in k1 ~ [-5.99 0.42], k2 ~ [-0.40 0.15] total integrated curvature = 0.503*4pi (6.320) --> 0 handles ICI = 1.5, FI = 11.5, variation=186.900 136 vertices thresholded to be in [-0.04 0.14] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.003 95 vertices thresholded to be in [-1.66 0.20] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.020, std = 0.040 done. PIDs (840812 840815 840818 840821 840824 840828 840831 840834 840838 840841 840845 840848) completed and logs appended. #-------------------------------------------- #@# Sphere lh Wed Oct 9 16:54:30 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Wed Oct 9 16:54:30 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 841456 of (841456 841459) to complete... Waiting for PID 841459 of (841456 841459) to complete... mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.314... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.27 pass 1: epoch 2 of 3 starting distance error %19.25 unfolding complete - removing small folds... starting distance error %19.19 removing remaining folds... final distance error %19.19 MRISunfold() return, current seed 1234 -01: dt=0.0000, 193 negative triangles VmPeak 773792 089: dt=0.9900, 193 negative triangles 090: dt=0.9900, 124 negative triangles 091: dt=0.9900, 97 negative triangles 092: dt=0.9900, 87 negative triangles 093: dt=0.9900, 79 negative triangles 094: dt=0.9900, 77 negative triangles 095: dt=0.9900, 63 negative triangles 096: dt=0.9900, 74 negative triangles 097: dt=0.9900, 73 negative triangles 098: dt=0.9900, 68 negative triangles 099: dt=0.9900, 58 negative triangles 100: dt=0.9900, 60 negative triangles 101: dt=0.9900, 55 negative triangles 102: dt=0.9900, 55 negative triangles 103: dt=0.9900, 61 negative triangles 104: dt=0.9900, 54 negative triangles 105: dt=0.9900, 46 negative triangles 106: dt=0.9900, 43 negative triangles 107: dt=0.9900, 53 negative triangles 108: dt=0.9900, 46 negative triangles 109: dt=0.9900, 38 negative triangles 110: dt=0.9900, 37 negative triangles 111: dt=0.9900, 32 negative triangles 112: dt=0.9900, 39 negative triangles 113: dt=0.9900, 30 negative triangles 114: dt=0.9900, 29 negative triangles 115: dt=0.9900, 32 negative triangles 116: dt=0.9900, 28 negative triangles 117: dt=0.9900, 24 negative triangles 118: dt=0.9900, 25 negative triangles 119: dt=0.9900, 25 negative triangles 120: dt=0.9900, 20 negative triangles 121: dt=0.9900, 18 negative triangles 122: dt=0.9900, 19 negative triangles 123: dt=0.9900, 21 negative triangles 124: dt=0.9900, 24 negative triangles 125: dt=0.9900, 18 negative triangles 126: dt=0.9900, 20 negative triangles 127: dt=0.9900, 21 negative triangles 128: dt=0.9900, 19 negative triangles 129: dt=0.9900, 14 negative triangles 130: dt=0.9900, 19 negative triangles 131: dt=0.9900, 16 negative triangles 132: dt=0.9900, 16 negative triangles 133: dt=0.9900, 13 negative triangles 134: dt=0.9900, 14 negative triangles 135: dt=0.9900, 13 negative triangles 136: dt=0.9900, 14 negative triangles 137: dt=0.9900, 12 negative triangles 138: dt=0.9900, 13 negative triangles 139: dt=0.9900, 10 negative triangles 140: dt=0.9900, 15 negative triangles 141: dt=0.9900, 12 negative triangles 142: dt=0.9900, 10 negative triangles 143: dt=0.9900, 11 negative triangles 144: dt=0.9900, 9 negative triangles 145: dt=0.9900, 15 negative triangles 146: dt=0.9900, 11 negative triangles 147: dt=0.9900, 10 negative triangles 148: dt=0.9900, 10 negative triangles 149: dt=0.9900, 11 negative triangles 150: dt=0.9900, 11 negative triangles 151: dt=0.9900, 8 negative triangles 152: dt=0.9900, 11 negative triangles 153: dt=0.9900, 8 negative triangles 154: dt=0.9900, 13 negative triangles 155: dt=0.9900, 11 negative triangles 156: dt=0.9900, 8 negative triangles 157: dt=0.9900, 11 negative triangles 158: dt=0.9900, 8 negative triangles 159: dt=0.9900, 8 negative triangles 160: dt=0.9900, 5 negative triangles 161: dt=0.9900, 7 negative triangles 162: dt=0.9900, 6 negative triangles 163: dt=0.9900, 6 negative triangles 164: dt=0.9900, 4 negative triangles 165: dt=0.9900, 6 negative triangles 166: dt=0.9900, 4 negative triangles 167: dt=0.9900, 6 negative triangles 168: dt=0.9900, 3 negative triangles 169: dt=0.9900, 4 negative triangles 170: dt=0.9900, 2 negative triangles 171: dt=0.9900, 1 negative triangles 172: dt=0.9900, 2 negative triangles 173: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.0500 hours FSRUNTIME@ mris_sphere 0.0500 hours 4 threads #VMPC# mris_sphere VmPeak 773792 mris_sphere done mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.302... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.36 pass 1: epoch 2 of 3 starting distance error %19.35 unfolding complete - removing small folds... starting distance error %19.29 removing remaining folds... final distance error %19.33 MRISunfold() return, current seed 1234 -01: dt=0.0000, 48 negative triangles VmPeak 777208 191: dt=0.9900, 48 negative triangles 192: dt=0.9900, 27 negative triangles 193: dt=0.9900, 22 negative triangles 194: dt=0.9900, 17 negative triangles 195: dt=0.9900, 11 negative triangles 196: dt=0.9900, 19 negative triangles 197: dt=0.9900, 14 negative triangles 198: dt=0.9900, 15 negative triangles 199: dt=0.9900, 15 negative triangles 200: dt=0.9900, 15 negative triangles 201: dt=0.9900, 14 negative triangles 202: dt=0.9900, 10 negative triangles 203: dt=0.9900, 13 negative triangles 204: dt=0.9900, 13 negative triangles 205: dt=0.9900, 12 negative triangles 206: dt=0.9900, 9 negative triangles 207: dt=0.9900, 13 negative triangles 208: dt=0.9900, 13 negative triangles 209: dt=0.9900, 12 negative triangles 210: dt=0.9900, 7 negative triangles 211: dt=0.9900, 5 negative triangles 212: dt=0.9900, 11 negative triangles 213: dt=0.9900, 9 negative triangles 214: dt=0.9900, 9 negative triangles 215: dt=0.9900, 11 negative triangles 216: dt=0.9900, 6 negative triangles 217: dt=0.9900, 8 negative triangles 218: dt=0.9900, 6 negative triangles 219: dt=0.9900, 12 negative triangles 220: dt=0.9900, 8 negative triangles 221: dt=0.9405, 7 negative triangles 222: dt=0.9405, 8 negative triangles 223: dt=0.9405, 7 negative triangles 224: dt=0.9405, 11 negative triangles 225: dt=0.9405, 6 negative triangles 226: dt=0.9405, 7 negative triangles 227: dt=0.9405, 7 negative triangles 228: dt=0.9405, 10 negative triangles 229: dt=0.9405, 9 negative triangles 230: dt=0.9405, 6 negative triangles 231: dt=0.8935, 6 negative triangles 232: dt=0.8935, 7 negative triangles 233: dt=0.8935, 5 negative triangles 234: dt=0.8935, 9 negative triangles 235: dt=0.8935, 5 negative triangles 236: dt=0.8935, 6 negative triangles 237: dt=0.8935, 4 negative triangles 238: dt=0.8935, 5 negative triangles 239: dt=0.8935, 5 negative triangles 240: dt=0.8935, 6 negative triangles 241: dt=0.8935, 4 negative triangles 242: dt=0.8935, 4 negative triangles 243: dt=0.8935, 1 negative triangles 244: dt=0.8935, 1 negative triangles 245: dt=0.8935, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.0773 hours FSRUNTIME@ mris_sphere 0.0773 hours 4 threads #VMPC# mris_sphere VmPeak 777208 mris_sphere done PIDs (841456 841459) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Wed Oct 9 16:59:08 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Wed Oct 9 16:59:08 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 844964 of (844964 844968) to complete... Waiting for PID 844968 of (844964 844968) to complete... mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts cmdline mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from ../surf/lh.sphere... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.295 curvature mean = 0.030, std = 0.823 curvature mean = 0.016, std = 0.883 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (8.00, -8.50, 1.50) sse = 166976.4, elapsed since starting=0.1226 min MRISrigidBodyAlignGlobal() done 0.12 min curvature mean = 0.032, std = 0.854 curvature mean = 0.007, std = 0.958 curvature mean = 0.031, std = 0.867 curvature mean = 0.003, std = 0.984 curvature mean = 0.031, std = 0.870 curvature mean = 0.001, std = 0.994 2 Reading smoothwm curvature mean = -0.022, std = 0.275 curvature mean = 0.043, std = 0.254 curvature mean = 0.060, std = 0.363 curvature mean = 0.038, std = 0.312 curvature mean = 0.026, std = 0.557 curvature mean = 0.037, std = 0.340 curvature mean = 0.012, std = 0.693 curvature mean = 0.037, std = 0.352 curvature mean = 0.003, std = 0.800 MRISregister() return, current seed 0 -01: dt=0.0000, 31 negative triangles VmPeak 773828 102: dt=0.9900, 31 negative triangles 103: dt=0.9900, 25 negative triangles 104: dt=0.9900, 20 negative triangles 105: dt=0.9900, 18 negative triangles 106: dt=0.9900, 20 negative triangles 107: dt=0.9900, 13 negative triangles 108: dt=0.9900, 13 negative triangles 109: dt=0.9900, 9 negative triangles 110: dt=0.9900, 10 negative triangles 111: dt=0.9900, 11 negative triangles 112: dt=0.9900, 9 negative triangles 113: dt=0.9900, 12 negative triangles 114: dt=0.9900, 9 negative triangles 115: dt=0.9900, 13 negative triangles 116: dt=0.9900, 9 negative triangles 117: dt=0.9900, 8 negative triangles 118: dt=0.9900, 7 negative triangles 119: dt=0.9900, 8 negative triangles 120: dt=0.9900, 7 negative triangles 121: dt=0.9900, 6 negative triangles 122: dt=0.9900, 4 negative triangles 123: dt=0.9900, 7 negative triangles 124: dt=0.9900, 3 negative triangles 125: dt=0.9900, 5 negative triangles 126: dt=0.9900, 2 negative triangles 127: dt=0.9900, 6 negative triangles 128: dt=0.9900, 2 negative triangles 129: dt=0.9900, 4 negative triangles 130: dt=0.9900, 2 negative triangles 131: dt=0.9900, 1 negative triangles 132: dt=0.9900, 2 negative triangles 133: dt=0.9900, 1 negative triangles 134: dt=0.9900, 1 negative triangles 135: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.06 hours #VMPC# mris_register VmPeak 773828 FSRUNTIME@ mris_register 0.0565 hours 4 threads mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts cmdline mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from ../surf/rh.sphere... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.309 curvature mean = 0.058, std = 0.825 curvature mean = 0.014, std = 0.882 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (9.00, -9.50, 3.00) sse = 237890.6, elapsed since starting=0.1181 min MRISrigidBodyAlignGlobal() done 0.12 min curvature mean = 0.046, std = 0.851 curvature mean = 0.005, std = 0.957 curvature mean = 0.045, std = 0.863 curvature mean = 0.002, std = 0.983 curvature mean = 0.045, std = 0.867 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.021, std = 0.271 curvature mean = 0.041, std = 0.247 curvature mean = 0.057, std = 0.381 curvature mean = 0.034, std = 0.307 curvature mean = 0.027, std = 0.566 curvature mean = 0.033, std = 0.335 curvature mean = 0.012, std = 0.704 curvature mean = 0.032, std = 0.348 curvature mean = 0.003, std = 0.811 MRISregister() return, current seed 0 -01: dt=0.0000, 37 negative triangles VmPeak 777244 110: dt=0.9900, 37 negative triangles expanding nbhd size to 1 111: dt=0.9900, 37 negative triangles 112: dt=0.9900, 33 negative triangles 113: dt=0.9900, 34 negative triangles 114: dt=0.9900, 32 negative triangles 115: dt=0.9900, 29 negative triangles 116: dt=0.9900, 25 negative triangles 117: dt=0.9900, 23 negative triangles 118: dt=0.9900, 21 negative triangles 119: dt=0.9900, 21 negative triangles 120: dt=0.9900, 21 negative triangles 121: dt=0.9900, 21 negative triangles 122: dt=0.9900, 17 negative triangles 123: dt=0.9900, 17 negative triangles 124: dt=0.9900, 15 negative triangles 125: dt=0.9900, 13 negative triangles 126: dt=0.9900, 10 negative triangles 127: dt=0.9900, 9 negative triangles 128: dt=0.9900, 9 negative triangles 129: dt=0.9900, 10 negative triangles 130: dt=0.9900, 12 negative triangles 131: dt=0.9900, 8 negative triangles 132: dt=0.9900, 7 negative triangles 133: dt=0.9900, 4 negative triangles 134: dt=0.9900, 3 negative triangles 135: dt=0.9900, 4 negative triangles 136: dt=0.9900, 5 negative triangles 137: dt=0.9900, 3 negative triangles 138: dt=0.9900, 3 negative triangles 139: dt=0.9900, 2 negative triangles 140: dt=0.9900, 2 negative triangles 141: dt=0.9900, 2 negative triangles 142: dt=0.9900, 2 negative triangles 143: dt=0.9900, 2 negative triangles 144: dt=0.9900, 5 negative triangles 145: dt=0.9900, 3 negative triangles 146: dt=0.9900, 2 negative triangles 147: dt=0.9900, 2 negative triangles 148: dt=0.9900, 2 negative triangles 149: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.07 hours #VMPC# mris_register VmPeak 777244 FSRUNTIME@ mris_register 0.0681 hours 4 threads PIDs (844964 844968) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Wed Oct 9 17:03:14 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Wed Oct 9 17:03:14 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 846717 of (846717 846720) to complete... Waiting for PID 846720 of (846717 846720) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (846717 846720) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Wed Oct 9 17:03:15 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Wed Oct 9 17:03:15 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 846801 of (846801 846804) to complete... Waiting for PID 846804 of (846801 846804) to complete... mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (846801 846804) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Wed Oct 9 17:03:16 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Wed Oct 9 17:03:16 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 846883 of (846883 846886) to complete... Waiting for PID 846886 of (846883 846886) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1285 labels changed using aseg relabeling using gibbs priors... 000: 2661 changed, 114660 examined... 001: 594 changed, 11507 examined... 002: 132 changed, 3464 examined... 003: 36 changed, 815 examined... 004: 10 changed, 229 examined... 005: 1 changed, 68 examined... 006: 1 changed, 7 examined... 007: 0 changed, 8 examined... 185 labels changed using aseg 000: 82 total segments, 33 labels (227 vertices) changed 001: 49 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1614 vertices marked for relabeling... 1614 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 9 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1459 labels changed using aseg relabeling using gibbs priors... 000: 2442 changed, 118918 examined... 001: 514 changed, 10785 examined... 002: 128 changed, 2986 examined... 003: 51 changed, 776 examined... 004: 20 changed, 315 examined... 005: 8 changed, 126 examined... 006: 3 changed, 50 examined... 007: 1 changed, 18 examined... 008: 0 changed, 7 examined... 257 labels changed using aseg 000: 86 total segments, 35 labels (191 vertices) changed 001: 52 total segments, 1 labels (1 vertices) changed 002: 51 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1160 vertices marked for relabeling... 1160 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 9 seconds. PIDs (846883 846886) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Wed Oct 9 17:03:25 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 229316 0.34321 0.12880 0.000559 1.8986 Corner 687948 60.00000 15.00132 0.287080 178.4964 Edge 343974 0.90333 0.21469 0.025294 3.5409 Hinge 343974 11.71132 12.89997 0.000000 179.9540 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25585, wmmin=5, clip=110 MRIfindBrightNonWM(): 372 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label MRISripNotLabel() ripped 10415/114660 vertices (104245 unripped) Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 412 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57330: xyz = (-52.904,1.68549,6.82003) oxyz = (-52.904,1.68549,6.82003) wxzy = (-52.904,1.68549,6.82003) pxyz = (0,0,0) CBVO Creating mask 114660 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 108.7521360; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=2 had to be increased for 260 vertices, nripped=10827 mean border=86.7, 969 (969) missing vertices, mean dist 0.4 [2.3 (%11.7)->0.8 (%88.3))] %27 local maxima, %63 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0375 min Finding expansion regions mean absolute distance = 0.95 +- 1.10 3416 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1090066.1, rms=6.704 001: dt: 0.5000, sse=502641.5, rms=4.060 (39.436%) 002: dt: 0.5000, sse=328253.9, rms=2.780 (31.541%) 003: dt: 0.5000, sse=276118.8, rms=2.312 (16.833%) 004: dt: 0.5000, sse=258758.1, rms=2.102 (9.080%) rms = 2.0621/2.1018, sse=258397.5/258758.1, time step reduction 1 of 3 to 0.250 0 0 1 005: dt: 0.5000, sse=258397.5, rms=2.062 (1.889%) 006: dt: 0.2500, sse=228999.0, rms=1.655 (19.718%) 007: dt: 0.2500, sse=221265.9, rms=1.583 (4.379%) rms = 1.5611/1.5830, sse=221710.3/221265.9, time step reduction 2 of 3 to 0.125 0 1 1 008: dt: 0.2500, sse=221710.3, rms=1.561 (1.381%) rms = 1.5451/1.5611, sse=220688.2/221710.3, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=220688.2, rms=1.545 (1.026%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 108.7521360; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=1 had to be increased for 175 vertices, nripped=10827 mean border=88.7, 416 (309) missing vertices, mean dist -0.3 [0.7 (%60.0)->0.3 (%40.0))] %45 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0283 min Finding expansion regions mean absolute distance = 0.52 +- 0.86 4334 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=432003.0, rms=3.488 010: dt: 0.5000, sse=293423.6, rms=2.372 (31.993%) 011: dt: 0.5000, sse=261973.7, rms=2.011 (15.233%) 012: dt: 0.5000, sse=254788.2, rms=1.905 (5.281%) rms = 1.8959/1.9046, sse=257822.2/254788.2, time step reduction 1 of 3 to 0.250 0 1 1 013: dt: 0.5000, sse=257822.2, rms=1.896 (0.456%) 014: dt: 0.2500, sse=226109.1, rms=1.515 (20.095%) 015: dt: 0.2500, sse=222386.1, rms=1.455 (3.945%) rms = 1.4401/1.4551, sse=220970.8/222386.1, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=220970.8, rms=1.440 (1.032%) rms = 1.4194/1.4401, sse=219940.2/220970.8, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=219940.2, rms=1.419 (1.440%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 108.7521360; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 223 vertices, nripped=10827 mean border=91.2, 343 (204) missing vertices, mean dist -0.3 [0.5 (%72.3)->0.3 (%27.7))] %70 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0163 min Finding expansion regions mean absolute distance = 0.40 +- 0.51 3460 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=441505.3, rms=3.582 018: dt: 0.5000, sse=280415.0, rms=2.163 (39.604%) 019: dt: 0.5000, sse=254225.3, rms=1.920 (11.239%) rms = 1.9056/1.9202, sse=254168.6/254225.3, time step reduction 1 of 3 to 0.250 0 0 1 020: dt: 0.5000, sse=254168.6, rms=1.906 (0.760%) 021: dt: 0.2500, sse=227810.8, rms=1.497 (21.433%) 022: dt: 0.2500, sse=221871.1, rms=1.430 (4.491%) rms = 1.4142/1.4299, sse=220190.1/221871.1, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=220190.1, rms=1.414 (1.101%) rms = 1.3970/1.4142, sse=217874.3/220190.1, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=217874.3, rms=1.397 (1.216%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 108.7521360; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 305 vertices, nripped=10827 mean border=92.2, 359 (168) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %78 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0108 min Finding expansion regions mean absolute distance = 0.28 +- 0.39 2600 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=244425.5, rms=1.841 025: dt: 0.5000, sse=221437.0, rms=1.429 (22.388%) rms = 1.5910/1.4287, sse=228780.8/221437.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=211312.5, rms=1.280 (10.428%) rms = 1.2479/1.2797, sse=210410.8/211312.5, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=210410.8, rms=1.248 (2.481%) rms = 1.2258/1.2479, sse=206176.8/210410.8, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=206176.8, rms=1.226 (1.774%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 1.74 minutes #VMPC# mris_place_surfaces VmPeak 2053352 mris_place_surface done @#@FSTIME 2024:10:09:17:03:25 mris_place_surface N 25 e 110.19 S 1.77 U 207.30 P 189% M 1628580 F 1 R 2048576 W 0 c 17727 w 1377 I 0 O 8064 L 4.87 7.76 8.95 @#@FSLOADPOST 2024:10:09:17:05:15 mris_place_surface N 25 4.43 6.64 8.41 #-------------------------------------------- #@# WhiteSurfs rh Wed Oct 9 17:05:15 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 237832 0.34177 0.13280 0.001025 2.2494 Corner 713496 60.00000 15.48342 0.455452 178.8182 Edge 356748 0.90185 0.22001 0.017547 3.5102 Hinge 356748 11.52667 13.13179 0.000000 179.9871 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25585, wmmin=5, clip=110 MRIfindBrightNonWM(): 372 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label MRISripNotLabel() ripped 10494/118918 vertices (108424 unripped) Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 322 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59459: xyz = (43.2823,5.36853,26.9466) oxyz = (43.2823,5.36853,26.9466) wxzy = (43.2823,5.36853,26.9466) pxyz = (0,0,0) CBVO Creating mask 118918 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 109.7521360; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=2 had to be increased for 303 vertices, nripped=10816 mean border=86.9, 1197 (1197) missing vertices, mean dist 0.5 [2.4 (%11.3)->0.8 (%88.7))] %31 local maxima, %59 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0418 min Finding expansion regions mean absolute distance = 0.99 +- 1.11 3601 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1305765.9, rms=7.270 001: dt: 0.5000, sse=637775.9, rms=4.681 (35.613%) 002: dt: 0.5000, sse=412509.7, rms=3.359 (28.241%) 003: dt: 0.5000, sse=342897.4, rms=2.841 (15.439%) 004: dt: 0.5000, sse=319417.8, rms=2.602 (8.388%) 005: dt: 0.5000, sse=308724.4, rms=2.515 (3.340%) 006: dt: 0.5000, sse=299955.9, rms=2.421 (3.736%) rms = 2.4056/2.4214, sse=300509.4/299955.9, time step reduction 1 of 3 to 0.250 0 1 1 007: dt: 0.5000, sse=300509.4, rms=2.406 (0.653%) 008: dt: 0.2500, sse=268962.6, rms=2.083 (13.420%) 009: dt: 0.2500, sse=264722.6, rms=2.029 (2.583%) rms = 2.0087/2.0290, sse=263889.9/264722.6, time step reduction 2 of 3 to 0.125 0 0 1 010: dt: 0.2500, sse=263889.9, rms=2.009 (0.998%) rms = 1.9956/2.0087, sse=262181.3/263889.9, time step reduction 3 of 3 to 0.062 0 0 1 011: dt: 0.1250, sse=262181.2, rms=1.996 (0.652%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 109.7521360; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=1 had to be increased for 253 vertices, nripped=10816 mean border=89.1, 999 (824) missing vertices, mean dist -0.3 [0.7 (%62.2)->0.3 (%37.8))] %49 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0322 min Finding expansion regions mean absolute distance = 0.54 +- 0.88 4076 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=513624.9, rms=3.892 012: dt: 0.5000, sse=354074.8, rms=2.779 (28.590%) 013: dt: 0.5000, sse=311911.9, rms=2.376 (14.499%) 014: dt: 0.5000, sse=294499.9, rms=2.212 (6.885%) 015: dt: 0.5000, sse=289143.2, rms=2.152 (2.715%) rms = 2.1519/2.1523, sse=298530.7/289143.2, time step reduction 1 of 3 to 0.250 0 1 1 016: dt: 0.5000, sse=298530.7, rms=2.152 (0.022%) 017: dt: 0.2500, sse=262673.1, rms=1.806 (16.086%) 018: dt: 0.2500, sse=259475.6, rms=1.754 (2.848%) rms = 1.7453/1.7543, sse=262129.4/259475.6, time step reduction 2 of 3 to 0.125 0 1 1 019: dt: 0.2500, sse=262129.4, rms=1.745 (0.514%) rms = 1.7336/1.7453, sse=262723.7/262129.4, time step reduction 3 of 3 to 0.062 0 1 1 020: dt: 0.1250, sse=262723.7, rms=1.734 (0.667%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 109.7521360; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 280 vertices, nripped=10816 mean border=91.8, 1024 (729) missing vertices, mean dist -0.3 [0.5 (%73.2)->0.3 (%26.8))] %72 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0183 min Finding expansion regions mean absolute distance = 0.42 +- 0.52 3026 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=500780.7, rms=3.784 021: dt: 0.5000, sse=316987.7, rms=2.371 (37.330%) rms = 2.0409/2.3711, sse=317582.7/316987.7, time step reduction 1 of 3 to 0.250 0 1 0 022: dt: 0.5000, sse=317582.7, rms=2.041 (13.926%) 023: dt: 0.2500, sse=279339.0, rms=1.723 (15.601%) 024: dt: 0.2500, sse=250835.1, rms=1.660 (3.648%) rms = 1.6483/1.6597, sse=250957.9/250835.1, time step reduction 2 of 3 to 0.125 0 1 1 025: dt: 0.2500, sse=250957.9, rms=1.648 (0.687%) rms = 1.6411/1.6483, sse=250773.0/250957.9, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=250773.0, rms=1.641 (0.435%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7521360; border_low = 80.0000000; outside_low = 68.0676800; outside_hi = 109.7521360; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 331 vertices, nripped=10816 mean border=92.8, 1035 (683) missing vertices, mean dist -0.1 [0.3 (%60.4)->0.2 (%39.6))] %80 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0123 min Finding expansion regions mean absolute distance = 0.29 +- 0.40 2758 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=280517.9, rms=2.063 027: dt: 0.5000, sse=274866.9, rms=1.653 (19.895%) rms = 1.7685/1.6529, sse=279924.9/274866.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=248970.7, rms=1.540 (6.845%) rms = 1.5221/1.5397, sse=244878.7/248970.7, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=244878.7, rms=1.522 (1.145%) rms = 1.5061/1.5221, sse=241377.1/244878.7, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=241377.1, rms=1.506 (1.050%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 2.07 minutes #VMPC# mris_place_surfaces VmPeak 2101252 mris_place_surface done @#@FSTIME 2024:10:09:17:05:16 mris_place_surface N 25 e 131.00 S 1.76 U 242.22 P 186% M 1678300 F 1 R 2081381 W 0 c 21060 w 1575 I 0 O 8368 L 4.43 6.64 8.41 @#@FSLOADPOST 2024:10:09:17:07:27 mris_place_surface N 25 4.44 5.99 7.94 #-------------------------------------------- #@# T1PialSurf lh Wed Oct 9 17:07:27 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 229316 0.34740 0.14430 0.000654 2.8130 Corner 687948 60.00000 16.36515 0.353919 177.9257 Edge 343974 0.91067 0.23678 0.028019 4.2204 Hinge 343974 11.81457 12.94501 0.000000 179.9540 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25585, wmmin=5, clip=110 MRIfindBrightNonWM(): 372 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 69.7255 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 8959/114660 vertices (105701 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57330: xyz = (-52.9608,1.68644,6.83275) oxyz = (-52.9608,1.68644,6.83275) wxzy = (-52.9608,1.68644,6.83275) pxyz = (-52.9608,1.68644,6.83275) CBVO Creating mask 114660 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.2478640; border_hi = 68.0676800; border_low = 44.2030450; outside_low = 10.0000000; outside_hi = 62.1015210; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=2 had to be increased for 302 vertices, nripped=8959 mean border=63.2, 934 (934) missing vertices, mean dist 2.3 [1.8 (%0.1)->2.6 (%99.9))] %38 local maxima, %41 large gradients and %12 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0362 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=18580834.0, rms=29.645 001: dt: 0.5000, sse=14532468.0, rms=26.184 (11.674%) 002: dt: 0.5000, sse=11394809.0, rms=23.148 (11.597%) 003: dt: 0.5000, sse=9076726.0, rms=20.618 (10.929%) 004: dt: 0.5000, sse=7360495.0, rms=18.523 (10.162%) 005: dt: 0.5000, sse=6007801.0, rms=16.686 (9.914%) 006: dt: 0.5000, sse=4826686.5, rms=14.899 (10.713%) 007: dt: 0.5000, sse=3800787.2, rms=13.150 (11.739%) 008: dt: 0.5000, sse=2930861.5, rms=11.458 (12.863%) 009: dt: 0.5000, sse=2247333.8, rms=9.928 (13.355%) 010: dt: 0.5000, sse=1757785.5, rms=8.666 (12.713%) 011: dt: 0.5000, sse=1432644.0, rms=7.713 (10.998%) 012: dt: 0.5000, sse=1216769.4, rms=7.007 (9.148%) 013: dt: 0.5000, sse=1074496.9, rms=6.499 (7.247%) 014: dt: 0.5000, sse=977860.6, rms=6.130 (5.690%) 015: dt: 0.5000, sse=912784.1, rms=5.866 (4.301%) 016: dt: 0.5000, sse=864685.8, rms=5.663 (3.467%) 017: dt: 0.5000, sse=827353.2, rms=5.500 (2.879%) 018: dt: 0.5000, sse=799462.7, rms=5.374 (2.288%) 019: dt: 0.5000, sse=774790.9, rms=5.260 (2.108%) 020: dt: 0.5000, sse=756359.4, rms=5.174 (1.650%) 021: dt: 0.5000, sse=740520.1, rms=5.098 (1.454%) rms = 5.0514/5.0985, sse=730931.8/740520.1, time step reduction 1 of 3 to 0.250 0 0 1 022: dt: 0.5000, sse=730931.8, rms=5.051 (0.922%) 023: dt: 0.2500, sse=497673.9, rms=3.766 (25.443%) 024: dt: 0.2500, sse=447609.5, rms=3.432 (8.885%) 025: dt: 0.2500, sse=436042.7, rms=3.349 (2.410%) rms = 3.3035/3.3489, sse=429747.9/436042.7, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=429747.9, rms=3.304 (1.355%) 027: dt: 0.1250, sse=401248.9, rms=3.088 (6.538%) rms = 3.0537/3.0875, sse=396915.6/401248.9, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=396915.6, rms=3.054 (1.096%) maximum number of reductions reached, breaking from loop positioning took 1.4 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.2478640; border_hi = 68.0676800; border_low = 44.2030450; outside_low = 10.0000000; outside_hi = 62.1015210; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=1 had to be increased for 2415 vertices, nripped=8959 mean border=60.1, 637 (62) missing vertices, mean dist 0.2 [0.1 (%33.0)->0.4 (%67.0))] %59 local maxima, %24 large gradients and % 9 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0121 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=864369.1, rms=5.404 029: dt: 0.5000, sse=755390.0, rms=4.898 (9.369%) rms = 4.9046/4.8979, sse=752508.8/755390.0, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 030: dt: 0.2500, sse=570696.4, rms=3.904 (20.300%) 031: dt: 0.2500, sse=504041.2, rms=3.480 (10.843%) 032: dt: 0.2500, sse=487501.4, rms=3.366 (3.288%) 033: dt: 0.2500, sse=479462.4, rms=3.310 (1.670%) rms = 3.2832/3.3097, sse=475685.9/479462.4, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=475685.9, rms=3.283 (0.799%) 035: dt: 0.1250, sse=451621.1, rms=3.102 (5.517%) rms = 3.0644/3.1021, sse=446678.0/451621.1, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=446678.0, rms=3.064 (1.215%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.2478640; border_hi = 68.0676800; border_low = 44.2030450; outside_low = 10.0000000; outside_hi = 62.1015210; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 2567 vertices, nripped=8959 mean border=58.4, 790 (46) missing vertices, mean dist 0.1 [0.1 (%36.0)->0.3 (%64.0))] %69 local maxima, %14 large gradients and % 9 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0075 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=556604.2, rms=3.803 rms = 4.7209/3.8034, sse=722527.0/556604.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=475635.7, rms=3.257 (14.362%) 038: dt: 0.2500, sse=458333.7, rms=3.128 (3.976%) rms = 3.1010/3.1277, sse=454341.2/458333.7, time step reduction 2 of 3 to 0.125 0 0 1 039: dt: 0.2500, sse=454341.2, rms=3.101 (0.852%) 040: dt: 0.1250, sse=438633.0, rms=2.977 (3.999%) rms = 2.9456/2.9770, sse=434619.6/438633.0, time step reduction 3 of 3 to 0.062 0 0 1 041: dt: 0.1250, sse=434619.6, rms=2.946 (1.053%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.2478640; border_hi = 68.0676800; border_low = 44.2030450; outside_low = 10.0000000; outside_hi = 62.1015210; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114660 Gdiag_no=-1 vno start=0, stop=114660 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 2226 vertices, nripped=8959 mean border=57.7, 1383 (41) missing vertices, mean dist 0.0 [0.2 (%44.8)->0.2 (%55.2))] %71 local maxima, %12 large gradients and % 8 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0050 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=453099.4, rms=3.095 rms = 3.8072/3.0945, sse=556132.3/453099.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 042: dt: 0.2500, sse=430195.7, rms=2.913 (5.865%) rms = 2.8719/2.9130, sse=424656.6/430195.7, time step reduction 2 of 3 to 0.125 0 0 1 043: dt: 0.2500, sse=424656.6, rms=2.872 (1.411%) 044: dt: 0.1250, sse=416913.5, rms=2.807 (2.260%) rms = 2.7745/2.8070, sse=412860.0/416913.5, time step reduction 3 of 3 to 0.062 0 0 1 045: dt: 0.1250, sse=412860.0, rms=2.774 (1.160%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 14 intersecting 001: 6 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 2.43 minutes #VMPC# mris_place_surfaces VmPeak 1460188 mris_place_surface done @#@FSTIME 2024:10:09:17:07:27 mris_place_surface N 28 e 151.71 S 1.28 U 302.80 P 200% M 1023504 F 1 R 1372205 W 0 c 26386 w 2018 I 0 O 8064 L 4.44 5.99 7.94 @#@FSLOADPOST 2024:10:09:17:09:58 mris_place_surface N 28 4.80 5.50 7.46 #-------------------------------------------- #@# T1PialSurf rh Wed Oct 9 17:09:58 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 237832 0.34578 0.14962 0.000310 2.6699 Corner 713496 60.00000 17.15498 0.537805 178.0129 Edge 356748 0.90926 0.24233 0.020937 3.8079 Hinge 356748 11.75099 13.59102 0.000000 179.9988 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=25585, wmmin=5, clip=110 MRIfindBrightNonWM(): 372 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 70.2255 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 9081/118918 vertices (109837 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59459: xyz = (43.246,5.37223,26.9483) oxyz = (43.246,5.37223,26.9483) wxzy = (43.246,5.37223,26.9483) pxyz = (43.246,5.37223,26.9483) CBVO Creating mask 118918 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2478640; border_hi = 68.0676800; border_low = 44.2030450; outside_low = 10.0000000; outside_hi = 62.1015210; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=2 had to be increased for 360 vertices, nripped=9081 mean border=63.7, 1234 (1234) missing vertices, mean dist 2.2 [6.1 (%0.1)->2.7 (%99.9))] %35 local maxima, %40 large gradients and %16 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0378 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=19355242.0, rms=29.717 001: dt: 0.5000, sse=15226203.0, rms=26.325 (11.414%) 002: dt: 0.5000, sse=12026292.0, rms=23.359 (11.267%) 003: dt: 0.5000, sse=9659447.0, rms=20.895 (10.549%) 004: dt: 0.5000, sse=7891519.5, rms=18.845 (9.814%) 005: dt: 0.5000, sse=6482650.5, rms=17.034 (9.608%) 006: dt: 0.5000, sse=5231324.5, rms=15.246 (10.495%) 007: dt: 0.5000, sse=4127397.0, rms=13.473 (11.629%) 008: dt: 0.5000, sse=3181692.8, rms=11.743 (12.847%) 009: dt: 0.5000, sse=2413295.8, rms=10.120 (13.821%) 010: dt: 0.5000, sse=1850151.6, rms=8.739 (13.639%) 011: dt: 0.5000, sse=1486765.5, rms=7.717 (11.699%) 012: dt: 0.5000, sse=1273680.0, rms=7.047 (8.677%) 013: dt: 0.5000, sse=1138403.5, rms=6.585 (6.565%) 014: dt: 0.5000, sse=1049059.2, rms=6.260 (4.934%) 015: dt: 0.5000, sse=982687.9, rms=6.006 (4.061%) 016: dt: 0.5000, sse=933623.2, rms=5.810 (3.255%) 017: dt: 0.5000, sse=892803.2, rms=5.642 (2.899%) 018: dt: 0.5000, sse=863621.1, rms=5.518 (2.197%) 019: dt: 0.5000, sse=839802.2, rms=5.414 (1.873%) 020: dt: 0.5000, sse=819110.4, rms=5.323 (1.689%) 021: dt: 0.5000, sse=801597.4, rms=5.244 (1.476%) 022: dt: 0.5000, sse=788492.7, rms=5.185 (1.137%) rms = 5.1368/5.1847, sse=778206.2/788492.7, time step reduction 1 of 3 to 0.250 0 0 1 023: dt: 0.5000, sse=778206.2, rms=5.137 (0.924%) 024: dt: 0.2500, sse=555170.6, rms=3.991 (22.308%) 025: dt: 0.2500, sse=507285.8, rms=3.702 (7.236%) 026: dt: 0.2500, sse=496209.3, rms=3.631 (1.923%) rms = 3.5891/3.6309, sse=489606.2/496209.3, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=489606.2, rms=3.589 (1.151%) 028: dt: 0.1250, sse=459291.5, rms=3.385 (5.673%) rms = 3.3459/3.3855, sse=453557.0/459291.5, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=453557.0, rms=3.346 (1.170%) maximum number of reductions reached, breaking from loop positioning took 1.4 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2478640; border_hi = 68.0676800; border_low = 44.2030450; outside_low = 10.0000000; outside_hi = 62.1015210; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=1 had to be increased for 3594 vertices, nripped=9081 mean border=61.0, 1433 (525) missing vertices, mean dist 0.2 [0.1 (%34.7)->0.4 (%65.3))] %53 local maxima, %25 large gradients and %13 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0121 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=846509.5, rms=5.187 030: dt: 0.5000, sse=790321.6, rms=4.929 (4.969%) 031: dt: 0.5000, sse=775112.4, rms=4.877 (1.057%) rms = 5.1553/4.8771, sse=837309.2/775112.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=590395.1, rms=3.902 (19.985%) 033: dt: 0.2500, sse=538910.4, rms=3.581 (8.247%) 034: dt: 0.2500, sse=526393.3, rms=3.500 (2.255%) rms = 3.4700/3.4998, sse=521981.2/526393.3, time step reduction 2 of 3 to 0.125 0 0 1 035: dt: 0.2500, sse=521981.2, rms=3.470 (0.853%) 036: dt: 0.1250, sse=495235.5, rms=3.286 (5.307%) rms = 3.2453/3.2858, sse=489508.0/495235.5, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=489508.0, rms=3.245 (1.233%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2478640; border_hi = 68.0676800; border_low = 44.2030450; outside_low = 10.0000000; outside_hi = 62.1015210; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 3847 vertices, nripped=9081 mean border=59.6, 1735 (482) missing vertices, mean dist 0.1 [0.1 (%38.2)->0.3 (%61.8))] %63 local maxima, %15 large gradients and %13 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0073 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=581875.4, rms=3.822 rms = 4.6785/3.8225, sse=741185.1/581875.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 038: dt: 0.2500, sse=516200.9, rms=3.404 (10.949%) 039: dt: 0.2500, sse=503267.8, rms=3.316 (2.573%) rms = 3.3070/3.3164, sse=501499.7/503267.8, time step reduction 2 of 3 to 0.125 0 0 1 040: dt: 0.2500, sse=501499.7, rms=3.307 (0.282%) 041: dt: 0.1250, sse=483651.8, rms=3.180 (3.851%) rms = 3.1447/3.1797, sse=478691.4/483651.8, time step reduction 3 of 3 to 0.062 0 0 1 042: dt: 0.1250, sse=478691.4, rms=3.145 (1.100%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2478640; border_hi = 68.0676800; border_low = 44.2030450; outside_low = 10.0000000; outside_hi = 62.1015210; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118918 Gdiag_no=-1 vno start=0, stop=118918 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 3242 vertices, nripped=9081 mean border=59.0, 2523 (469) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.2 (%54.9))] %65 local maxima, %12 large gradients and %13 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0051 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=495016.3, rms=3.265 rms = 3.8732/3.2650, sse=588856.4/495016.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 043: dt: 0.2500, sse=474337.5, rms=3.116 (4.566%) rms = 3.0889/3.1160, sse=470149.2/474337.5, time step reduction 2 of 3 to 0.125 0 0 1 044: dt: 0.2500, sse=470149.2, rms=3.089 (0.868%) 045: dt: 0.1250, sse=461514.4, rms=3.024 (2.108%) rms = 2.9946/3.0238, sse=457462.2/461514.4, time step reduction 3 of 3 to 0.062 0 0 1 046: dt: 0.1250, sse=457462.2, rms=2.995 (0.966%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 10 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.44 minutes #VMPC# mris_place_surfaces VmPeak 1485160 mris_place_surface done @#@FSTIME 2024:10:09:17:09:59 mris_place_surface N 28 e 152.18 S 1.21 U 314.09 P 207% M 1050268 F 2 R 1489423 W 0 c 27250 w 1798 I 8368 O 8368 L 4.80 5.50 7.46 @#@FSLOADPOST 2024:10:09:17:12:31 mris_place_surface N 28 4.82 5.21 7.04 #@# white curv lh Wed Oct 9 17:12:31 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2024:10:09:17:12:31 mris_place_surface N 5 e 1.47 S 0.07 U 1.64 P 116% M 158496 F 1 R 42694 W 0 c 156 w 103 I 0 O 896 L 4.82 5.21 7.04 @#@FSLOADPOST 2024:10:09:17:12:32 mris_place_surface N 5 4.82 5.21 7.04 #@# white area lh Wed Oct 9 17:12:32 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2024:10:09:17:12:33 mris_place_surface N 3 e 0.77 S 0.08 U 0.80 P 114% M 158512 F 2 R 42666 W 0 c 79 w 120 I 96 O 896 L 4.82 5.21 7.04 @#@FSLOADPOST 2024:10:09:17:12:33 mris_place_surface N 3 4.82 5.21 7.04 #@# pial curv lh Wed Oct 9 17:12:33 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2024:10:09:17:12:33 mris_place_surface N 5 e 1.41 S 0.10 U 1.59 P 119% M 158552 F 2 R 42677 W 0 c 151 w 139 I 96 O 896 L 4.82 5.21 7.04 @#@FSLOADPOST 2024:10:09:17:12:35 mris_place_surface N 5 4.76 5.19 7.02 #@# pial area lh Wed Oct 9 17:12:35 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2024:10:09:17:12:35 mris_place_surface N 3 e 0.60 S 0.09 U 0.81 P 148% M 158464 F 4 R 42657 W 0 c 86 w 108 I 96 O 896 L 4.76 5.19 7.02 @#@FSLOADPOST 2024:10:09:17:12:36 mris_place_surface N 3 4.76 5.19 7.02 #@# thickness lh Wed Oct 9 17:12:36 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 114660 vertices processed 25000 of 114660 vertices processed 50000 of 114660 vertices processed 75000 of 114660 vertices processed 100000 of 114660 vertices processed 0 of 114660 vertices processed 25000 of 114660 vertices processed 50000 of 114660 vertices processed 75000 of 114660 vertices processed 100000 of 114660 vertices processed thickness calculation complete, 163:1388 truncations. 60839 vertices at 0 distance 95436 vertices at 1 distance 50240 vertices at 2 distance 15599 vertices at 3 distance 4561 vertices at 4 distance 1521 vertices at 5 distance 549 vertices at 6 distance 222 vertices at 7 distance 116 vertices at 8 distance 86 vertices at 9 distance 37 vertices at 10 distance 22 vertices at 11 distance 25 vertices at 12 distance 16 vertices at 13 distance 16 vertices at 14 distance 9 vertices at 15 distance 5 vertices at 16 distance 3 vertices at 17 distance 3 vertices at 18 distance 3 vertices at 19 distance 12 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2024:10:09:17:12:36 mris_place_surface N 6 e 24.40 S 0.18 U 24.61 P 101% M 158448 F 1 R 134438 W 0 c 2226 w 120 I 96 O 896 L 4.76 5.19 7.02 @#@FSLOADPOST 2024:10:09:17:13:00 mris_place_surface N 6 4.46 5.09 6.94 #@# area and vertex vol lh Wed Oct 9 17:13:00 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume PIB23-310_VYr0_Bay3prisma lh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Total face volume 208388 Total vertex volume 208141 (mask=0) #@# PIB23-310_VYr0_Bay3prisma lh 208141 vertexvol Done @#@FSTIME 2024:10:09:17:13:00 vertexvol N 4 e 1.66 S 0.19 U 1.49 P 101% M 263460 F 1 R 75049 W 0 c 162 w 341 I 192 O 2688 L 4.46 5.09 6.94 @#@FSLOADPOST 2024:10:09:17:13:02 vertexvol N 4 4.46 5.09 6.94 #@# white curv rh Wed Oct 9 17:13:02 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2024:10:09:17:13:02 mris_place_surface N 5 e 1.43 S 0.09 U 1.66 P 123% M 164184 F 2 R 44261 W 0 c 157 w 118 I 0 O 936 L 4.46 5.09 6.94 @#@FSLOADPOST 2024:10:09:17:13:04 mris_place_surface N 5 4.46 5.09 6.94 #@# white area rh Wed Oct 9 17:13:04 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2024:10:09:17:13:04 mris_place_surface N 3 e 0.60 S 0.08 U 0.82 P 150% M 163964 F 1 R 44276 W 0 c 85 w 101 I 96 O 936 L 4.46 5.09 6.94 @#@FSLOADPOST 2024:10:09:17:13:04 mris_place_surface N 3 4.66 5.12 6.94 #@# pial curv rh Wed Oct 9 17:13:04 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2024:10:09:17:13:05 mris_place_surface N 5 e 1.87 S 0.09 U 1.65 P 93% M 164400 F 2 R 44243 W 0 c 154 w 152 I 8464 O 936 L 4.66 5.12 6.94 @#@FSLOADPOST 2024:10:09:17:13:06 mris_place_surface N 5 4.66 5.12 6.94 #@# pial area rh Wed Oct 9 17:13:06 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2024:10:09:17:13:07 mris_place_surface N 3 e 0.62 S 0.09 U 0.83 P 150% M 164208 F 1 R 44249 W 0 c 84 w 110 I 96 O 936 L 4.66 5.12 6.94 @#@FSLOADPOST 2024:10:09:17:13:07 mris_place_surface N 3 4.66 5.12 6.94 #@# thickness rh Wed Oct 9 17:13:07 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 118918 vertices processed 25000 of 118918 vertices processed 50000 of 118918 vertices processed 75000 of 118918 vertices processed 100000 of 118918 vertices processed 0 of 118918 vertices processed 25000 of 118918 vertices processed 50000 of 118918 vertices processed 75000 of 118918 vertices processed 100000 of 118918 vertices processed thickness calculation complete, 108:1272 truncations. 60295 vertices at 0 distance 97080 vertices at 1 distance 53645 vertices at 2 distance 17752 vertices at 3 distance 5540 vertices at 4 distance 1915 vertices at 5 distance 779 vertices at 6 distance 334 vertices at 7 distance 162 vertices at 8 distance 90 vertices at 9 distance 68 vertices at 10 distance 61 vertices at 11 distance 31 vertices at 12 distance 18 vertices at 13 distance 13 vertices at 14 distance 11 vertices at 15 distance 9 vertices at 16 distance 13 vertices at 17 distance 5 vertices at 18 distance 5 vertices at 19 distance 10 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2024:10:09:17:13:07 mris_place_surface N 6 e 26.51 S 0.25 U 26.70 P 101% M 163932 F 2 R 145281 W 0 c 2367 w 143 I 96 O 936 L 4.66 5.12 6.94 @#@FSLOADPOST 2024:10:09:17:13:34 mris_place_surface N 6 4.25 4.98 6.85 #@# area and vertex vol rh Wed Oct 9 17:13:34 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume PIB23-310_VYr0_Bay3prisma rh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Total face volume 218086 Total vertex volume 217784 (mask=0) #@# PIB23-310_VYr0_Bay3prisma rh 217784 vertexvol Done @#@FSTIME 2024:10:09:17:13:34 vertexvol N 4 e 1.43 S 0.16 U 1.60 P 123% M 272672 F 3 R 77713 W 0 c 164 w 374 I 192 O 2808 L 5.11 5.15 6.89 @#@FSLOADPOST 2024:10:09:17:13:35 vertexvol N 4 5.11 5.15 6.89 #----------------------------------------- #@# Curvature Stats lh Wed Oct 9 17:13:35 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PIB23-310_VYr0_Bay3prisma lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ PIB23-310_VYr0_Bay3prisma/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 257 ] Gb_filter = 0 @#@FSTIME 2024:10:09:17:13:36 mris_curvature_stats N 11 e 2.47 S 0.12 U 2.27 P 97% M 158672 F 2 R 42874 W 0 c 213 w 484 I 768 O 7208 L 5.11 5.15 6.89 @#@FSLOADPOST 2024:10:09:17:13:38 mris_curvature_stats N 11 5.11 5.15 6.89 #----------------------------------------- #@# Curvature Stats rh Wed Oct 9 17:13:38 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PIB23-310_VYr0_Bay3prisma rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ PIB23-310_VYr0_Bay3prisma/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 259 ] Gb_filter = 0 WARN: S lookup min: -0.109996 WARN: S explicit min: 0.000000 vertex = 10 @#@FSTIME 2024:10:09:17:13:38 mris_curvature_stats N 11 e 2.48 S 0.12 U 2.49 P 105% M 164340 F 1 R 76105 W 0 c 240 w 473 I 768 O 7528 L 5.11 5.15 6.89 @#@FSLOADPOST 2024:10:09:17:13:41 mris_curvature_stats N 11 5.02 5.13 6.87 #-------------------------------------------- #@# Cortical ribbon mask Wed Oct 9 17:13:41 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon PIB23-310_VYr0_Bay3prisma SUBJECTS_DIR is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing loading input data... Running hemis serially Processing left hemi computing distance to left white surface computing distance to left pial surface Processing right hemi computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 56 writing volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz mris_volmask took 6.04 minutes writing ribbon files @#@FSTIME 2024:10:09:17:13:41 mris_volmask N 12 e 362.42 S 1.28 U 362.33 P 100% M 909680 F 1 R 1307447 W 0 c 32261 w 295 I 0 O 816 L 5.02 5.13 6.87 @#@FSLOADPOST 2024:10:09:17:19:43 mris_volmask N 12 2.82 4.60 6.16 #----------------------------------------- #@# Cortical Parc 2 lh Wed Oct 9 17:19:43 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Wed Oct 9 17:19:43 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 854792 of (854792 854795) to complete... Waiting for PID 854795 of (854792 854795) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 3.0 using min determinant for regularization = 0.088 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 691 labels changed using aseg relabeling using gibbs priors... 000: 7428 changed, 114660 examined... 001: 1705 changed, 29153 examined... 002: 460 changed, 9223 examined... 003: 180 changed, 2723 examined... 004: 89 changed, 1060 examined... 005: 43 changed, 546 examined... 006: 19 changed, 256 examined... 007: 20 changed, 114 examined... 008: 11 changed, 113 examined... 009: 4 changed, 59 examined... 010: 2 changed, 29 examined... 011: 0 changed, 14 examined... 131 labels changed using aseg 000: 205 total segments, 117 labels (1336 vertices) changed 001: 89 total segments, 3 labels (166 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 26 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1037 vertices marked for relabeling... 1037 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.021 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 919 labels changed using aseg relabeling using gibbs priors... 000: 7865 changed, 118918 examined... 001: 1753 changed, 30739 examined... 002: 514 changed, 9345 examined... 003: 238 changed, 2997 examined... 004: 143 changed, 1366 examined... 005: 67 changed, 821 examined... 006: 48 changed, 398 examined... 007: 26 changed, 269 examined... 008: 8 changed, 144 examined... 009: 3 changed, 53 examined... 010: 1 changed, 21 examined... 011: 1 changed, 6 examined... 012: 0 changed, 7 examined... 105 labels changed using aseg 000: 228 total segments, 141 labels (1496 vertices) changed 001: 90 total segments, 4 labels (4 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 880 vertices marked for relabeling... 880 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 13 seconds. PIDs (854792 854795) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Wed Oct 9 17:19:56 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Wed Oct 9 17:19:56 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 854920 of (854920 854923) to complete... Waiting for PID 854923 of (854920 854923) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1524 labels changed using aseg relabeling using gibbs priors... 000: 1705 changed, 114660 examined... 001: 405 changed, 8179 examined... 002: 125 changed, 2362 examined... 003: 61 changed, 739 examined... 004: 25 changed, 336 examined... 005: 23 changed, 138 examined... 006: 14 changed, 118 examined... 007: 10 changed, 78 examined... 008: 10 changed, 58 examined... 009: 8 changed, 45 examined... 010: 6 changed, 38 examined... 011: 6 changed, 32 examined... 012: 4 changed, 32 examined... 013: 3 changed, 20 examined... 014: 4 changed, 18 examined... 015: 1 changed, 20 examined... 016: 3 changed, 7 examined... 017: 2 changed, 13 examined... 018: 3 changed, 13 examined... 019: 4 changed, 15 examined... 020: 3 changed, 17 examined... 021: 5 changed, 18 examined... 022: 4 changed, 22 examined... 023: 2 changed, 20 examined... 024: 1 changed, 15 examined... 025: 4 changed, 7 examined... 026: 6 changed, 16 examined... 027: 3 changed, 24 examined... 028: 3 changed, 17 examined... 029: 2 changed, 19 examined... 030: 0 changed, 10 examined... 395 labels changed using aseg 000: 43 total segments, 10 labels (74 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 7 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 549 vertices marked for relabeling... 549 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1816 labels changed using aseg relabeling using gibbs priors... 000: 1805 changed, 118918 examined... 001: 399 changed, 8455 examined... 002: 119 changed, 2318 examined... 003: 66 changed, 691 examined... 004: 42 changed, 386 examined... 005: 25 changed, 229 examined... 006: 23 changed, 136 examined... 007: 18 changed, 124 examined... 008: 8 changed, 96 examined... 009: 8 changed, 43 examined... 010: 7 changed, 41 examined... 011: 9 changed, 35 examined... 012: 5 changed, 43 examined... 013: 3 changed, 33 examined... 014: 2 changed, 21 examined... 015: 2 changed, 14 examined... 016: 3 changed, 13 examined... 017: 3 changed, 18 examined... 018: 3 changed, 19 examined... 019: 1 changed, 14 examined... 020: 0 changed, 7 examined... 349 labels changed using aseg 000: 60 total segments, 27 labels (271 vertices) changed 001: 34 total segments, 1 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 537 vertices marked for relabeling... 537 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. PIDs (854920 854923) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Wed Oct 9 17:20:06 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts pctsurfcon --s PIB23-310_VYr0_Bay3prisma --lh-only #----------------------------------------- #@# WM/GM Contrast rh Wed Oct 9 17:20:06 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts pctsurfcon --s PIB23-310_VYr0_Bay3prisma --rh-only Waiting for PID 855035 of (855035 855038) to complete... Waiting for PID 855038 of (855035 855038) to complete... pctsurfcon --s PIB23-310_VYr0_Bay3prisma --lh-only mv: cannot stat '/data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/pctsurfcon.log': No such file or directory Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/pctsurfcon.log Wed Oct 9 17:20:06 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/pctsurfcon pctsurfcon 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855035/lh.wm.mgh --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 74632 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855035/lh.wm.mgh Dim: 114660 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855035/lh.gm.mgh --projfrac 0.3 --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 87988 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855035/lh.gm.mgh Dim: 114660 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855035/lh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855035/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/lh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/lh.w-g.pct.stats --snr sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Seg base 1000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh Vertex Area is 0.694785 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s PIB23-310_VYr0_Bay3prisma --rh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/pctsurfcon.log Wed Oct 9 17:20:06 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/pctsurfcon pctsurfcon 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855038/rh.wm.mgh --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 76781 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855038/rh.wm.mgh Dim: 118918 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855038/rh.gm.mgh --projfrac 0.3 --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 91122 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855038/rh.gm.mgh Dim: 118918 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855038/rh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.855038/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/rh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/rh.w-g.pct.stats --snr sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Seg base 2000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh Vertex Area is 0.691539 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (855035 855038) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Wed Oct 9 17:20:10 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2614 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2683 voxels changed to hypointensity... 5010 hypointense voxels neighboring cortex changed @#@FSTIME 2024:10:09:17:20:10 mri_relabel_hypointensities N 3 e 15.94 S 0.65 U 16.62 P 108% M 453664 F 2 R 541840 W 0 c 1550 w 146 I 0 O 672 L 2.71 4.41 6.04 @#@FSLOADPOST 2024:10:09:17:20:26 mri_relabel_hypointensities N 3 2.33 4.24 5.96 #----------------------------------------- #@# APas-to-ASeg Wed Oct 9 17:20:26 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz --threads 4 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aseg.mgz 72 avail.processors, using 4 Loading aseg.presurf.hypos.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Done loading 0 192 64 128 65 193 1 2 194 66 3 195 67 4 196 129 5 197 68 6 198 69 7 199 70 8 200 9 71 201 10 202 72 130 11 203 12 204 73 13 205 14 206 74 15 207 75 208 16 131 209 17 210 18 76 19 211 20 212 77 21 213 22 214 132 78 23 215 24 216 79 25 217 26 218 133 80 27 219 28 220 29 221 81 30 222 134 31 223 82 32 224 33 225 34 135 226 83 35 227 36 228 37 84 229 136 38 230 39 231 40 85 232 41 137 233 42 234 86 43 235 44 138 236 45 237 46 238 87 47 239 48 139 240 49 241 50 88 242 51 243 52 140 244 53 245 54 89 246 55 141 247 56 248 57 249 58 90 142 250 59 60 251 61 252 143 253 91 62 254 63 255 144 92 93 145 94 146 147 95 148 96 149 97 150 98 151 99 152 153 100 154 155 101 156 157 102 158 159 160 103 161 162 104 163 105 164 165 106 166 107 167 108 168 109 169 170 110 171 111 172 112 173 113 174 175 114 176 177 115 178 179 116 180 117 181 182 183 118 184 185 186 119 187 188 189 120 190 191 121 122 123 124 125 126 127 nrelabeled = 109526 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 998396 mri_surf2volseg done @#@FSTIME 2024:10:09:17:20:26 mri_surf2volseg N 20 e 6.80 S 0.52 U 11.43 P 175% M 812272 F 1 R 449746 W 0 c 1094 w 281 I 0 O 704 L 2.33 4.24 5.96 @#@FSLOADPOST 2024:10:09:17:20:33 mri_surf2volseg N 20 2.22 4.18 5.94 mri_brainvol_stats PIB23-310_VYr0_Bay3prisma ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1607897.0 #CBVS2 BrainSegVol 1086090.0 #CBVS2 BrainSegVolNotVent 964893.0 #CBVS2 SupraTentVol 960593.0 #CBVS2 SupraTentVolNotVent 839396.0 #CBVS2 lhCtxGM 208435.8 #CBVS2 rhCtxGM 217868.8 #CBVS2 lhCerebralWM 181136.5 #CBVS2 rhCerebralWM 182939.5 #CBVS2 SubCortGMVol 49818.0 #CBVS2 CerebellumVol 125497.0 #CBVS2 CerebellumGMVol 100708.0 #CBVS2 VentChorVol 112973.0 #CBVS2 3rd4th5thCSF 8224.0 #CBVS2 AllCSF 121197.0 #CBVS2 CCVol 3869.0 @#@FSTIME 2024:10:09:17:20:33 mri_brainvol_stats N 1 e 2.81 S 0.34 U 4.63 P 176% M 213208 F 1 R 201357 W 0 c 450 w 157 I 0 O 8 L 2.22 4.18 5.94 @#@FSLOADPOST 2024:10:09:17:20:36 mri_brainvol_stats N 1 2.12 4.13 5.91 #----------------------------------------- #@# AParc-to-ASeg aparc Wed Oct 9 17:20:36 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10415 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10494 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Done loading 0 64 192 128 1 193 2 194 3 195 4 196 5 197 6 198 7 199 8 200 65 9 201 10 202 11 203 12 204 13 205 14 206 15 207 16 208 17 209 18 210 19 211 20 212 21 213 22 66 214 23 215 24 216 25 217 26 218 27 219 28 220 29 30 221 31 222 32 223 33 224 34 225 35 226 36 227 37 228 38 229 39 230 40 231 41 232 67 42 233 43 234 44 235 45 236 46 237 47 238 48 239 49 240 50 51 241 52 242 53 243 54 244 55 245 56 246 57 247 58 248 59 249 60 250 61 251 62 68 252 253 254 255 63 129 69 70 71 130 72 131 73 74 132 75 133 76 134 77 135 78 136 79 137 80 81 138 82 139 83 140 141 84 142 85 143 86 144 145 87 146 88 147 148 89 149 90 150 151 91 152 153 92 154 155 93 156 94 157 158 95 159 96 160 161 97 162 98 163 99 164 165 100 166 101 167 102 168 169 103 170 104 171 172 105 173 106 174 107 175 176 108 177 109 178 110 179 111 180 112 181 182 113 183 114 184 185 186 187 188 115 189 190 191 116 117 118 119 120 121 122 123 124 125 126 127 nrelabeled = 425488 ndotcheck = 13758 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 982444 mri_surf2volseg done @#@FSTIME 2024:10:09:17:20:36 mri_surf2volseg N 25 e 52.95 S 0.77 U 94.19 P 179% M 797184 F 2 R 848977 W 0 c 8510 w 376 I 0 O 800 L 2.12 4.13 5.91 @#@FSLOADPOST 2024:10:09:17:21:29 mri_surf2volseg N 25 2.64 3.98 5.76 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Wed Oct 9 17:21:29 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc.a2009s+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10415 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.a2009s.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10494 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.a2009s.annot Done loading 0 64 128 192 1 193 194 2 195 3 196 4 197 5 198 6 199 7 200 8 65 201 9 202 10 203 11 204 12 205 13 206 14 207 15 208 16 209 17 210 18 211 212 19 213 20 214 21 66 215 22 216 23 217 24 218 25 219 26 220 27 221 28 222 29 223 30 224 31 225 32 226 33 227 34 228 35 229 36 230 37 231 38 232 39 233 67 40 234 41 235 42 236 43 237 44 238 239 45 240 46 241 47 242 48 243 49 244 50 245 51 246 52 247 53 248 54 249 55 250 56 251 57 252 58 253 59 254 60 255 61 68 62 63 129 69 70 71 130 72 131 73 74 132 75 133 76 134 77 135 78 136 79 137 80 81 138 82 139 83 140 84 141 142 85 143 86 144 87 145 146 88 147 89 148 149 90 150 151 91 152 92 153 154 93 155 156 94 157 95 158 159 96 160 97 161 98 162 163 99 164 100 165 101 166 167 102 168 103 169 104 170 171 105 172 106 173 107 174 175 108 176 109 177 110 178 111 179 112 180 113 181 182 114 183 115 184 185 186 187 188 189 190 191 116 117 118 119 120 121 122 123 124 125 126 127 nrelabeled = 425488 ndotcheck = 13758 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 982540 mri_surf2volseg done @#@FSTIME 2024:10:09:17:21:29 mri_surf2volseg N 25 e 53.16 S 0.75 U 95.29 P 180% M 797464 F 3 R 835505 W 0 c 8628 w 353 I 0 O 864 L 2.83 4.00 5.76 @#@FSLOADPOST 2024:10:09:17:22:22 mri_surf2volseg N 25 2.96 3.86 5.62 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Wed Oct 9 17:22:22 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc.DKTatlas+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10415 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.DKTatlas.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10494 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.DKTatlas.annot Done loading 0 192 64 128 1 193 2 194 3 195 4 196 5 197 6 198 7 199 8 200 9 65 201 10 202 11 203 12 204 13 205 14 206 15 207 16 208 17 209 18 210 19 211 20 212 21 213 22 23 214 66 24 215 25 216 26 217 27 218 28 219 29 220 30 221 31 222 32 223 33 224 34 225 35 226 36 227 37 228 38 229 39 230 40 231 41 232 42 43 233 67 44 234 45 235 46 236 47 237 48 238 49 239 50 240 51 241 52 242 53 243 54 244 55 245 56 246 57 58 247 59 248 60 249 61 250 251 62 252 253 254 68 63 255 129 69 70 71 130 72 131 73 74 132 75 133 76 134 77 135 78 136 79 137 80 138 81 82 139 83 140 141 84 142 85 143 86 144 145 87 146 88 147 148 89 149 90 150 151 91 152 153 92 154 155 93 156 157 94 158 95 159 96 160 161 97 162 98 163 99 164 165 100 166 101 167 102 168 169 103 170 104 171 172 105 173 106 174 175 107 176 108 177 109 178 110 179 111 180 112 181 182 113 183 114 184 185 186 187 188 115 189 190 191 116 117 118 119 120 121 122 123 124 125 126 127 nrelabeled = 425488 ndotcheck = 13758 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 982440 mri_surf2volseg done @#@FSTIME 2024:10:09:17:22:23 mri_surf2volseg N 25 e 53.92 S 0.86 U 95.93 P 179% M 797332 F 1 R 843519 W 0 c 8685 w 382 I 0 O 792 L 2.96 3.86 5.62 @#@FSLOADPOST 2024:10:09:17:23:17 mri_surf2volseg N 25 2.34 3.54 5.41 #----------------------------------------- #@# WMParc Wed Oct 9 17:23:17 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot 3000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot 4000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol wmparc.mgz 72 avail.processors, using 4 Loading aparc+aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10415 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10494 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Done loading 0 128 192 64 193 1 65 194 2 66 195 3 196 4 67 197 5 198 6 199 7 68 200 8 201 9 202 10 69 203 11 204 12 205 13 206 14 207 15 70 208 16 209 17 210 18 211 19 212 20 213 21 214 71 22 215 23 216 24 217 25 218 219 26 72 129 220 27 221 28 222 29 223 30 224 31 225 32 226 33 227 34 228 35 229 36 230 37 231 38 232 39 73 233 40 234 41 235 42 236 43 237 44 130 238 45 239 46 240 47 241 48 242 49 243 50 244 51 245 52 246 53 247 74 54 248 55 249 56 250 57 251 58 252 59 253 60 254 61 255 131 62 63 75 76 132 77 133 78 134 79 135 80 136 81 82 137 83 138 84 139 85 140 86 87 141 88 142 89 90 143 91 144 92 145 93 146 94 147 95 148 96 149 97 150 98 151 99 152 100 153 101 154 102 155 103 156 104 157 105 158 159 106 160 107 161 108 162 163 109 164 110 165 111 166 167 112 168 113 169 170 114 171 115 172 173 116 174 175 117 176 118 177 178 119 179 180 120 181 182 183 121 184 185 186 187 188 189 190 122 191 123 124 125 126 127 nrelabeled = 360207 ndotcheck = 4784 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 982440 mri_surf2volseg done @#@FSTIME 2024:10:09:17:23:17 mri_surf2volseg N 25 e 21.36 S 0.64 U 39.99 P 190% M 797348 F 1 R 631175 W 0 c 3656 w 323 I 0 O 880 L 2.34 3.54 5.41 @#@FSLOADPOST 2024:10:09:17:23:38 mri_surf2volseg N 25 2.47 3.49 5.35 mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject PIB23-310_VYr0_Bay3prisma --surf-wm-vol --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 7.3.2 cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject PIB23-310_VYr0_Bay3prisma --surf-wm-vol --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/WMParcStatsLUT.txt --etiv sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2024:10:09:17:23:38 mri_segstats N 24 e 200.40 S 0.92 U 413.26 P 206% M 240000 F 0 R 1650193 W 0 c 36216 w 799 I 0 O 24 L 2.47 3.49 5.35 @#@FSLOADPOST 2024:10:09:17:26:59 mri_segstats N 24 2.52 3.09 4.83 #----------------------------------------- #@# Parcellation Stats lh Wed Oct 9 17:26:59 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh pial #----------------------------------------- #@# Parcellation Stats rh Wed Oct 9 17:26:59 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh pial Waiting for PID 857044 of (857044 857047 857050 857053) to complete... Waiting for PID 857047 of (857044 857047 857050 857053) to complete... Waiting for PID 857050 of (857044 857047 857050 857053) to complete... Waiting for PID 857053 of (857044 857047 857050 857053) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208388 Total vertex volume 208141 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1295 872 2107 2.440 0.497 0.082 0.017 5 0.9 bankssts 749 570 1940 3.190 0.725 0.159 0.041 17 1.3 caudalanteriorcingulate 2673 1977 5687 2.536 0.477 0.123 0.031 28 3.6 caudalmiddlefrontal 1794 1184 2485 1.980 0.506 0.143 0.036 25 2.5 cuneus 634 445 1398 2.484 0.847 0.128 0.045 8 1.2 entorhinal 3735 2673 8341 2.620 0.658 0.126 0.030 47 4.5 fusiform 5230 3820 10765 2.525 0.554 0.132 0.032 70 6.9 inferiorparietal 3651 2797 9287 2.674 0.727 0.134 0.033 50 5.1 inferiortemporal 1179 766 1624 2.154 0.793 0.121 0.031 16 1.6 isthmuscingulate 6047 4049 10063 2.273 0.529 0.135 0.033 73 7.9 lateraloccipital 2934 2130 6627 2.696 0.765 0.136 0.036 34 4.3 lateralorbitofrontal 4169 2790 6239 2.057 0.560 0.130 0.035 54 5.9 lingual 2481 1802 4857 2.390 0.840 0.143 0.038 41 3.5 medialorbitofrontal 3965 2753 8875 2.676 0.617 0.117 0.027 50 4.3 middletemporal 1134 703 2060 2.440 0.622 0.083 0.021 6 0.8 parahippocampal 1886 1168 3260 2.535 0.556 0.095 0.022 12 1.7 paracentral 1933 1326 3684 2.469 0.498 0.109 0.025 17 2.0 parsopercularis 705 537 2020 2.788 0.634 0.144 0.034 9 1.0 parsorbitalis 1618 1161 3227 2.395 0.580 0.117 0.027 17 1.8 parstriangularis 2009 1312 2047 1.620 0.470 0.128 0.035 21 3.0 pericalcarine 5820 3854 8866 2.067 0.615 0.106 0.026 50 5.7 postcentral 1122 814 2289 2.686 0.592 0.135 0.033 20 1.7 posteriorcingulate 6904 4741 12771 2.473 0.575 0.120 0.031 65 9.0 precentral 4143 2981 8261 2.591 0.526 0.136 0.034 52 5.6 precuneus 1258 930 2509 2.437 1.133 0.159 0.060 31 3.7 rostralanteriorcingulate 5651 4320 13108 2.472 0.627 0.133 0.033 82 7.5 rostralmiddlefrontal 7651 5790 18816 2.654 0.664 0.131 0.037 110 11.8 superiorfrontal 6189 4386 12041 2.493 0.482 0.124 0.029 69 7.5 superiorparietal 5622 3741 11178 2.571 0.613 0.095 0.020 47 4.6 superiortemporal 5132 3653 9534 2.360 0.519 0.124 0.029 57 6.1 supramarginal 314 245 1335 3.159 0.796 0.160 0.054 9 0.7 frontalpole 639 513 3007 3.349 0.923 0.148 0.055 12 1.4 temporalpole 765 405 967 2.187 0.547 0.095 0.028 6 0.8 transversetemporal 3214 2182 6865 2.972 0.966 0.121 0.038 31 5.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208388 Total vertex volume 208141 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1295 808 2107 2.440 0.497 0.087 0.017 8 0.8 bankssts 749 712 1940 3.190 0.725 0.160 0.036 11 0.9 caudalanteriorcingulate 2673 2405 5687 2.536 0.477 0.139 0.026 32 2.8 caudalmiddlefrontal 1794 1425 2485 1.980 0.506 0.131 0.037 28 2.3 cuneus 634 713 1398 2.484 0.847 0.236 0.074 17 2.5 entorhinal 3735 3511 8341 2.620 0.658 0.151 0.033 50 5.1 fusiform 5230 4591 10765 2.525 0.554 0.143 0.031 71 6.3 inferiorparietal 3651 3769 9287 2.674 0.727 0.164 0.046 66 5.2 inferiortemporal 1179 849 1624 2.154 0.793 0.144 0.045 22 1.9 isthmuscingulate 6047 4815 10063 2.273 0.529 0.137 0.033 187 7.6 lateraloccipital 2934 2660 6627 2.696 0.765 0.157 0.038 51 4.3 lateralorbitofrontal 4169 3428 6239 2.057 0.560 0.135 0.035 64 5.4 lingual 2481 2261 4857 2.390 0.840 0.154 0.037 39 3.5 medialorbitofrontal 3965 3676 8875 2.676 0.617 0.139 0.027 42 4.4 middletemporal 1134 1020 2060 2.440 0.622 0.127 0.029 10 1.3 parahippocampal 1886 1423 3260 2.535 0.556 0.114 0.024 22 1.9 paracentral 1933 1603 3684 2.469 0.498 0.127 0.023 19 1.7 parsopercularis 705 885 2020 2.788 0.634 0.194 0.039 9 1.3 parsorbitalis 1618 1480 3227 2.395 0.580 0.143 0.026 16 1.7 parstriangularis 2009 1212 2047 1.620 0.470 0.116 0.029 31 2.2 pericalcarine 5820 4743 8866 2.067 0.615 0.115 0.020 46 4.8 postcentral 1122 961 2289 2.686 0.592 0.137 0.031 11 1.5 posteriorcingulate 6904 5479 12771 2.473 0.575 0.116 0.022 62 6.2 precentral 4143 3329 8261 2.591 0.526 0.145 0.036 80 6.1 precuneus 1258 1130 2509 2.437 1.133 0.158 0.068 65 2.2 rostralanteriorcingulate 5651 5838 13108 2.472 0.627 0.165 0.031 81 7.1 rostralmiddlefrontal 7651 7897 18816 2.654 0.664 0.162 0.035 118 10.0 superiorfrontal 6189 5250 12041 2.493 0.482 0.136 0.030 172 7.5 superiorparietal 5622 4805 11178 2.571 0.613 0.115 0.024 41 4.8 superiortemporal 5132 4336 9534 2.360 0.519 0.136 0.026 53 5.5 supramarginal 314 601 1335 3.159 0.796 0.281 0.048 5 0.8 frontalpole 639 1099 3007 3.349 0.923 0.237 0.040 8 1.2 temporalpole 765 497 967 2.187 0.547 0.083 0.013 3 0.4 transversetemporal 3214 2315 6865 2.972 0.966 0.148 0.044 68 5.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 218086 Total vertex volume 217784 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1231 823 2023 2.550 0.534 0.082 0.016 5 0.8 bankssts 827 578 1483 2.765 0.843 0.119 0.026 13 1.0 caudalanteriorcingulate 2935 2134 6096 2.533 0.498 0.125 0.028 30 3.5 caudalmiddlefrontal 2263 1452 3228 2.014 0.472 0.141 0.035 32 3.2 cuneus 704 497 1881 2.918 0.756 0.133 0.042 9 1.0 entorhinal 3777 2788 8357 2.570 0.645 0.128 0.028 51 4.3 fusiform 6874 4859 13991 2.581 0.511 0.124 0.029 81 7.9 inferiorparietal 3990 2982 9925 2.805 0.670 0.135 0.034 55 5.3 inferiortemporal 858 529 1137 2.083 0.739 0.109 0.030 8 1.1 isthmuscingulate 6339 4252 10330 2.271 0.590 0.130 0.030 72 7.9 lateraloccipital 2808 2092 6511 2.707 0.726 0.142 0.040 35 4.4 lateralorbitofrontal 5045 3416 7511 2.060 0.583 0.132 0.035 67 7.2 lingual 2572 1875 5186 2.348 0.773 0.136 0.041 51 4.0 medialorbitofrontal 4421 3048 10318 2.825 0.595 0.109 0.025 46 4.4 middletemporal 1098 706 2222 2.669 0.734 0.105 0.026 12 1.0 parahippocampal 2169 1384 3641 2.488 0.502 0.113 0.027 19 2.3 paracentral 1589 1187 3745 2.643 0.553 0.130 0.034 19 2.1 parsopercularis 864 670 2542 2.713 0.658 0.144 0.037 13 1.2 parsorbitalis 1640 1195 3394 2.403 0.612 0.115 0.027 17 1.8 parstriangularis 2390 1508 2444 1.710 0.537 0.135 0.043 76 4.0 pericalcarine 6195 3900 9027 2.113 0.600 0.095 0.021 47 5.5 postcentral 948 661 1826 2.628 0.631 0.128 0.029 15 1.1 posteriorcingulate 6449 4311 12354 2.679 0.555 0.110 0.027 51 7.2 precentral 4749 3515 9474 2.521 0.522 0.127 0.030 59 6.0 precuneus 662 478 1895 2.855 0.899 0.129 0.032 10 0.9 rostralanteriorcingulate 5472 4339 13522 2.492 0.719 0.143 0.038 90 8.7 rostralmiddlefrontal 8066 6187 19803 2.608 0.683 0.136 0.036 118 12.2 superiorfrontal 6220 4270 12077 2.585 0.425 0.118 0.026 67 6.5 superiorparietal 5596 3568 10805 2.490 0.642 0.086 0.017 43 3.8 superiortemporal 4806 3335 9116 2.541 0.534 0.116 0.025 48 5.0 supramarginal 360 310 1473 3.062 0.685 0.186 0.050 10 1.0 frontalpole 610 479 2805 3.508 0.830 0.142 0.048 9 0.9 temporalpole 630 321 886 2.363 0.487 0.111 0.032 7 0.7 transversetemporal 3267 2214 6753 2.862 0.847 0.112 0.032 31 3.8 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 218086 Total vertex volume 217784 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1231 734 2023 2.550 0.534 0.087 0.017 10 0.8 bankssts 827 555 1483 2.765 0.843 0.112 0.027 16 0.7 caudalanteriorcingulate 2935 2584 6096 2.533 0.498 0.131 0.024 29 2.6 caudalmiddlefrontal 2263 1837 3228 2.014 0.472 0.140 0.032 31 3.2 cuneus 704 807 1881 2.918 0.756 0.226 0.065 17 2.1 entorhinal 3777 3565 8357 2.570 0.645 0.153 0.034 59 5.3 fusiform 6874 5875 13991 2.581 0.511 0.136 0.030 102 8.6 inferiorparietal 3990 3958 9925 2.805 0.670 0.162 0.036 97 6.1 inferiortemporal 858 610 1137 2.083 0.739 0.133 0.042 14 1.1 isthmuscingulate 6339 4898 10330 2.271 0.590 0.128 0.031 109 7.9 lateraloccipital 2808 2634 6511 2.707 0.726 0.170 0.045 49 5.2 lateralorbitofrontal 5045 4112 7511 2.060 0.583 0.142 0.036 138 6.8 lingual 2572 2491 5186 2.348 0.773 0.161 0.039 59 3.9 medialorbitofrontal 4421 4117 10318 2.825 0.595 0.135 0.027 57 4.5 middletemporal 1098 951 2222 2.669 0.734 0.144 0.032 16 1.5 parahippocampal 2169 1542 3641 2.488 0.502 0.112 0.027 39 2.0 paracentral 1589 1594 3745 2.643 0.553 0.161 0.031 19 2.0 parsopercularis 864 1152 2542 2.713 0.658 0.202 0.037 12 1.5 parsorbitalis 1640 1577 3394 2.403 0.612 0.159 0.031 23 2.1 parstriangularis 2390 1353 2444 1.710 0.537 0.133 0.051 76 3.8 pericalcarine 6195 4691 9027 2.113 0.600 0.100 0.019 37 4.7 postcentral 948 812 1826 2.628 0.631 0.198 0.093 261 1.9 posteriorcingulate 6449 4765 12354 2.679 0.555 0.104 0.020 65 5.3 precentral 4749 3953 9474 2.521 0.522 0.136 0.030 63 5.5 precuneus 662 779 1895 2.855 0.899 0.197 0.037 8 1.0 rostralanteriorcingulate 5472 6090 13522 2.492 0.719 0.185 0.036 83 8.7 rostralmiddlefrontal 8066 8407 19803 2.608 0.683 0.167 0.036 142 11.8 superiorfrontal 6220 5070 12077 2.585 0.425 0.133 0.033 128 7.6 superiorparietal 5596 4843 10805 2.490 0.642 0.114 0.019 40 5.0 superiortemporal 4806 3800 9116 2.541 0.534 0.124 0.024 47 4.7 supramarginal 360 683 1473 3.062 0.685 0.292 0.051 7 0.9 frontalpole 610 1083 2805 3.508 0.830 0.276 0.063 12 1.7 temporalpole 630 426 886 2.363 0.487 0.094 0.017 3 0.4 transversetemporal 3267 2341 6753 2.862 0.847 0.139 0.041 57 5.3 insula PIDs (857044 857047 857050 857053) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Oct 9 17:27:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 2 rh Wed Oct 9 17:27:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma rh white Waiting for PID 857281 of (857281 857284) to complete... Waiting for PID 857284 of (857281 857284) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208388 Total vertex volume 208141 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 834 620 2161 2.694 0.811 0.131 0.031 10 1.2 G_and_S_frontomargin 1236 831 2650 2.586 0.529 0.137 0.030 17 1.4 G_and_S_occipital_inf 1517 1010 3064 2.413 0.652 0.118 0.029 15 1.9 G_and_S_paracentral 1100 761 2673 2.868 0.553 0.137 0.040 13 1.7 G_and_S_subcentral 517 419 1875 2.944 0.698 0.159 0.046 12 0.8 G_and_S_transv_frontopol 2024 1519 4251 2.620 0.755 0.135 0.034 30 3.0 G_and_S_cingul-Ant 1101 777 2081 2.732 0.826 0.142 0.046 18 2.4 G_and_S_cingul-Mid-Ant 1131 775 1997 2.590 0.582 0.119 0.034 19 1.6 G_and_S_cingul-Mid-Post 492 336 852 2.587 0.664 0.147 0.030 9 0.8 G_cingul-Post-dorsal 303 198 440 2.068 0.576 0.134 0.044 6 0.5 G_cingul-Post-ventral 1762 1118 2531 1.953 0.470 0.143 0.037 27 2.5 G_cuneus 1044 721 2452 2.597 0.495 0.126 0.034 13 1.5 G_front_inf-Opercular 313 229 870 2.807 0.436 0.149 0.032 5 0.4 G_front_inf-Orbital 882 667 2471 2.737 0.555 0.151 0.039 16 1.5 G_front_inf-Triangul 3161 2642 9600 2.652 0.600 0.156 0.042 75 5.3 G_front_middle 5002 3932 14925 2.815 0.703 0.144 0.043 85 8.8 G_front_sup 668 465 1748 3.300 0.810 0.138 0.044 10 1.2 G_Ins_lg_and_S_cent_ins 590 405 1992 3.804 0.730 0.152 0.055 9 1.2 G_insular_short 1647 1110 3921 2.620 0.536 0.142 0.041 27 2.6 G_occipital_middle 1107 750 2136 2.405 0.647 0.139 0.035 14 1.5 G_occipital_sup 1545 1074 3884 2.749 0.520 0.133 0.035 28 2.1 G_oc-temp_lat-fusifor 2914 1881 4732 2.117 0.528 0.137 0.041 48 4.6 G_oc-temp_med-Lingual 1484 964 3282 2.611 0.754 0.115 0.038 17 2.1 G_oc-temp_med-Parahip 1685 1283 5022 2.854 0.773 0.146 0.042 27 2.5 G_orbital 2146 1656 5418 2.604 0.483 0.150 0.036 44 3.0 G_pariet_inf-Angular 2297 1674 5212 2.504 0.541 0.135 0.031 31 2.8 G_pariet_inf-Supramar 2208 1664 5299 2.564 0.464 0.141 0.036 34 3.4 G_parietal_sup 2125 1313 3395 2.088 0.524 0.106 0.028 23 1.9 G_postcentral 2406 1596 5526 2.617 0.541 0.130 0.038 32 3.5 G_precentral 2273 1697 5608 2.697 0.562 0.158 0.043 42 3.7 G_precuneus 794 594 2329 2.725 0.914 0.151 0.046 15 1.2 G_rectus 729 480 667 1.585 0.812 0.155 0.069 20 2.4 G_subcallosal 567 265 805 2.339 0.521 0.087 0.029 5 0.6 G_temp_sup-G_T_transv 1940 1314 5424 2.972 0.569 0.125 0.030 30 2.2 G_temp_sup-Lateral 720 484 1416 2.639 0.577 0.059 0.011 1 0.3 G_temp_sup-Plan_polar 910 625 1590 2.345 0.530 0.103 0.025 8 1.0 G_temp_sup-Plan_tempo 1791 1452 5867 2.890 0.773 0.147 0.040 33 3.0 G_temporal_inf 2306 1599 5904 2.811 0.605 0.127 0.032 37 2.8 G_temporal_middle 219 154 254 1.731 0.347 0.091 0.017 1 0.1 Lat_Fis-ant-Horizont 348 246 501 2.279 0.334 0.078 0.013 1 0.2 Lat_Fis-ant-Vertical 1065 728 1366 2.235 0.527 0.112 0.028 6 1.3 Lat_Fis-post 1893 1217 2514 1.893 0.466 0.132 0.033 23 2.5 Pole_occipital 1344 1127 5979 3.245 0.858 0.163 0.054 28 2.8 Pole_temporal 2342 1573 2383 1.654 0.552 0.119 0.029 19 3.0 S_calcarine 3533 2481 4344 2.003 0.599 0.109 0.026 23 4.0 S_central 1023 679 1366 2.367 0.330 0.092 0.013 4 0.7 S_cingul-Marginalis 413 281 668 2.764 0.663 0.097 0.030 2 0.5 S_circular_insula_ant 1669 1085 2471 2.485 0.890 0.080 0.017 6 1.3 S_circular_insula_inf 1591 1062 2198 2.397 0.563 0.099 0.025 7 1.8 S_circular_insula_sup 808 556 1366 2.478 0.722 0.098 0.020 6 0.8 S_collat_transv_ant 351 268 496 2.147 0.374 0.136 0.029 2 0.6 S_collat_transv_post 1992 1353 2925 2.214 0.426 0.098 0.020 11 1.7 S_front_inf 956 691 1503 2.226 0.496 0.128 0.027 9 1.2 S_front_middle 1900 1314 3213 2.508 0.434 0.099 0.022 9 1.7 S_front_sup 291 209 438 2.257 0.427 0.108 0.022 1 0.3 S_interm_prim-Jensen 2453 1676 3555 2.361 0.488 0.111 0.026 18 2.9 S_intrapariet_and_P_trans 917 661 1272 2.252 0.386 0.129 0.028 7 1.1 S_oc_middle_and_Lunatus 1111 778 1718 2.569 0.417 0.121 0.025 9 1.2 S_oc_sup_and_transversal 552 401 800 2.414 0.395 0.118 0.024 3 0.7 S_occipital_ant 714 499 1111 2.415 0.413 0.104 0.017 3 0.6 S_oc-temp_lat 2001 1411 2816 2.201 0.525 0.107 0.020 11 1.8 S_oc-temp_med_and_Lingual 279 208 405 2.173 0.338 0.128 0.030 2 0.4 S_orbital_lateral 560 398 735 2.101 0.622 0.134 0.030 5 0.8 S_orbital_med-olfact 1066 788 2254 2.727 0.742 0.141 0.033 10 1.7 S_orbital-H_Shaped 1367 944 2120 2.504 0.504 0.117 0.024 10 1.4 S_parieto_occipital 645 413 682 2.057 1.031 0.103 0.027 6 0.7 S_pericallosal 2769 1916 3889 2.097 0.414 0.100 0.019 18 2.5 S_postcentral 1478 985 2166 2.428 0.453 0.096 0.018 8 1.2 S_precentral-inf-part 1196 809 1868 2.481 0.486 0.092 0.019 5 1.0 S_precentral-sup-part 787 587 1406 2.550 0.758 0.154 0.033 13 1.1 S_suborbital 735 501 1262 2.566 0.420 0.126 0.035 10 0.9 S_subparietal 1257 921 1921 2.313 0.543 0.127 0.022 11 1.4 S_temporal_inf 5045 3363 7745 2.403 0.488 0.092 0.018 26 3.9 S_temporal_sup 304 212 361 1.887 0.465 0.109 0.021 2 0.3 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 218086 Total vertex volume 217784 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 682 530 1680 2.436 0.682 0.146 0.040 12 1.1 G_and_S_frontomargin 1237 873 2489 2.549 0.535 0.141 0.031 15 1.6 G_and_S_occipital_inf 1487 939 2640 2.347 0.527 0.119 0.030 17 1.8 G_and_S_paracentral 1183 807 2642 2.835 0.519 0.117 0.026 12 1.3 G_and_S_subcentral 845 686 2715 2.810 0.778 0.142 0.039 16 1.5 G_and_S_transv_frontopol 2330 1690 5117 2.627 0.708 0.123 0.029 30 2.8 G_and_S_cingul-Ant 1225 826 2025 2.455 0.510 0.121 0.030 16 1.4 G_and_S_cingul-Mid-Ant 1155 798 1955 2.539 0.542 0.125 0.027 14 1.3 G_and_S_cingul-Mid-Post 247 162 367 2.326 0.775 0.139 0.041 5 0.4 G_cingul-Post-dorsal 295 184 437 2.343 0.641 0.132 0.044 4 0.5 G_cingul-Post-ventral 2111 1379 3119 1.976 0.467 0.140 0.036 30 3.1 G_cuneus 1103 861 3324 2.890 0.568 0.153 0.043 20 1.8 G_front_inf-Opercular 280 213 871 2.797 0.539 0.136 0.033 4 0.4 G_front_inf-Orbital 675 505 1850 2.716 0.527 0.121 0.029 8 0.7 G_front_inf-Triangul 2880 2403 8847 2.718 0.644 0.166 0.046 65 5.4 G_front_middle 5130 4098 15308 2.757 0.753 0.152 0.044 96 9.6 G_front_sup 682 488 1798 3.080 0.656 0.137 0.038 12 0.9 G_Ins_lg_and_S_cent_ins 539 387 1888 3.849 0.793 0.146 0.056 8 1.0 G_insular_short 1812 1268 4406 2.798 0.459 0.127 0.029 28 2.0 G_occipital_middle 1303 837 2466 2.369 0.540 0.115 0.026 16 1.4 G_occipital_sup 1698 1180 4252 2.785 0.585 0.128 0.028 27 1.8 G_oc-temp_lat-fusifor 3010 2006 5002 2.127 0.551 0.131 0.037 43 4.2 G_oc-temp_med-Lingual 1454 937 3674 2.923 0.766 0.126 0.041 23 1.9 G_oc-temp_med-Parahip 1897 1479 6116 2.965 0.737 0.150 0.046 32 3.2 G_orbital 2563 1799 6593 2.761 0.441 0.145 0.037 45 3.8 G_pariet_inf-Angular 2156 1532 4982 2.669 0.571 0.124 0.028 27 2.4 G_pariet_inf-Supramar 1897 1352 4639 2.677 0.461 0.134 0.032 28 2.4 G_parietal_sup 2221 1264 3324 2.115 0.522 0.095 0.026 22 2.1 G_postcentral 2402 1500 5706 2.873 0.494 0.117 0.032 26 2.9 G_precentral 2049 1604 5286 2.636 0.544 0.158 0.043 44 3.7 G_precuneus 812 636 2197 2.554 0.741 0.169 0.058 26 1.8 G_rectus 424 274 589 2.200 0.988 0.107 0.036 5 0.5 G_subcallosal 488 220 779 2.580 0.423 0.105 0.031 5 0.5 G_temp_sup-G_T_transv 1869 1170 4864 2.814 0.620 0.112 0.028 29 1.8 G_temp_sup-Lateral 887 589 1654 2.597 0.753 0.071 0.018 3 0.6 G_temp_sup-Plan_polar 788 509 1487 2.674 0.567 0.086 0.016 5 0.5 G_temp_sup-Plan_tempo 2014 1557 6357 2.978 0.751 0.152 0.046 39 3.2 G_temporal_inf 2559 1762 7127 2.982 0.575 0.123 0.030 39 3.1 G_temporal_middle 264 179 312 1.985 0.462 0.089 0.014 1 0.2 Lat_Fis-ant-Horizont 171 137 254 1.968 0.427 0.116 0.016 1 0.1 Lat_Fis-ant-Vertical 1452 956 1846 2.280 0.462 0.100 0.022 7 1.4 Lat_Fis-post 3356 2108 4133 1.864 0.491 0.133 0.036 45 4.7 Pole_occipital 1639 1301 6300 3.128 0.752 0.151 0.040 27 2.5 Pole_temporal 2976 1929 3130 1.786 0.662 0.133 0.039 82 5.2 S_calcarine 3132 2190 3806 2.023 0.630 0.100 0.022 15 3.2 S_central 1120 774 1683 2.484 0.356 0.094 0.013 5 0.7 S_cingul-Marginalis 477 319 779 2.859 0.727 0.119 0.044 5 0.8 S_circular_insula_ant 1400 926 1695 2.111 0.591 0.080 0.017 5 0.9 S_circular_insula_inf 1227 798 1847 2.671 0.503 0.090 0.020 4 1.1 S_circular_insula_sup 1115 818 1818 2.212 0.580 0.112 0.025 10 1.3 S_collat_transv_ant 301 224 399 2.145 0.389 0.127 0.020 2 0.3 S_collat_transv_post 1655 1167 2447 2.174 0.505 0.109 0.027 13 2.1 S_front_inf 1336 1037 2726 2.313 0.640 0.128 0.029 15 1.6 S_front_middle 2130 1489 3611 2.468 0.456 0.104 0.021 13 2.0 S_front_sup 325 233 557 2.376 0.516 0.115 0.027 3 0.4 S_interm_prim-Jensen 2416 1695 4113 2.608 0.414 0.112 0.022 17 2.2 S_intrapariet_and_P_trans 648 490 1034 2.581 0.406 0.140 0.027 6 0.8 S_oc_middle_and_Lunatus 1059 720 1572 2.567 0.322 0.098 0.020 6 0.8 S_oc_sup_and_transversal 559 411 893 2.415 0.468 0.104 0.024 3 0.5 S_occipital_ant 762 545 1215 2.486 0.430 0.099 0.016 3 0.5 S_oc-temp_lat 1735 1304 2865 2.336 0.527 0.116 0.020 14 1.4 S_oc-temp_med_and_Lingual 274 210 544 2.224 0.718 0.134 0.025 3 0.3 S_orbital_lateral 615 431 986 2.215 0.741 0.111 0.021 4 0.5 S_orbital_med-olfact 1066 808 1998 2.387 0.610 0.145 0.039 12 1.8 S_orbital-H_Shaped 1949 1352 3030 2.428 0.446 0.110 0.022 15 1.9 S_parieto_occipital 559 348 639 2.375 1.157 0.103 0.026 6 0.8 S_pericallosal 2717 1765 3550 2.317 0.460 0.089 0.015 14 1.9 S_postcentral 1290 882 1885 2.474 0.442 0.105 0.022 7 1.3 S_precentral-inf-part 1306 877 2032 2.561 0.449 0.098 0.019 6 1.2 S_precentral-sup-part 318 224 430 2.017 0.589 0.115 0.015 2 0.3 S_suborbital 971 678 1787 2.487 0.522 0.111 0.022 6 0.9 S_subparietal 1193 841 1850 2.619 0.404 0.121 0.023 8 1.3 S_temporal_inf 6236 4197 9119 2.368 0.486 0.091 0.018 31 4.7 S_temporal_sup 286 195 330 1.867 0.306 0.111 0.018 2 0.3 S_temporal_transverse PIDs (857281 857284) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Oct 9 17:27:23 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 3 rh Wed Oct 9 17:27:23 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma rh white Waiting for PID 857557 of (857557 857560) to complete... Waiting for PID 857560 of (857557 857560) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208388 Total vertex volume 208141 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1150 845 2443 2.910 0.799 0.158 0.049 22 2.6 caudalanteriorcingulate 2883 2128 6162 2.540 0.480 0.122 0.030 30 3.8 caudalmiddlefrontal 2405 1584 3465 2.091 0.520 0.135 0.032 30 3.1 cuneus 600 409 1303 2.534 0.892 0.126 0.045 8 1.1 entorhinal 3449 2439 7035 2.554 0.603 0.123 0.028 42 3.9 fusiform 5316 3893 11032 2.530 0.552 0.132 0.032 71 7.1 inferiorparietal 3747 2885 10081 2.718 0.743 0.138 0.036 54 5.9 inferiortemporal 1156 750 1545 2.136 0.790 0.119 0.031 15 1.6 isthmuscingulate 5966 4008 10068 2.299 0.541 0.136 0.033 73 7.8 lateraloccipital 3221 2365 7803 2.746 0.827 0.140 0.037 42 4.8 lateralorbitofrontal 4269 2861 6409 2.050 0.556 0.130 0.035 56 6.0 lingual 2003 1455 4338 2.478 0.851 0.145 0.040 35 3.0 medialorbitofrontal 5224 3628 11180 2.622 0.611 0.112 0.025 59 5.3 middletemporal 1173 733 2135 2.432 0.635 0.084 0.020 6 0.9 parahippocampal 2191 1368 3952 2.565 0.598 0.099 0.024 17 2.1 paracentral 1768 1200 3313 2.487 0.463 0.107 0.025 15 1.8 parsopercularis 770 577 1697 2.490 0.579 0.134 0.032 9 1.0 parsorbitalis 1941 1396 3925 2.416 0.569 0.118 0.027 21 2.2 parstriangularis 2012 1306 2042 1.622 0.471 0.128 0.035 21 3.0 pericalcarine 6549 4372 10203 2.099 0.618 0.108 0.026 57 6.8 postcentral 1228 875 2379 2.626 0.572 0.131 0.034 24 1.9 posteriorcingulate 6854 4686 12586 2.477 0.572 0.119 0.031 63 8.8 precentral 4129 2988 8438 2.585 0.535 0.139 0.035 55 5.6 precuneus 1725 1276 3402 2.451 1.058 0.153 0.051 38 4.4 rostralanteriorcingulate 4280 3260 9867 2.458 0.609 0.130 0.033 57 5.5 rostralmiddlefrontal 8048 6202 20623 2.651 0.675 0.134 0.036 120 11.9 superiorfrontal 4921 3506 9603 2.498 0.464 0.123 0.029 55 6.0 superiorparietal 7190 4870 15717 2.630 0.678 0.100 0.024 64 6.7 superiortemporal 4629 3309 8380 2.338 0.515 0.125 0.029 52 5.6 supramarginal 750 396 940 2.180 0.548 0.096 0.028 6 0.8 transversetemporal 2698 1821 6078 3.061 0.973 0.113 0.035 24 3.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 218086 Total vertex volume 217784 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 907 629 1632 2.754 0.804 0.124 0.027 15 1.2 caudalanteriorcingulate 3026 2191 6240 2.540 0.497 0.124 0.028 31 3.6 caudalmiddlefrontal 2696 1765 3955 2.082 0.452 0.132 0.031 33 3.4 cuneus 655 461 1803 2.976 0.777 0.129 0.043 9 0.9 entorhinal 3372 2483 7167 2.553 0.626 0.126 0.027 43 3.9 fusiform 6772 4806 13604 2.568 0.506 0.125 0.029 80 7.9 inferiorparietal 4467 3339 11467 2.798 0.680 0.136 0.034 64 5.8 inferiortemporal 891 543 1197 2.097 0.741 0.111 0.031 9 1.1 isthmuscingulate 6450 4298 10454 2.264 0.593 0.130 0.031 75 8.1 lateraloccipital 3238 2438 7867 2.679 0.742 0.149 0.042 48 5.5 lateralorbitofrontal 4956 3365 7373 2.062 0.586 0.134 0.036 67 7.4 lingual 1835 1367 3967 2.399 0.798 0.145 0.044 40 3.1 medialorbitofrontal 5381 3697 12070 2.802 0.592 0.105 0.023 50 5.1 middletemporal 1158 744 2319 2.640 0.740 0.104 0.025 14 1.0 parahippocampal 2275 1454 3897 2.508 0.506 0.114 0.027 21 2.5 paracentral 1781 1341 4098 2.585 0.581 0.131 0.033 21 2.3 parsopercularis 768 576 1927 2.540 0.670 0.134 0.038 10 1.1 parsorbitalis 1536 1107 3187 2.411 0.619 0.111 0.026 14 1.5 parstriangularis 2328 1465 2379 1.714 0.540 0.133 0.043 74 3.9 pericalcarine 6880 4353 10151 2.136 0.590 0.096 0.021 52 6.1 postcentral 991 696 1917 2.626 0.625 0.128 0.029 15 1.2 posteriorcingulate 6180 4133 11856 2.681 0.559 0.111 0.028 50 7.0 precentral 4830 3580 9738 2.511 0.537 0.128 0.031 61 6.1 precuneus 935 657 2378 2.676 0.973 0.120 0.030 12 1.1 rostralanteriorcingulate 3957 3202 9850 2.492 0.705 0.151 0.040 73 6.8 rostralmiddlefrontal 10024 7676 24820 2.610 0.688 0.133 0.035 143 14.9 superiorfrontal 4897 3367 9680 2.626 0.423 0.120 0.027 55 5.1 superiorparietal 7056 4595 14832 2.574 0.695 0.093 0.021 58 5.5 superiortemporal 4604 3211 8811 2.549 0.532 0.116 0.025 44 4.9 supramarginal 627 321 881 2.353 0.500 0.109 0.031 6 0.7 transversetemporal 2951 2001 6265 2.901 0.863 0.109 0.031 26 3.3 insula PIDs (857557 857560) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Wed Oct 9 17:27:34 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/ASegStatsLUT.txt --subject PIB23-310_VYr0_Bay3prisma setting seed for random number genererator to 1234 7.3.2 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/ASegStatsLUT.txt --subject PIB23-310_VYr0_Bay3prisma sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) Computing euler number orig.nofix lheno = -82, rheno = -66 orig.nofix lhholes = 42, rhholes = 34 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2024:10:09:17:27:34 mri_segstats N 32 e 63.43 S 0.61 U 238.56 P 377% M 282756 F 2 R 980896 W 0 c 20705 w 162 I 0 O 24 L 4.18 3.45 4.89 @#@FSLOADPOST 2024:10:09:17:28:38 mri_segstats N 32 4.42 3.70 4.88 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed Oct 9 17:28:38 CDT 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 858074 of (858074 858077 858081 858084 858088) to complete... Waiting for PID 858077 of (858074 858077 858081 858084 858088) to complete... Waiting for PID 858081 of (858074 858077 858081 858084 858088) to complete... Waiting for PID 858084 of (858074 858077 858081 858084 858088) to complete... Waiting for PID 858088 of (858074 858077 858081 858084 858088) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4241 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8016 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4171 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 117 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6100 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5932 mri_label2label: Done PIDs (858074 858077 858081 858084 858088) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 858198 of (858198 858201 858205 858208) to complete... Waiting for PID 858201 of (858198 858201 858205 858208) to complete... Waiting for PID 858205 of (858198 858201 858205 858208) to complete... Waiting for PID 858208 of (858198 858201 858205 858208) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4211 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 279 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13868 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4232 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 193 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3615 mri_label2label: Done PIDs (858198 858201 858205 858208) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 858308 of (858308 858311 858314 858318 858321) to complete... Waiting for PID 858311 of (858308 858311 858314 858318 858321) to complete... Waiting for PID 858314 of (858308 858311 858314 858318 858321) to complete... Waiting for PID 858318 of (858308 858311 858314 858318 858321) to complete... Waiting for PID 858321 of (858308 858311 858314 858318 858321) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 788 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5429 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 1194 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9308 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2129 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1368 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1266 mri_label2label: Done PIDs (858308 858311 858314 858318 858321) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 858444 of (858444 858447 858451 858454 858457 858461 858464 858467) to complete... Waiting for PID 858447 of (858444 858447 858451 858454 858457 858461 858464 858467) to complete... Waiting for PID 858451 of (858444 858447 858451 858454 858457 858461 858464 858467) to complete... Waiting for PID 858454 of (858444 858447 858451 858454 858457 858461 858464 858467) to complete... Waiting for PID 858457 of (858444 858447 858451 858454 858457 858461 858464 858467) to complete... Waiting for PID 858461 of (858444 858447 858451 858454 858457 858461 858464 858467) to complete... Waiting for PID 858464 of (858444 858447 858451 858454 858457 858461 858464 858467) to complete... Waiting for PID 858467 of (858444 858447 858451 858454 858457 858461 858464 858467) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 414 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 494 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 703 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 767 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1873 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 91 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1964 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2101 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3877 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 682 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4559 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2919 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 439 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3358 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1286 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 250 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1536 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1006 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 218 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1224 mri_label2label: Done PIDs (858444 858447 858451 858454 858457 858461 858464 858467) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt Number of ctab entries 9 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 101181 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.mpm.vpnl.annot @#@FSTIME 2024:10:09:17:29:02 mris_label2annot N 26 e 0.58 S 0.07 U 0.66 P 126% M 134396 F 0 R 36586 W 0 c 68 w 176 I 0 O 1800 L 5.18 3.94 4.93 @#@FSLOADPOST 2024:10:09:17:29:02 mris_label2annot N 26 5.18 3.94 4.93 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 858645 of (858645 858648 858653 858656 858659) to complete... Waiting for PID 858648 of (858645 858648 858653 858656 858659) to complete... Waiting for PID 858653 of (858645 858648 858653 858656 858659) to complete... Waiting for PID 858656 of (858645 858648 858653 858656 858659) to complete... Waiting for PID 858659 of (858645 858648 858653 858656 858659) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1064 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2138 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1514 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2041 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2379 mri_label2label: Done PIDs (858645 858648 858653 858656 858659) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 858757 of (858757 858760 858763 858767) to complete... Waiting for PID 858760 of (858757 858760 858763 858767) to complete... Waiting for PID 858763 of (858757 858760 858763 858767) to complete... Waiting for PID 858767 of (858757 858760 858763 858767) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1633 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7140 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1928 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1213 mri_label2label: Done PIDs (858757 858760 858763 858767) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 858864 of (858864 858868 858872 858875 858878) to complete... Waiting for PID 858868 of (858864 858868 858872 858875 858878) to complete... Waiting for PID 858872 of (858864 858868 858872 858875 858878) to complete... Waiting for PID 858875 of (858864 858868 858872 858875 858878) to complete... Waiting for PID 858878 of (858864 858868 858872 858875 858878) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 626 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4031 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 518 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 3852 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 551 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 497 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 114660 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 489 mri_label2label: Done PIDs (858864 858868 858872 858875 858878) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 79055 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.BA_exvivo.annot @#@FSTIME 2024:10:09:17:29:17 mris_label2annot N 38 e 0.57 S 0.09 U 0.67 P 134% M 134876 F 1 R 36594 W 0 c 69 w 203 I 0 O 1800 L 5.21 4.01 4.93 @#@FSLOADPOST 2024:10:09:17:29:17 mris_label2annot N 38 5.21 4.01 4.93 mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 93110 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2024:10:09:17:29:18 mris_label2annot N 38 e 0.54 S 0.10 U 0.63 P 138% M 134556 F 0 R 36565 W 0 c 65 w 216 I 0 O 1800 L 5.21 4.01 4.93 @#@FSLOADPOST 2024:10:09:17:29:18 mris_label2annot N 38 5.21 4.01 4.93 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 208388 Total vertex volume 208141 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1091 635 1949 2.285 0.535 0.124 0.036 17 1.3 BA1_exvivo 3499 2426 5799 2.196 0.521 0.104 0.021 27 3.1 BA2_exvivo 1097 820 1124 1.734 0.285 0.133 0.027 8 1.4 BA3a_exvivo 2258 1528 3294 1.910 0.656 0.104 0.025 18 2.4 BA3b_exvivo 1485 932 3087 2.743 0.588 0.110 0.031 14 1.9 BA4a_exvivo 1463 958 2328 2.551 0.501 0.109 0.034 12 1.9 BA4p_exvivo 7366 5391 17422 2.635 0.597 0.131 0.037 95 11.3 BA6_exvivo 1898 1277 3600 2.521 0.469 0.109 0.027 16 2.1 BA44_exvivo 2386 1746 4957 2.400 0.548 0.117 0.027 26 2.7 BA45_exvivo 3405 2206 3707 1.638 0.463 0.128 0.037 39 4.9 V1_exvivo 6719 4499 10315 2.097 0.523 0.139 0.034 88 9.4 V2_exvivo 1606 1093 3119 2.514 0.460 0.128 0.030 19 1.9 MT_exvivo 691 509 1695 2.727 0.834 0.125 0.038 6 1.0 perirhinal_exvivo 641 428 1352 2.439 0.902 0.110 0.036 7 1.0 entorhinal_exvivo @#@FSTIME 2024:10:09:17:29:18 mris_anatomical_stats N 12 e 3.12 S 0.27 U 4.24 P 144% M 406168 F 2 R 208681 W 0 c 411 w 289 I 0 O 136 L 5.21 4.01 4.93 @#@FSLOADPOST 2024:10:09:17:29:21 mris_anatomical_stats N 12 4.87 3.96 4.91 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 208388 Total vertex volume 208141 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 748 401 1243 2.234 0.421 0.128 0.040 12 0.9 BA1_exvivo 1501 1015 2185 2.018 0.445 0.083 0.015 7 0.9 BA2_exvivo 917 688 920 1.726 0.273 0.137 0.030 8 1.2 BA3a_exvivo 1463 993 1601 1.585 0.314 0.088 0.019 8 1.2 BA3b_exvivo 1460 969 2950 2.672 0.584 0.116 0.035 13 2.2 BA4a_exvivo 1236 808 1956 2.546 0.471 0.111 0.033 10 1.6 BA4p_exvivo 4021 2848 9556 2.675 0.593 0.125 0.035 48 5.4 BA6_exvivo 1190 808 2386 2.557 0.491 0.118 0.030 12 1.6 BA44_exvivo 906 695 2337 2.622 0.566 0.124 0.030 12 1.0 BA45_exvivo 3615 2340 4020 1.651 0.465 0.126 0.037 41 5.2 V1_exvivo 3355 2235 4612 1.940 0.463 0.144 0.038 45 5.2 V2_exvivo 438 308 793 2.405 0.427 0.124 0.026 3 0.7 MT_exvivo 313 214 713 2.892 0.771 0.135 0.041 3 0.5 perirhinal_exvivo 387 273 758 2.327 0.921 0.105 0.023 2 0.4 entorhinal_exvivo @#@FSTIME 2024:10:09:17:29:22 mris_anatomical_stats N 12 e 3.21 S 0.29 U 4.31 P 143% M 405812 F 2 R 211424 W 0 c 429 w 262 I 0 O 136 L 4.87 3.96 4.91 @#@FSLOADPOST 2024:10:09:17:29:25 mris_anatomical_stats N 12 4.64 3.92 4.90 #-------------------------------------------- #@# BA_exvivo Labels rh Wed Oct 9 17:29:25 CDT 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 859180 of (859180 859183 859186 859190 859193) to complete... Waiting for PID 859183 of (859180 859183 859186 859190 859193) to complete... Waiting for PID 859186 of (859180 859183 859186 859190 859193) to complete... Waiting for PID 859190 of (859180 859183 859186 859190 859193) to complete... Waiting for PID 859193 of (859180 859183 859186 859190 859193) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6872 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4051 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4641 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5913 mri_label2label: Done PIDs (859180 859183 859186 859190 859193) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 859301 of (859301 859304 859308 859311) to complete... Waiting for PID 859304 of (859301 859304 859308 859311) to complete... Waiting for PID 859308 of (859301 859304 859308 859311) to complete... Waiting for PID 859311 of (859301 859304 859308 859311) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 160 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4633 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 258 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12514 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7004 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5489 mri_label2label: Done PIDs (859301 859304 859308 859311) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 859406 of (859406 859410 859413 859417 859420) to complete... Waiting for PID 859410 of (859406 859410 859413 859417 859420) to complete... Waiting for PID 859413 of (859406 859410 859413 859417 859420) to complete... Waiting for PID 859417 of (859406 859410 859413 859417 859420) to complete... Waiting for PID 859420 of (859406 859410 859413 859417 859420) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 1430 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6157 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 2157 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10173 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2128 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1124 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 816 mri_label2label: Done PIDs (859406 859410 859413 859417 859420) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 859542 of (859542 859545 859549 859552 859556 859559 859562 859565) to complete... Waiting for PID 859545 of (859542 859545 859549 859552 859556 859559 859562 859565) to complete... Waiting for PID 859549 of (859542 859545 859549 859552 859556 859559 859562 859565) to complete... Waiting for PID 859552 of (859542 859545 859549 859552 859556 859559 859562 859565) to complete... Waiting for PID 859556 of (859542 859545 859549 859552 859556 859559 859562 859565) to complete... Waiting for PID 859559 of (859542 859545 859549 859552 859556 859559 859562 859565) to complete... Waiting for PID 859562 of (859542 859545 859549 859552 859556 859559 859562 859565) to complete... Waiting for PID 859565 of (859542 859545 859549 859552 859556 859559 859562 859565) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 541 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 644 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 721 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 827 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1523 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1602 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1586 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1710 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3667 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 1095 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4762 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2719 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 859 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3578 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1228 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 450 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1678 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1025 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1353 mri_label2label: Done PIDs (859542 859545 859549 859552 859556 859559 859562 859565) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt Number of ctab entries 9 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 104288 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.mpm.vpnl.annot @#@FSTIME 2024:10:09:17:29:48 mris_label2annot N 26 e 0.55 S 0.08 U 0.69 P 141% M 139244 F 1 R 38014 W 0 c 71 w 169 I 0 O 1864 L 4.92 4.03 4.91 @#@FSLOADPOST 2024:10:09:17:29:48 mris_label2annot N 26 4.92 4.03 4.91 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 859752 of (859752 859755 859759 859762 859765) to complete... Waiting for PID 859755 of (859752 859755 859759 859762 859765) to complete... Waiting for PID 859759 of (859752 859755 859759 859762 859765) to complete... Waiting for PID 859762 of (859752 859755 859759 859762 859765) to complete... Waiting for PID 859765 of (859752 859755 859759 859762 859765) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 941 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2751 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 5 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1703 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2226 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1427 mri_label2label: Done PIDs (859752 859755 859759 859762 859765) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 859864 of (859864 859867 859870 859873) to complete... Waiting for PID 859867 of (859864 859867 859870 859873) to complete... Waiting for PID 859870 of (859864 859867 859870 859873) to complete... Waiting for PID 859873 of (859864 859867 859870 859873) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1599 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7030 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1044 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1194 mri_label2label: Done PIDs (859864 859867 859870 859873) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 859966 of (859966 859969 859973 859976 859979) to complete... Waiting for PID 859969 of (859966 859969 859973 859976 859979) to complete... Waiting for PID 859973 of (859966 859969 859973 859976 859979) to complete... Waiting for PID 859976 of (859966 859969 859973 859976 859979) to complete... Waiting for PID 859979 of (859966 859969 859973 859976 859979) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 958 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4190 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 1171 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4608 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 315 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 747 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 118918 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 320 mri_label2label: Done PIDs (859966 859969 859973 859976 859979) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 81627 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.BA_exvivo.annot @#@FSTIME 2024:10:09:17:30:02 mris_label2annot N 38 e 0.64 S 0.09 U 0.71 P 125% M 139616 F 2 R 38060 W 0 c 77 w 269 I 0 O 1864 L 5.24 4.14 4.93 @#@FSLOADPOST 2024:10:09:17:30:03 mris_label2annot N 38 5.24 4.14 4.93 mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 96611 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2024:10:09:17:30:03 mris_label2annot N 38 e 0.57 S 0.08 U 0.69 P 135% M 139436 F 2 R 38064 W 0 c 77 w 251 I 0 O 1864 L 5.24 4.14 4.93 @#@FSLOADPOST 2024:10:09:17:30:04 mris_label2annot N 38 5.24 4.14 4.93 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 218086 Total vertex volume 217784 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1000 510 1655 2.338 0.488 0.115 0.038 15 1.3 BA1_exvivo 3232 2094 4653 2.256 0.459 0.084 0.015 18 2.1 BA2_exvivo 1076 766 1115 1.819 0.431 0.109 0.022 6 1.1 BA3a_exvivo 2037 1332 2532 1.751 0.445 0.093 0.020 13 1.7 BA3b_exvivo 1473 902 2724 2.653 0.541 0.110 0.032 13 1.9 BA4a_exvivo 1333 870 2230 2.693 0.553 0.111 0.033 11 1.7 BA4p_exvivo 6574 4774 15101 2.653 0.607 0.131 0.034 84 9.7 BA6_exvivo 2773 1983 5708 2.621 0.550 0.124 0.031 29 3.6 BA44_exvivo 2958 2235 6657 2.412 0.625 0.126 0.030 34 3.6 BA45_exvivo 4101 2595 4936 1.816 0.538 0.137 0.044 102 7.4 V1_exvivo 7865 5197 11262 2.023 0.558 0.135 0.033 103 10.6 V2_exvivo 1801 1270 3329 2.567 0.503 0.128 0.028 20 2.1 MT_exvivo 416 299 940 3.048 0.609 0.121 0.026 3 0.5 perirhinal_exvivo 652 441 1780 2.893 0.811 0.107 0.039 5 0.7 entorhinal_exvivo @#@FSTIME 2024:10:09:17:30:04 mris_anatomical_stats N 12 e 3.25 S 0.29 U 4.31 P 141% M 420356 F 3 R 211743 W 0 c 420 w 274 I 0 O 136 L 5.24 4.14 4.93 @#@FSLOADPOST 2024:10:09:17:30:07 mris_anatomical_stats N 12 4.98 4.11 4.92 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 218086 Total vertex volume 217784 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 738 358 1033 2.094 0.476 0.105 0.036 11 0.8 BA1_exvivo 1946 1235 2834 2.191 0.499 0.077 0.013 10 1.3 BA2_exvivo 975 707 983 1.808 0.397 0.113 0.021 5 1.0 BA3a_exvivo 1598 1056 1725 1.629 0.334 0.086 0.017 8 1.2 BA3b_exvivo 908 546 1772 2.674 0.546 0.117 0.038 10 1.3 BA4a_exvivo 1144 743 1961 2.804 0.561 0.111 0.035 9 1.7 BA4p_exvivo 4237 2986 9439 2.686 0.566 0.122 0.029 47 5.3 BA6_exvivo 697 548 1979 2.725 0.588 0.156 0.046 12 1.3 BA44_exvivo 769 618 2075 2.548 0.592 0.134 0.030 10 0.8 BA45_exvivo 3939 2498 4692 1.822 0.560 0.136 0.044 99 7.1 V1_exvivo 4405 2824 5786 1.909 0.522 0.138 0.036 62 6.5 V2_exvivo 284 195 534 2.248 0.495 0.132 0.034 4 0.4 MT_exvivo 39 30 77 3.183 0.323 0.136 0.026 0 0.0 perirhinal_exvivo 628 437 1507 2.854 0.670 0.104 0.030 4 0.6 entorhinal_exvivo @#@FSTIME 2024:10:09:17:30:07 mris_anatomical_stats N 12 e 3.41 S 0.31 U 4.71 P 147% M 420232 F 4 R 246023 W 0 c 459 w 329 I 0 O 136 L 4.98 4.11 4.92 @#@FSLOADPOST 2024:10:09:17:30:11 mris_anatomical_stats N 12 4.74 4.07 4.90 Started at Wed Oct 9 15:50:40 CDT 2024 Ended at Wed Oct 9 17:30:11 CDT 2024 #@#%# recon-all-run-time-hours 1.659 recon-all -s PIB23-310_VYr0_Bay3prisma finished without error at Wed Oct 9 17:30:11 CDT 2024 #New# invocation of recon-all Fri Oct 11 16:08:50 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/recon-all -3T -parallel -s PIB23-310_VYr0_Bay3prisma -autorecon2 -autorecon3 subjid PIB23-310_VYr0_Bay3prisma setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Actual FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 build-stamp.txt: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 1029556 maxlocks unlimited maxsignal 1029556 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 251Gi 164Gi 38Gi 21Mi 48Gi 85Gi Swap: 111Gi 4.8Gi 106Gi ######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275) 7.3.2 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:50-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/11-21:08:51-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 #New# invocation of recon-all Mon Oct 14 11:35:05 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/recon-all -3T -parallel -s PIB23-310_VYr0_Bay3prisma -autorecon2-noaseg -autorecon3 subjid PIB23-310_VYr0_Bay3prisma setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Actual FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 build-stamp.txt: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 1029556 maxlocks unlimited maxsignal 1029556 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 251Gi 136Gi 31Gi 23Mi 83Gi 113Gi Swap: 111Gi 4.8Gi 106Gi ######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275) 7.3.2 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:05-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:06-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:06-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:06-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:06-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:06-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:07-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:07-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:07-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:07-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:08-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:08-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:08-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:08-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:08-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:08-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:08-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:09-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:09-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:09-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:09-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:09-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:09-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:10-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:10-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:10-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:10-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:11-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:11-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:11-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:11-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:11-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:11-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:11-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:11-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:12-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:12-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:12-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:12-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:13-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:13-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:13-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:13-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:13-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:13-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:14-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:14-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:14-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:14-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:14-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:14-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:15-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:15-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:15-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:15-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:15-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:15-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:16-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:16-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:16-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:16-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:16-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:16-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:16-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:17-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:17-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:17-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:17-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:17-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:17-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:17-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:17-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/10/14-16:35:18-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: grossens Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Mon Oct 14 11:35:18 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 1074 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 108 gm peak at 82 (82), valley at 58 (58) csf peak at 23, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 83 (83), valley at 65 (65) csf peak at 24, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 56 seconds. @#@FSTIME 2024:10:14:11:35:18 mri_normalize N 9 e 178.31 S 2.14 U 186.83 P 105% M 1210732 F 15 R 1470197 W 0 c 18674 w 217 I 4528 O 2744 L 114.70 89.65 63.27 @#@FSLOADPOST 2024:10:14:11:38:16 mri_normalize N 9 69.45 87.84 67.55 #-------------------------------------------- #@# Mask BFS Mon Oct 14 11:38:16 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1592378 voxels in mask (pct= 9.49) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:10:14:11:38:17 mri_mask N 5 e 1.35 S 0.04 U 1.50 P 114% M 74304 F 7 R 18791 W 0 c 143 w 91 I 2216 O 2728 L 69.45 87.84 67.55 @#@FSLOADPOST 2024:10:14:11:38:18 mri_mask N 5 69.45 87.84 67.55 #-------------------------------------------- #@# WM Segmentation Mon Oct 14 11:38:18 CDT 2024 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname chopin machine x86_64 user grossens input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 270 values in range Counting number of voxels in first frame Found 269 voxels in final mask Writing output to wm255.mgz Count: 269 268.999984 16777216 0.001603 mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname chopin machine x86_64 user grossens input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Writing output to wm1.mgz Count: -1 -1.000000 16777216 -0.000006 mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: -1 deletes, 269 fills cp wm.mgz wm.seg.mgz AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2024:10:14:11:38:23 AntsDenoiseImageFs N 4 e 57.30 S 0.24 U 55.68 P 97% M 351272 F 26 R 229323 W 0 c 5211 w 148 I 4104 O 2696 L 71.25 87.91 67.68 @#@FSLOADPOST 2024:10:14:11:39:20 AntsDenoiseImageFs N 4 47.49 77.98 65.52 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz preserving editing changes in output volume... wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (101.0): 101.4 +- 5.8 [79.0 --> 125.0] CCS GM (77.0) : 74.3 +- 14.0 [30.0 --> 95.0] white_mean 101.379 white_sigma 5.80253 gray_mean 74.2698 gray_sigma 14.0083 setting bottom of white matter range wm_low to 88.3 setting top of gray matter range gray_hi to 100.4 wm_low 88.2781 wm_hi 125 gray_low 30 gray_hi 100.379 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 88.2781 wm_hi 125 gray_low 30 gray_hi 100.379 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 100.379, wm_low = 88.2781 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=100.379, wmlow=88.2781 164851 voxels processed (0.98%) 83812 voxels white (0.50%) 81039 voxels non-white (0.48%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=83.2781, gray_hi=100.379, wsize=13 328590 voxels tested (1.96%) 55127 voxels changed (0.33%) 48144 multi-scale searches (0.29%) Recovering bright white MRIrecoverBrightWhite() wm_low 88.2781 wm_hi 125 slack 5.80253 pct_thresh 0.33 intensity_thresh 130.803 nvox_thresh 8.58 50 voxels tested (0.00%) 23 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=83.2781, hithr=100.379 smoothing input volume with sigma = 0.250 155152 voxels tested (0.92%) 17443 voxels changed (0.10%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 2746 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 2821 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 4531 filled MRIfindBrightNonWM(): 227 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:10:14:11:39:20 mri_segment N 6 e 99.48 S 0.36 U 98.62 P 99% M 162496 F 8 R 292189 W 0 c 9473 w 82 I 344 O 776 L 47.49 77.98 65.52 @#@FSLOADPOST 2024:10:14:11:41:00 mri_segment N 6 43.33 70.15 64.14 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.62 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 8594 additional wm voxels added 0 additional wm voxels added SEG EDIT: 180250 voxels turned on, 32995 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:10:14:11:41:00 mri_edit_wm_with_aseg N 5 e 37.53 S 0.45 U 38.61 P 104% M 464060 F 4 R 469523 W 0 c 3519 w 155 I 864 O 728 L 43.33 70.15 64.14 @#@FSLOADPOST 2024:10:14:11:41:37 mri_edit_wm_with_aseg N 5 30.79 64.05 62.32 mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 37 found - 37 modified | TOTAL: 37 pass 2 (xy+): 0 found - 37 modified | TOTAL: 37 pass 1 (xy-): 54 found - 54 modified | TOTAL: 91 pass 2 (xy-): 0 found - 54 modified | TOTAL: 91 pass 1 (yz+): 49 found - 49 modified | TOTAL: 140 pass 2 (yz+): 0 found - 49 modified | TOTAL: 140 pass 1 (yz-): 42 found - 42 modified | TOTAL: 182 pass 2 (yz-): 0 found - 42 modified | TOTAL: 182 pass 1 (xz+): 28 found - 28 modified | TOTAL: 210 pass 2 (xz+): 0 found - 28 modified | TOTAL: 210 pass 1 (xz-): 35 found - 35 modified | TOTAL: 245 pass 2 (xz-): 0 found - 35 modified | TOTAL: 245 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 11 found - 11 modified | TOTAL: 29 pass 2 (+++): 0 found - 11 modified | TOTAL: 29 pass 1 (+++): 10 found - 10 modified | TOTAL: 39 pass 2 (+++): 0 found - 10 modified | TOTAL: 39 pass 1 (+++): 4 found - 4 modified | TOTAL: 43 pass 2 (+++): 0 found - 4 modified | TOTAL: 43 Iteration Number : 1 pass 1 (++): 97 found - 97 modified | TOTAL: 97 pass 2 (++): 0 found - 97 modified | TOTAL: 97 pass 1 (+-): 86 found - 86 modified | TOTAL: 183 pass 2 (+-): 0 found - 86 modified | TOTAL: 183 pass 1 (--): 126 found - 126 modified | TOTAL: 309 pass 2 (--): 0 found - 126 modified | TOTAL: 309 pass 1 (-+): 97 found - 97 modified | TOTAL: 406 pass 2 (-+): 0 found - 97 modified | TOTAL: 406 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 6 found - 6 modified | TOTAL: 12 pass 2 (xy-): 0 found - 6 modified | TOTAL: 12 pass 1 (yz+): 7 found - 7 modified | TOTAL: 19 pass 2 (yz+): 0 found - 7 modified | TOTAL: 19 pass 1 (yz-): 3 found - 3 modified | TOTAL: 22 pass 2 (yz-): 0 found - 3 modified | TOTAL: 22 pass 1 (xz+): 3 found - 3 modified | TOTAL: 25 pass 2 (xz+): 0 found - 3 modified | TOTAL: 25 pass 1 (xz-): 5 found - 5 modified | TOTAL: 30 pass 2 (xz-): 0 found - 5 modified | TOTAL: 30 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 0 found - 0 modified | TOTAL: 8 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 2 found - 2 modified | TOTAL: 6 pass 2 (+-): 0 found - 2 modified | TOTAL: 6 pass 1 (--): 2 found - 2 modified | TOTAL: 8 pass 2 (--): 0 found - 2 modified | TOTAL: 8 pass 1 (-+): 5 found - 5 modified | TOTAL: 13 pass 2 (-+): 0 found - 5 modified | TOTAL: 13 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 748 (out of 536994: 0.139294) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 270 WM ON voxels kept 0 WM OFF voxels mri_pretess done @#@FSTIME 2024:10:14:11:41:37 mri_pretess N 5 e 5.73 S 0.07 U 6.63 P 116% M 106400 F 18 R 42373 W 0 c 649 w 103 I 2280 O 728 L 30.79 64.05 62.32 @#@FSLOADPOST 2024:10:14:11:41:43 mri_pretess N 5 35.37 64.45 62.45 #-------------------------------------------- #@# Fill Mon Oct 14 11:41:43 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/SubCorticalMassLUT.txt -auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01708 0.03299 0.01521 -9.14641; -0.03326 1.05500 0.21471 -43.02063; -0.00859 -0.18744 0.96628 16.29088; 0.00000 0.00000 0.00000 1.00000; Using auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt ndiff 16218 voxel to talairach voxel transform 1.01708 0.03299 0.01521 -9.14641; -0.03326 1.05500 0.21471 -43.02063; -0.00859 -0.18744 0.96628 16.29088; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 2125 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) need search nearby using seed (128, 119, 157), TAL = (0.0, 29.0, 9.0) talairach voxel to voxel transform 0.98208 -0.03219 -0.00831 7.73326; 0.02807 0.91094 -0.20286 42.75090; 0.01417 0.17642 0.99548 -8.49771; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (128, 119, 157) --> (0.0, 29.0, 9.0) done. filling took 1.2 minutes talairach cc position changed to (0.00, 29.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(18.00, 29.00, 9.00) SRC: (110.63, 122.39, 170.35) search lh wm seed point around talairach space (-18.00, 29.00, 9.00), SRC: (145.98, 123.40, 170.86) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... DoAutoMan 1 Applying edits to the output Applied 16218 edits Writing edits to ../tmp/filled.edits.txt Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2024:10:14:11:41:43 mri_fill N 14 e 72.85 S 2.06 U 70.78 P 99% M 989980 F 7 R 1153281 W 0 c 6808 w 112 I 1096 O 816 L 35.37 64.45 62.45 @#@FSLOADPOST 2024:10:14:11:42:56 mri_fill N 14 36.33 57.83 60.26 #-------------------------------------------- #@# Tessellate lh Mon Oct 14 11:42:56 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 16 found - 16 modified | TOTAL: 29 pass 2 (xy-): 0 found - 16 modified | TOTAL: 29 pass 1 (yz+): 15 found - 15 modified | TOTAL: 44 pass 2 (yz+): 0 found - 15 modified | TOTAL: 44 pass 1 (yz-): 9 found - 9 modified | TOTAL: 53 pass 2 (yz-): 0 found - 9 modified | TOTAL: 53 pass 1 (xz+): 11 found - 11 modified | TOTAL: 64 pass 2 (xz+): 0 found - 11 modified | TOTAL: 64 pass 1 (xz-): 12 found - 12 modified | TOTAL: 76 pass 2 (xz-): 0 found - 12 modified | TOTAL: 76 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 4 found - 4 modified | TOTAL: 11 pass 2 (+-): 0 found - 4 modified | TOTAL: 11 pass 1 (--): 6 found - 6 modified | TOTAL: 17 pass 2 (--): 0 found - 6 modified | TOTAL: 17 pass 1 (-+): 4 found - 4 modified | TOTAL: 21 pass 2 (-+): 0 found - 4 modified | TOTAL: 21 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 105 (out of 258986: 0.040543) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:10:14:11:42:56 mri_pretess N 4 e 3.19 S 0.03 U 3.29 P 103% M 40616 F 0 R 13198 W 0 c 332 w 49 I 0 O 232 L 36.33 57.83 60.26 @#@FSLOADPOST 2024:10:14:11:43:00 mri_pretess N 4 39.99 58.23 60.38 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.3.2 7.3.2 slice 50: 1188 vertices, 1296 faces slice 60: 6672 vertices, 6921 faces slice 70: 14738 vertices, 15009 faces slice 80: 23291 vertices, 23576 faces slice 90: 31838 vertices, 32121 faces slice 100: 40104 vertices, 40452 faces slice 110: 49530 vertices, 49912 faces slice 120: 59001 vertices, 59363 faces slice 130: 67889 vertices, 68238 faces slice 140: 76548 vertices, 76920 faces slice 150: 85429 vertices, 85800 faces slice 160: 92717 vertices, 93005 faces slice 170: 99349 vertices, 99621 faces slice 180: 105024 vertices, 105246 faces slice 190: 109393 vertices, 109592 faces slice 200: 111907 vertices, 112032 faces slice 210: 112304 vertices, 112362 faces slice 220: 112304 vertices, 112362 faces slice 230: 112304 vertices, 112362 faces slice 240: 112304 vertices, 112362 faces slice 250: 112304 vertices, 112362 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:10:14:11:43:00 mri_tessellate N 3 e 2.29 S 0.03 U 2.40 P 106% M 35656 F 5 R 9356 W 0 c 268 w 123 I 800 O 5272 L 39.99 58.23 60.38 @#@FSLOADPOST 2024:10:14:11:43:02 mri_tessellate N 3 39.99 58.23 60.38 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 112096 voxel in cpt #1: X=-82 [v=112096,e=336534,f=224356] located at (-25.489214, -10.768796, 1.343911) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (-11.000000, -67.000000, -9.000000) 8 voxel in cpt #3: X=2 [v=8,e=18,f=12] located at (-11.000000, -66.000000, -14.000000) 66 voxel in cpt #4: X=2 [v=66,e=192,f=128] located at (-11.590909, -60.454544, -7.606061) 8 voxel in cpt #5: X=2 [v=8,e=18,f=12] located at (-9.000000, -63.000000, -19.000000) 8 voxel in cpt #6: X=2 [v=8,e=18,f=12] located at (-9.000000, -60.000000, -8.000000) 8 voxel in cpt #7: X=2 [v=8,e=18,f=12] located at (-9.000000, -60.000000, -10.000000) 28 voxel in cpt #8: X=2 [v=28,e=78,f=52] located at (-11.857142, -57.285713, -18.214285) 8 voxel in cpt #9: X=2 [v=8,e=18,f=12] located at (-15.000000, -49.000000, -24.000000) 30 voxel in cpt #10: X=2 [v=30,e=84,f=56] located at (-30.100000, 26.200001, 16.700001) 12 voxel in cpt #11: X=2 [v=12,e=30,f=20] located at (-13.000000, 29.000000, -9.500000) 8 voxel in cpt #12: X=2 [v=8,e=18,f=12] located at (-15.000000, 30.000000, -10.000000) 16 voxel in cpt #13: X=2 [v=16,e=42,f=28] located at (-33.375000, 44.000000, -32.375000) For the whole surface: X=-58 [v=112304,e=337086,f=224724] 13 components have been found keeping component #1 with 112096 vertices done @#@FSTIME 2024:10:14:11:43:02 mris_extract_main_component N 2 e 1.20 S 0.15 U 1.02 P 97% M 224332 F 18 R 59168 W 0 c 154 w 363 I 2648 O 7888 L 39.99 58.23 60.38 @#@FSLOADPOST 2024:10:14:11:43:03 mris_extract_main_component N 2 44.31 58.82 60.56 #-------------------------------------------- #@# Tessellate rh Mon Oct 14 11:43:03 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 14 found - 14 modified | TOTAL: 31 pass 2 (xy-): 0 found - 14 modified | TOTAL: 31 pass 1 (yz+): 15 found - 15 modified | TOTAL: 46 pass 2 (yz+): 0 found - 15 modified | TOTAL: 46 pass 1 (yz-): 11 found - 11 modified | TOTAL: 57 pass 2 (yz-): 0 found - 11 modified | TOTAL: 57 pass 1 (xz+): 11 found - 11 modified | TOTAL: 68 pass 2 (xz+): 0 found - 11 modified | TOTAL: 68 pass 1 (xz-): 7 found - 7 modified | TOTAL: 75 pass 2 (xz-): 0 found - 7 modified | TOTAL: 75 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 3 found - 3 modified | TOTAL: 9 pass 2 (+++): 0 found - 3 modified | TOTAL: 9 pass 1 (+++): 4 found - 4 modified | TOTAL: 13 pass 2 (+++): 0 found - 4 modified | TOTAL: 13 Iteration Number : 1 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 7 found - 7 modified | TOTAL: 11 pass 2 (+-): 0 found - 7 modified | TOTAL: 11 pass 1 (--): 9 found - 9 modified | TOTAL: 20 pass 2 (--): 0 found - 9 modified | TOTAL: 20 pass 1 (-+): 6 found - 6 modified | TOTAL: 26 pass 2 (-+): 0 found - 6 modified | TOTAL: 26 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 123 (out of 259934: 0.047320) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:10:14:11:43:03 mri_pretess N 4 e 4.13 S 0.02 U 4.42 P 107% M 40564 F 0 R 14599 W 0 c 446 w 39 I 0 O 232 L 44.31 58.82 60.56 @#@FSLOADPOST 2024:10:14:11:43:08 mri_pretess N 4 44.31 58.82 60.56 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 50: 783 vertices, 866 faces slice 60: 6162 vertices, 6380 faces slice 70: 13448 vertices, 13699 faces slice 80: 22748 vertices, 23096 faces slice 90: 31604 vertices, 31845 faces slice 100: 40108 vertices, 40399 faces slice 110: 49313 vertices, 49633 faces slice 120: 58670 vertices, 59007 faces slice 130: 67643 vertices, 67979 faces slice 140: 76409 vertices, 76744 faces slice 150: 85206 vertices, 85529 faces slice 160: 93403 vertices, 93691 faces slice 170: 100486 vertices, 100721 faces slice 180: 106913 vertices, 107111 faces slice 190: 111293 vertices, 111463 faces slice 200: 114996 vertices, 115119 faces slice 210: 116310 vertices, 116336 faces slice 220: 116310 vertices, 116336 faces slice 230: 116310 vertices, 116336 faces slice 240: 116310 vertices, 116336 faces slice 250: 116310 vertices, 116336 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2024:10:14:11:43:08 mri_tessellate N 3 e 2.11 S 0.01 U 2.16 P 103% M 36092 F 0 R 7986 W 0 c 201 w 53 I 0 O 5456 L 44.31 58.82 60.56 @#@FSLOADPOST 2024:10:14:11:43:10 mri_tessellate N 3 42.69 58.25 60.37 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 116124 voxel in cpt #1: X=-64 [v=116124,e=348564,f=232376] located at (29.092625, -8.121482, 2.894948) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (21.000000, -61.000000, -8.000000) 8 voxel in cpt #3: X=2 [v=8,e=18,f=12] located at (21.000000, -61.000000, -10.000000) 8 voxel in cpt #4: X=2 [v=8,e=18,f=12] located at (20.000000, -61.000000, -12.000000) 8 voxel in cpt #5: X=2 [v=8,e=18,f=12] located at (19.000000, -60.000000, -18.000000) 30 voxel in cpt #6: X=2 [v=30,e=84,f=56] located at (19.000000, -57.500000, -10.500000) 8 voxel in cpt #7: X=2 [v=8,e=18,f=12] located at (20.000000, -57.000000, -8.000000) 8 voxel in cpt #8: X=2 [v=8,e=18,f=12] located at (25.000000, -55.000000, -25.000000) 8 voxel in cpt #9: X=2 [v=8,e=18,f=12] located at (21.000000, -54.000000, -8.000000) 8 voxel in cpt #10: X=2 [v=8,e=18,f=12] located at (22.000000, -54.000000, -16.000000) 12 voxel in cpt #11: X=2 [v=12,e=30,f=20] located at (21.000000, -51.500000, -11.000000) 8 voxel in cpt #12: X=2 [v=8,e=18,f=12] located at (28.000000, -51.000000, -5.000000) 8 voxel in cpt #13: X=2 [v=8,e=18,f=12] located at (30.000000, -51.000000, -6.000000) 8 voxel in cpt #14: X=2 [v=8,e=18,f=12] located at (21.000000, -51.000000, -23.000000) 8 voxel in cpt #15: X=2 [v=8,e=18,f=12] located at (22.000000, -49.000000, -9.000000) 8 voxel in cpt #16: X=2 [v=8,e=18,f=12] located at (25.000000, -39.000000, -18.000000) 12 voxel in cpt #17: X=2 [v=12,e=30,f=20] located at (42.000000, 12.000000, 11.500000) 8 voxel in cpt #18: X=2 [v=8,e=18,f=12] located at (32.000000, 27.000000, -12.000000) 8 voxel in cpt #19: X=2 [v=8,e=18,f=12] located at (32.000000, 28.000000, -10.000000) 12 voxel in cpt #20: X=2 [v=12,e=30,f=20] located at (15.000000, 29.500000, 28.000000) For the whole surface: X=-26 [v=116310,e=349008,f=232672] 20 components have been found keeping component #1 with 116124 vertices done @#@FSTIME 2024:10:14:11:43:10 mris_extract_main_component N 2 e 1.16 S 0.16 U 1.02 P 101% M 231884 F 0 R 61193 W 0 c 225 w 222 I 0 O 8176 L 42.69 58.25 60.37 @#@FSLOADPOST 2024:10:14:11:43:11 mris_extract_main_component N 2 42.69 58.25 60.37 #-------------------------------------------- #@# Smooth1 lh Mon Oct 14 11:43:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Mon Oct 14 11:43:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 3969861 of (3969861 3969864) to complete... Waiting for PID 3969864 of (3969861 3969864) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (3969861 3969864) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Mon Oct 14 11:43:14 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Mon Oct 14 11:43:14 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 3971571 of (3971571 3971575) to complete... Waiting for PID 3971575 of (3971571 3971575) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.7 mm, total surface area = 60242 mm^2 step 000: RMS=0.155 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.070 (target=0.015) step 025: RMS=0.064 (target=0.015) step 030: RMS=0.058 (target=0.015) step 035: RMS=0.056 (target=0.015) step 040: RMS=0.053 (target=0.015) step 045: RMS=0.051 (target=0.015) step 050: RMS=0.051 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.051 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 28.788064 mris_inflate stimesec 1.326311 mris_inflate ru_maxrss 179720 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 600584 mris_inflate ru_majflt 18 mris_inflate ru_nswap 0 mris_inflate ru_inblock 2208 mris_inflate ru_oublock 7912 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2894 mris_inflate ru_nivcsw 2981 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.2 mm, total surface area = 62674 mm^2 step 000: RMS=0.153 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.062 (target=0.015) step 030: RMS=0.057 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.051 (target=0.015) step 045: RMS=0.050 (target=0.015) step 050: RMS=0.049 (target=0.015) step 055: RMS=0.050 (target=0.015) step 060: RMS=0.050 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 29.921409 mris_inflate stimesec 1.442328 mris_inflate ru_maxrss 185596 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 605949 mris_inflate ru_majflt 13 mris_inflate ru_nswap 0 mris_inflate ru_inblock 448 mris_inflate ru_oublock 8192 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 4739 mris_inflate ru_nivcsw 3597 PIDs (3971571 3971575) completed and logs appended. #-------------------------------------------- #@# QSphere lh Mon Oct 14 11:43:31 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Mon Oct 14 11:43:31 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 3984821 of (3984821 3984824) to complete... Waiting for PID 3984824 of (3984821 3984824) to complete... mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 scaling brain by 0.344... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.09 +- 0.61 (0.00-->6.06) (max @ vno 86685 --> 87493) face area 0.03 +- 0.04 (-0.17-->0.68) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.166, avgs=0 005/300: dt: 0.9000, rms radial error=175.909, avgs=0 010/300: dt: 0.9000, rms radial error=175.356, avgs=0 015/300: dt: 0.9000, rms radial error=174.630, avgs=0 020/300: dt: 0.9000, rms radial error=173.804, avgs=0 025/300: dt: 0.9000, rms radial error=172.919, avgs=0 030/300: dt: 0.9000, rms radial error=172.002, avgs=0 035/300: dt: 0.9000, rms radial error=171.068, avgs=0 040/300: dt: 0.9000, rms radial error=170.127, avgs=0 045/300: dt: 0.9000, rms radial error=169.183, avgs=0 050/300: dt: 0.9000, rms radial error=168.239, avgs=0 055/300: dt: 0.9000, rms radial error=167.298, avgs=0 060/300: dt: 0.9000, rms radial error=166.359, avgs=0 065/300: dt: 0.9000, rms radial error=165.425, avgs=0 070/300: dt: 0.9000, rms radial error=164.494, avgs=0 075/300: dt: 0.9000, rms radial error=163.568, avgs=0 080/300: dt: 0.9000, rms radial error=162.649, avgs=0 085/300: dt: 0.9000, rms radial error=161.737, avgs=0 090/300: dt: 0.9000, rms radial error=160.830, avgs=0 095/300: dt: 0.9000, rms radial error=159.928, avgs=0 100/300: dt: 0.9000, rms radial error=159.031, avgs=0 105/300: dt: 0.9000, rms radial error=158.138, avgs=0 110/300: dt: 0.9000, rms radial error=157.251, avgs=0 115/300: dt: 0.9000, rms radial error=156.368, avgs=0 120/300: dt: 0.9000, rms radial error=155.490, avgs=0 125/300: dt: 0.9000, rms radial error=154.618, avgs=0 130/300: dt: 0.9000, rms radial error=153.750, avgs=0 135/300: dt: 0.9000, rms radial error=152.886, avgs=0 140/300: dt: 0.9000, rms radial error=152.028, avgs=0 145/300: dt: 0.9000, rms radial error=151.174, avgs=0 150/300: dt: 0.9000, rms radial error=150.324, avgs=0 155/300: dt: 0.9000, rms radial error=149.480, avgs=0 160/300: dt: 0.9000, rms radial error=148.640, avgs=0 165/300: dt: 0.9000, rms radial error=147.804, avgs=0 170/300: dt: 0.9000, rms radial error=146.973, avgs=0 175/300: dt: 0.9000, rms radial error=146.147, avgs=0 180/300: dt: 0.9000, rms radial error=145.325, avgs=0 185/300: dt: 0.9000, rms radial error=144.508, avgs=0 190/300: dt: 0.9000, rms radial error=143.695, avgs=0 195/300: dt: 0.9000, rms radial error=142.886, avgs=0 200/300: dt: 0.9000, rms radial error=142.083, avgs=0 205/300: dt: 0.9000, rms radial error=141.283, avgs=0 210/300: dt: 0.9000, rms radial error=140.488, avgs=0 215/300: dt: 0.9000, rms radial error=139.698, avgs=0 220/300: dt: 0.9000, rms radial error=138.912, avgs=0 225/300: dt: 0.9000, rms radial error=138.130, avgs=0 230/300: dt: 0.9000, rms radial error=137.352, avgs=0 235/300: dt: 0.9000, rms radial error=136.579, avgs=0 240/300: dt: 0.9000, rms radial error=135.810, avgs=0 245/300: dt: 0.9000, rms radial error=135.046, avgs=0 250/300: dt: 0.9000, rms radial error=134.285, avgs=0 255/300: dt: 0.9000, rms radial error=133.529, avgs=0 260/300: dt: 0.9000, rms radial error=132.777, avgs=0 265/300: dt: 0.9000, rms radial error=132.029, avgs=0 270/300: dt: 0.9000, rms radial error=131.286, avgs=0 275/300: dt: 0.9000, rms radial error=130.546, avgs=0 280/300: dt: 0.9000, rms radial error=129.811, avgs=0 285/300: dt: 0.9000, rms radial error=129.080, avgs=0 290/300: dt: 0.9000, rms radial error=128.353, avgs=0 295/300: dt: 0.9000, rms radial error=127.630, avgs=0 300/300: dt: 0.9000, rms radial error=126.911, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12597.93 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00039 epoch 2 (K=40.0), pass 1, starting sse = 1888.62 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00079 epoch 3 (K=160.0), pass 1, starting sse = 155.07 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/15 = 0.00935 epoch 4 (K=640.0), pass 1, starting sse = 9.23 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/18 = 0.00449 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0249 hours FSRUNTIME@ mris_sphere 0.0249 hours 4 threads #VMPC# mris_sphere VmPeak 772004 mris_sphere done mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 scaling brain by 0.331... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.07 +- 0.61 (0.00-->8.22) (max @ vno 52575 --> 53512) face area 0.03 +- 0.04 (-0.12-->0.80) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.557, avgs=0 005/300: dt: 0.9000, rms radial error=176.299, avgs=0 010/300: dt: 0.9000, rms radial error=175.746, avgs=0 015/300: dt: 0.9000, rms radial error=175.018, avgs=0 020/300: dt: 0.9000, rms radial error=174.193, avgs=0 025/300: dt: 0.9000, rms radial error=173.311, avgs=0 030/300: dt: 0.9000, rms radial error=172.397, avgs=0 035/300: dt: 0.9000, rms radial error=171.466, avgs=0 040/300: dt: 0.9000, rms radial error=170.526, avgs=0 045/300: dt: 0.9000, rms radial error=169.584, avgs=0 050/300: dt: 0.9000, rms radial error=168.641, avgs=0 055/300: dt: 0.9000, rms radial error=167.701, avgs=0 060/300: dt: 0.9000, rms radial error=166.764, avgs=0 065/300: dt: 0.9000, rms radial error=165.832, avgs=0 070/300: dt: 0.9000, rms radial error=164.903, avgs=0 075/300: dt: 0.9000, rms radial error=163.980, avgs=0 080/300: dt: 0.9000, rms radial error=163.061, avgs=0 085/300: dt: 0.9000, rms radial error=162.147, avgs=0 090/300: dt: 0.9000, rms radial error=161.238, avgs=0 095/300: dt: 0.9000, rms radial error=160.334, avgs=0 100/300: dt: 0.9000, rms radial error=159.435, avgs=0 105/300: dt: 0.9000, rms radial error=158.541, avgs=0 110/300: dt: 0.9000, rms radial error=157.651, avgs=0 115/300: dt: 0.9000, rms radial error=156.766, avgs=0 120/300: dt: 0.9000, rms radial error=155.885, avgs=0 125/300: dt: 0.9000, rms radial error=155.010, avgs=0 130/300: dt: 0.9000, rms radial error=154.139, avgs=0 135/300: dt: 0.9000, rms radial error=153.273, avgs=0 140/300: dt: 0.9000, rms radial error=152.411, avgs=0 145/300: dt: 0.9000, rms radial error=151.555, avgs=0 150/300: dt: 0.9000, rms radial error=150.703, avgs=0 155/300: dt: 0.9000, rms radial error=149.856, avgs=0 160/300: dt: 0.9000, rms radial error=149.013, avgs=0 165/300: dt: 0.9000, rms radial error=148.175, avgs=0 170/300: dt: 0.9000, rms radial error=147.341, avgs=0 175/300: dt: 0.9000, rms radial error=146.512, avgs=0 180/300: dt: 0.9000, rms radial error=145.688, avgs=0 185/300: dt: 0.9000, rms radial error=144.868, avgs=0 190/300: dt: 0.9000, rms radial error=144.052, avgs=0 195/300: dt: 0.9000, rms radial error=143.242, avgs=0 200/300: dt: 0.9000, rms radial error=142.435, avgs=0 205/300: dt: 0.9000, rms radial error=141.633, avgs=0 210/300: dt: 0.9000, rms radial error=140.836, avgs=0 215/300: dt: 0.9000, rms radial error=140.043, avgs=0 220/300: dt: 0.9000, rms radial error=139.255, avgs=0 225/300: dt: 0.9000, rms radial error=138.471, avgs=0 230/300: dt: 0.9000, rms radial error=137.691, avgs=0 235/300: dt: 0.9000, rms radial error=136.915, avgs=0 240/300: dt: 0.9000, rms radial error=136.144, avgs=0 245/300: dt: 0.9000, rms radial error=135.377, avgs=0 250/300: dt: 0.9000, rms radial error=134.615, avgs=0 255/300: dt: 0.9000, rms radial error=133.856, avgs=0 260/300: dt: 0.9000, rms radial error=133.102, avgs=0 265/300: dt: 0.9000, rms radial error=132.353, avgs=0 270/300: dt: 0.9000, rms radial error=131.607, avgs=0 275/300: dt: 0.9000, rms radial error=130.866, avgs=0 280/300: dt: 0.9000, rms radial error=130.128, avgs=0 285/300: dt: 0.9000, rms radial error=129.395, avgs=0 290/300: dt: 0.9000, rms radial error=128.666, avgs=0 295/300: dt: 0.9000, rms radial error=127.941, avgs=0 300/300: dt: 0.9000, rms radial error=127.220, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13239.80 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00031 epoch 2 (K=40.0), pass 1, starting sse = 2048.65 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00088 epoch 3 (K=160.0), pass 1, starting sse = 179.32 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/14 = 0.00860 epoch 4 (K=640.0), pass 1, starting sse = 10.87 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/17 = 0.00315 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0250 hours FSRUNTIME@ mris_sphere 0.0250 hours 4 threads #VMPC# mris_sphere VmPeak 775236 mris_sphere done PIDs (3984821 3984824) completed and logs appended. #@# Fix Topology lh Mon Oct 14 11:45:01 CDT 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma lh #@# Fix Topology rh Mon Oct 14 11:45:01 CDT 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma rh Waiting for PID 4067102 of (4067102 4067106) to complete... Waiting for PID 4067106 of (4067102 4067106) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-82 (nv=112096, nf=224356, ne=336534, g=42) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 14 iterations marking ambiguous vertices... 4512 ambiguous faces found in tessellation segmenting defects... 67 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 67 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7741 (-4.3870) -vertex loglikelihood: -6.2920 (-3.1460) -normal dot loglikelihood: -3.6149 (-3.6149) -quad curv loglikelihood: -5.8110 (-2.9055) Total Loglikelihood : -24.4919 CORRECTING DEFECT 0 (vertices=14, convex hull=25, v0=4196) After retessellation of defect 0 (v0=4196), euler #=-63 (109207,326263,216993) : difference with theory (-64) = -1 CORRECTING DEFECT 1 (vertices=9, convex hull=20, v0=6264) After retessellation of defect 1 (v0=6264), euler #=-62 (109208,326272,217002) : difference with theory (-63) = -1 CORRECTING DEFECT 2 (vertices=72, convex hull=101, v0=9072) After retessellation of defect 2 (v0=9072), euler #=-61 (109251,326441,217129) : difference with theory (-62) = -1 CORRECTING DEFECT 3 (vertices=5, convex hull=17, v0=9442) After retessellation of defect 3 (v0=9442), euler #=-60 (109251,326445,217134) : difference with theory (-61) = -1 CORRECTING DEFECT 4 (vertices=55, convex hull=87, v0=10124) After retessellation of defect 4 (v0=10124), euler #=-59 (109275,326554,217220) : difference with theory (-60) = -1 CORRECTING DEFECT 5 (vertices=32, convex hull=58, v0=11354) After retessellation of defect 5 (v0=11354), euler #=-58 (109291,326623,217274) : difference with theory (-59) = -1 CORRECTING DEFECT 6 (vertices=30, convex hull=77, v0=12282) After retessellation of defect 6 (v0=12282), euler #=-57 (109311,326715,217347) : difference with theory (-58) = -1 CORRECTING DEFECT 7 (vertices=53, convex hull=63, v0=14475) After retessellation of defect 7 (v0=14475), euler #=-56 (109336,326815,217423) : difference with theory (-57) = -1 CORRECTING DEFECT 8 (vertices=45, convex hull=73, v0=14714) After retessellation of defect 8 (v0=14714), euler #=-55 (109363,326927,217509) : difference with theory (-56) = -1 CORRECTING DEFECT 9 (vertices=69, convex hull=34, v0=18174) After retessellation of defect 9 (v0=18174), euler #=-54 (109369,326956,217533) : difference with theory (-55) = -1 CORRECTING DEFECT 10 (vertices=7, convex hull=17, v0=19410) After retessellation of defect 10 (v0=19410), euler #=-53 (109370,326963,217540) : difference with theory (-54) = -1 CORRECTING DEFECT 11 (vertices=49, convex hull=97, v0=22278) After retessellation of defect 11 (v0=22278), euler #=-52 (109400,327095,217643) : difference with theory (-53) = -1 CORRECTING DEFECT 12 (vertices=61, convex hull=91, v0=22400) After retessellation of defect 12 (v0=22400), euler #=-51 (109438,327251,217762) : difference with theory (-52) = -1 CORRECTING DEFECT 13 (vertices=197, convex hull=141, v0=22570) After retessellation of defect 13 (v0=22570), euler #=-50 (109465,327402,217887) : difference with theory (-51) = -1 CORRECTING DEFECT 14 (vertices=10, convex hull=19, v0=23049) After retessellation of defect 14 (v0=23049), euler #=-49 (109466,327411,217896) : difference with theory (-50) = -1 CORRECTING DEFECT 15 (vertices=22, convex hull=53, v0=25062) After retessellation of defect 15 (v0=25062), euler #=-48 (109477,327465,217940) : difference with theory (-49) = -1 CORRECTING DEFECT 16 (vertices=9, convex hull=14, v0=25287) After retessellation of defect 16 (v0=25287), euler #=-47 (109478,327471,217946) : difference with theory (-48) = -1 CORRECTING DEFECT 17 (vertices=8, convex hull=23, v0=28516) After retessellation of defect 17 (v0=28516), euler #=-46 (109479,327481,217956) : difference with theory (-47) = -1 CORRECTING DEFECT 18 (vertices=34, convex hull=80, v0=30297) After retessellation of defect 18 (v0=30297), euler #=-45 (109501,327579,218033) : difference with theory (-46) = -1 CORRECTING DEFECT 19 (vertices=25, convex hull=53, v0=30331) After retessellation of defect 19 (v0=30331), euler #=-44 (109517,327648,218087) : difference with theory (-45) = -1 CORRECTING DEFECT 20 (vertices=27, convex hull=27, v0=31342) After retessellation of defect 20 (v0=31342), euler #=-43 (109525,327680,218112) : difference with theory (-44) = -1 CORRECTING DEFECT 21 (vertices=27, convex hull=69, v0=32412) After retessellation of defect 21 (v0=32412), euler #=-42 (109537,327743,218164) : difference with theory (-43) = -1 CORRECTING DEFECT 22 (vertices=21, convex hull=54, v0=33280) After retessellation of defect 22 (v0=33280), euler #=-41 (109546,327788,218201) : difference with theory (-42) = -1 CORRECTING DEFECT 23 (vertices=45, convex hull=72, v0=35425) After retessellation of defect 23 (v0=35425), euler #=-40 (109570,327893,218283) : difference with theory (-41) = -1 CORRECTING DEFECT 24 (vertices=21, convex hull=51, v0=35596) After retessellation of defect 24 (v0=35596), euler #=-39 (109579,327939,218321) : difference with theory (-40) = -1 CORRECTING DEFECT 25 (vertices=17, convex hull=55, v0=39474) After retessellation of defect 25 (v0=39474), euler #=-38 (109590,327993,218365) : difference with theory (-39) = -1 CORRECTING DEFECT 26 (vertices=24, convex hull=34, v0=39784) After retessellation of defect 26 (v0=39784), euler #=-37 (109596,328022,218389) : difference with theory (-38) = -1 CORRECTING DEFECT 27 (vertices=19, convex hull=21, v0=42622) After retessellation of defect 27 (v0=42622), euler #=-36 (109601,328044,218407) : difference with theory (-37) = -1 CORRECTING DEFECT 28 (vertices=49, convex hull=77, v0=44475) After retessellation of defect 28 (v0=44475), euler #=-35 (109610,328102,218457) : difference with theory (-36) = -1 CORRECTING DEFECT 29 (vertices=179, convex hull=77, v0=45698) After retessellation of defect 29 (v0=45698), euler #=-34 (109619,328158,218505) : difference with theory (-35) = -1 CORRECTING DEFECT 30 (vertices=63, convex hull=134, v0=48731) After retessellation of defect 30 (v0=48731), euler #=-33 (109645,328291,218613) : difference with theory (-34) = -1 CORRECTING DEFECT 31 (vertices=6, convex hull=21, v0=51071) After retessellation of defect 31 (v0=51071), euler #=-32 (109647,328304,218625) : difference with theory (-33) = -1 CORRECTING DEFECT 32 (vertices=51, convex hull=68, v0=53332) After retessellation of defect 32 (v0=53332), euler #=-31 (109659,328361,218671) : difference with theory (-32) = -1 CORRECTING DEFECT 33 (vertices=62, convex hull=54, v0=56154) After retessellation of defect 33 (v0=56154), euler #=-30 (109680,328447,218737) : difference with theory (-31) = -1 CORRECTING DEFECT 34 (vertices=37, convex hull=21, v0=56291) After retessellation of defect 34 (v0=56291), euler #=-29 (109683,328463,218751) : difference with theory (-30) = -1 CORRECTING DEFECT 35 (vertices=10, convex hull=17, v0=62752) After retessellation of defect 35 (v0=62752), euler #=-28 (109684,328471,218759) : difference with theory (-29) = -1 CORRECTING DEFECT 36 (vertices=42, convex hull=83, v0=63612) After retessellation of defect 36 (v0=63612), euler #=-27 (109709,328579,218843) : difference with theory (-28) = -1 CORRECTING DEFECT 37 (vertices=29, convex hull=31, v0=64546) After retessellation of defect 37 (v0=64546), euler #=-26 (109712,328596,218858) : difference with theory (-27) = -1 CORRECTING DEFECT 38 (vertices=19, convex hull=16, v0=66016) After retessellation of defect 38 (v0=66016), euler #=-25 (109713,328602,218864) : difference with theory (-26) = -1 CORRECTING DEFECT 39 (vertices=18, convex hull=21, v0=66965) After retessellation of defect 39 (v0=66965), euler #=-24 (109714,328613,218875) : difference with theory (-25) = -1 CORRECTING DEFECT 40 (vertices=17, convex hull=19, v0=68741) After retessellation of defect 40 (v0=68741), euler #=-23 (109717,328625,218885) : difference with theory (-24) = -1 CORRECTING DEFECT 41 (vertices=33, convex hull=44, v0=72203) After retessellation of defect 41 (v0=72203), euler #=-22 (109730,328682,218930) : difference with theory (-23) = -1 CORRECTING DEFECT 42 (vertices=7, convex hull=15, v0=73472) After retessellation of defect 42 (v0=73472), euler #=-21 (109730,328686,218935) : difference with theory (-22) = -1 CORRECTING DEFECT 43 (vertices=111, convex hull=114, v0=75146) After retessellation of defect 43 (v0=75146), euler #=-21 (109739,328768,219008) : difference with theory (-21) = 0 CORRECTING DEFECT 44 (vertices=25, convex hull=24, v0=76609) After retessellation of defect 44 (v0=76609), euler #=-20 (109744,328790,219026) : difference with theory (-20) = 0 CORRECTING DEFECT 45 (vertices=21, convex hull=35, v0=79955) After retessellation of defect 45 (v0=79955), euler #=-19 (109747,328814,219048) : difference with theory (-19) = 0 CORRECTING DEFECT 46 (vertices=150, convex hull=91, v0=80087) After retessellation of defect 46 (v0=80087), euler #=-18 (109786,328975,219171) : difference with theory (-18) = 0 CORRECTING DEFECT 47 (vertices=57, convex hull=76, v0=80152) After retessellation of defect 47 (v0=80152), euler #=-17 (109813,329093,219263) : difference with theory (-17) = 0 CORRECTING DEFECT 48 (vertices=19, convex hull=27, v0=81397) After retessellation of defect 48 (v0=81397), euler #=-16 (109817,329117,219284) : difference with theory (-16) = 0 CORRECTING DEFECT 49 (vertices=27, convex hull=27, v0=83042) After retessellation of defect 49 (v0=83042), euler #=-15 (109824,329146,219307) : difference with theory (-15) = 0 CORRECTING DEFECT 50 (vertices=49, convex hull=23, v0=83687) After retessellation of defect 50 (v0=83687), euler #=-14 (109831,329176,219331) : difference with theory (-14) = 0 CORRECTING DEFECT 51 (vertices=50, convex hull=65, v0=84217) After retessellation of defect 51 (v0=84217), euler #=-13 (109846,329245,219386) : difference with theory (-13) = 0 CORRECTING DEFECT 52 (vertices=54, convex hull=84, v0=86411) After retessellation of defect 52 (v0=86411), euler #=-12 (109879,329378,219487) : difference with theory (-12) = 0 CORRECTING DEFECT 53 (vertices=14, convex hull=16, v0=86985) After retessellation of defect 53 (v0=86985), euler #=-11 (109882,329390,219497) : difference with theory (-11) = 0 CORRECTING DEFECT 54 (vertices=7, convex hull=21, v0=89195) After retessellation of defect 54 (v0=89195), euler #=-10 (109883,329398,219505) : difference with theory (-10) = 0 CORRECTING DEFECT 55 (vertices=22, convex hull=31, v0=89661) After retessellation of defect 55 (v0=89661), euler #=-9 (109887,329417,219521) : difference with theory (-9) = 0 CORRECTING DEFECT 56 (vertices=52, convex hull=43, v0=90368) After retessellation of defect 56 (v0=90368), euler #=-8 (109895,329458,219555) : difference with theory (-8) = 0 CORRECTING DEFECT 57 (vertices=19, convex hull=24, v0=90615) After retessellation of defect 57 (v0=90615), euler #=-7 (109896,329468,219565) : difference with theory (-7) = 0 CORRECTING DEFECT 58 (vertices=28, convex hull=26, v0=91907) After retessellation of defect 58 (v0=91907), euler #=-6 (109901,329490,219583) : difference with theory (-6) = 0 CORRECTING DEFECT 59 (vertices=5, convex hull=18, v0=92262) After retessellation of defect 59 (v0=92262), euler #=-5 (109902,329496,219589) : difference with theory (-5) = 0 CORRECTING DEFECT 60 (vertices=100, convex hull=126, v0=93614) After retessellation of defect 60 (v0=93614), euler #=-4 (109927,329626,219695) : difference with theory (-4) = 0 CORRECTING DEFECT 61 (vertices=104, convex hull=101, v0=93753) After retessellation of defect 61 (v0=93753), euler #=-3 (109967,329790,219820) : difference with theory (-3) = 0 CORRECTING DEFECT 62 (vertices=28, convex hull=65, v0=95399) After retessellation of defect 62 (v0=95399), euler #=-2 (109985,329867,219880) : difference with theory (-2) = 0 CORRECTING DEFECT 63 (vertices=155, convex hull=47, v0=100189) After retessellation of defect 63 (v0=100189), euler #=-1 (109994,329909,219914) : difference with theory (-1) = 0 CORRECTING DEFECT 64 (vertices=6, convex hull=27, v0=103916) After retessellation of defect 64 (v0=103916), euler #=0 (109996,329925,219929) : difference with theory (0) = 0 CORRECTING DEFECT 65 (vertices=135, convex hull=91, v0=108407) After retessellation of defect 65 (v0=108407), euler #=1 (110008,330004,219997) : difference with theory (1) = 0 CORRECTING DEFECT 66 (vertices=21, convex hull=44, v0=111145) After retessellation of defect 66 (v0=111145), euler #=2 (110018,330048,220032) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.03-->7.12) (max @ vno 105213 --> 107521) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.03-->7.12) (max @ vno 105213 --> 107521) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 253 mutations (36.3%), 444 crossovers (63.7%), 215 vertices were eliminated building final representation... 2078 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=110018, nf=220032, ne=330048, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 355 intersecting 001: 16 intersecting terminating search with 0 intersecting topology fixing took 2.9 minutes FSRUNTIME@ mris_fix_topology lh 0.0477 hours 4 threads #VMPC# mris_fix_topology VmPeak 949224 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-64 (nv=116124, nf=232376, ne=348564, g=33) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... 4656 ambiguous faces found in tessellation segmenting defects... 53 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 17 into 13 -merging segment 23 into 19 51 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7387 (-4.3693) -vertex loglikelihood: -6.2258 (-3.1129) -normal dot loglikelihood: -3.5771 (-3.5771) -quad curv loglikelihood: -6.1681 (-3.0840) Total Loglikelihood : -24.7097 CORRECTING DEFECT 0 (vertices=929, convex hull=316, v0=1075) After retessellation of defect 0 (v0=1075), euler #=-49 (113321,338918,225548) : difference with theory (-48) = 1 CORRECTING DEFECT 1 (vertices=64, convex hull=79, v0=7519) After retessellation of defect 1 (v0=7519), euler #=-48 (113345,339021,225628) : difference with theory (-47) = 1 CORRECTING DEFECT 2 (vertices=63, convex hull=103, v0=12765) After retessellation of defect 2 (v0=12765), euler #=-47 (113380,339166,225739) : difference with theory (-46) = 1 CORRECTING DEFECT 3 (vertices=12, convex hull=29, v0=15663) After retessellation of defect 3 (v0=15663), euler #=-46 (113384,339189,225759) : difference with theory (-45) = 1 CORRECTING DEFECT 4 (vertices=26, convex hull=27, v0=16294) After retessellation of defect 4 (v0=16294), euler #=-45 (113388,339209,225776) : difference with theory (-44) = 1 CORRECTING DEFECT 5 (vertices=24, convex hull=23, v0=18758) After retessellation of defect 5 (v0=18758), euler #=-44 (113390,339222,225788) : difference with theory (-43) = 1 CORRECTING DEFECT 6 (vertices=25, convex hull=45, v0=26282) After retessellation of defect 6 (v0=26282), euler #=-43 (113401,339274,225830) : difference with theory (-42) = 1 CORRECTING DEFECT 7 (vertices=25, convex hull=69, v0=32656) After retessellation of defect 7 (v0=32656), euler #=-42 (113417,339349,225890) : difference with theory (-41) = 1 CORRECTING DEFECT 8 (vertices=5, convex hull=18, v0=33503) After retessellation of defect 8 (v0=33503), euler #=-41 (113417,339352,225894) : difference with theory (-40) = 1 CORRECTING DEFECT 9 (vertices=38, convex hull=25, v0=33528) After retessellation of defect 9 (v0=33528), euler #=-40 (113424,339383,225919) : difference with theory (-39) = 1 CORRECTING DEFECT 10 (vertices=95, convex hull=30, v0=38540) After retessellation of defect 10 (v0=38540), euler #=-39 (113433,339420,225948) : difference with theory (-38) = 1 CORRECTING DEFECT 11 (vertices=187, convex hull=57, v0=43823) After retessellation of defect 11 (v0=43823), euler #=-38 (113444,339472,225990) : difference with theory (-37) = 1 CORRECTING DEFECT 12 (vertices=71, convex hull=96, v0=46060) After retessellation of defect 12 (v0=46060), euler #=-37 (113471,339593,226085) : difference with theory (-36) = 1 CORRECTING DEFECT 13 (vertices=18, convex hull=52, v0=48977) After retessellation of defect 13 (v0=48977), euler #=-35 (113475,339621,226111) : difference with theory (-35) = 0 CORRECTING DEFECT 14 (vertices=27, convex hull=20, v0=50155) After retessellation of defect 14 (v0=50155), euler #=-34 (113479,339638,226125) : difference with theory (-34) = 0 CORRECTING DEFECT 15 (vertices=8, convex hull=30, v0=51287) After retessellation of defect 15 (v0=51287), euler #=-33 (113480,339652,226139) : difference with theory (-33) = 0 CORRECTING DEFECT 16 (vertices=7, convex hull=13, v0=52484) After retessellation of defect 16 (v0=52484), euler #=-32 (113484,339666,226150) : difference with theory (-32) = 0 CORRECTING DEFECT 17 (vertices=5, convex hull=23, v0=53381) After retessellation of defect 17 (v0=53381), euler #=-31 (113486,339678,226161) : difference with theory (-31) = 0 CORRECTING DEFECT 18 (vertices=50, convex hull=89, v0=53679) After retessellation of defect 18 (v0=53679), euler #=-29 (113507,339786,226250) : difference with theory (-30) = -1 CORRECTING DEFECT 19 (vertices=61, convex hull=47, v0=53723) After retessellation of defect 19 (v0=53723), euler #=-28 (113519,339838,226291) : difference with theory (-29) = -1 CORRECTING DEFECT 20 (vertices=29, convex hull=71, v0=54081) After retessellation of defect 20 (v0=54081), euler #=-27 (113539,339927,226361) : difference with theory (-28) = -1 CORRECTING DEFECT 21 (vertices=26, convex hull=65, v0=56288) After retessellation of defect 21 (v0=56288), euler #=-26 (113554,339997,226417) : difference with theory (-27) = -1 CORRECTING DEFECT 22 (vertices=46, convex hull=36, v0=57588) After retessellation of defect 22 (v0=57588), euler #=-25 (113562,340032,226445) : difference with theory (-26) = -1 CORRECTING DEFECT 23 (vertices=37, convex hull=57, v0=61410) After retessellation of defect 23 (v0=61410), euler #=-24 (113571,340083,226488) : difference with theory (-25) = -1 CORRECTING DEFECT 24 (vertices=14, convex hull=24, v0=69785) After retessellation of defect 24 (v0=69785), euler #=-23 (113574,340102,226505) : difference with theory (-24) = -1 CORRECTING DEFECT 25 (vertices=69, convex hull=135, v0=76274) After retessellation of defect 25 (v0=76274), euler #=-22 (113599,340232,226611) : difference with theory (-23) = -1 CORRECTING DEFECT 26 (vertices=43, convex hull=37, v0=76360) After retessellation of defect 26 (v0=76360), euler #=-21 (113611,340281,226649) : difference with theory (-22) = -1 CORRECTING DEFECT 27 (vertices=21, convex hull=62, v0=77216) After retessellation of defect 27 (v0=77216), euler #=-20 (113621,340335,226694) : difference with theory (-21) = -1 CORRECTING DEFECT 28 (vertices=17, convex hull=23, v0=79927) After retessellation of defect 28 (v0=79927), euler #=-19 (113626,340355,226710) : difference with theory (-20) = -1 CORRECTING DEFECT 29 (vertices=11, convex hull=12, v0=80441) After retessellation of defect 29 (v0=80441), euler #=-18 (113626,340357,226713) : difference with theory (-19) = -1 CORRECTING DEFECT 30 (vertices=28, convex hull=38, v0=84821) After retessellation of defect 30 (v0=84821), euler #=-17 (113635,340400,226748) : difference with theory (-18) = -1 CORRECTING DEFECT 31 (vertices=49, convex hull=85, v0=91215) After retessellation of defect 31 (v0=91215), euler #=-16 (113661,340514,226837) : difference with theory (-17) = -1 CORRECTING DEFECT 32 (vertices=63, convex hull=46, v0=91708) After retessellation of defect 32 (v0=91708), euler #=-15 (113672,340564,226877) : difference with theory (-16) = -1 CORRECTING DEFECT 33 (vertices=19, convex hull=33, v0=92875) After retessellation of defect 33 (v0=92875), euler #=-14 (113675,340583,226894) : difference with theory (-15) = -1 CORRECTING DEFECT 34 (vertices=34, convex hull=58, v0=93637) After retessellation of defect 34 (v0=93637), euler #=-13 (113684,340632,226935) : difference with theory (-14) = -1 CORRECTING DEFECT 35 (vertices=68, convex hull=117, v0=94040) After retessellation of defect 35 (v0=94040), euler #=-12 (113719,340785,227054) : difference with theory (-13) = -1 CORRECTING DEFECT 36 (vertices=10, convex hull=25, v0=94110) After retessellation of defect 36 (v0=94110), euler #=-11 (113721,340802,227070) : difference with theory (-12) = -1 CORRECTING DEFECT 37 (vertices=61, convex hull=127, v0=98755) After retessellation of defect 37 (v0=98755), euler #=-10 (113733,340893,227150) : difference with theory (-11) = -1 CORRECTING DEFECT 38 (vertices=56, convex hull=85, v0=98796) After retessellation of defect 38 (v0=98796), euler #=-9 (113752,340985,227224) : difference with theory (-10) = -1 CORRECTING DEFECT 39 (vertices=64, convex hull=71, v0=99460) After retessellation of defect 39 (v0=99460), euler #=-8 (113764,341049,227277) : difference with theory (-9) = -1 CORRECTING DEFECT 40 (vertices=31, convex hull=49, v0=100153) After retessellation of defect 40 (v0=100153), euler #=-7 (113775,341101,227319) : difference with theory (-8) = -1 CORRECTING DEFECT 41 (vertices=59, convex hull=109, v0=100237) After retessellation of defect 41 (v0=100237), euler #=-6 (113798,341216,227412) : difference with theory (-7) = -1 CORRECTING DEFECT 42 (vertices=50, convex hull=31, v0=101487) After retessellation of defect 42 (v0=101487), euler #=-5 (113804,341248,227439) : difference with theory (-6) = -1 CORRECTING DEFECT 43 (vertices=30, convex hull=75, v0=102040) After retessellation of defect 43 (v0=102040), euler #=-4 (113821,341330,227505) : difference with theory (-5) = -1 CORRECTING DEFECT 44 (vertices=21, convex hull=33, v0=104215) After retessellation of defect 44 (v0=104215), euler #=-3 (113826,341359,227530) : difference with theory (-4) = -1 CORRECTING DEFECT 45 (vertices=59, convex hull=59, v0=108102) After retessellation of defect 45 (v0=108102), euler #=-3 (113845,341443,227595) : difference with theory (-3) = 0 CORRECTING DEFECT 46 (vertices=29, convex hull=65, v0=110223) After retessellation of defect 46 (v0=110223), euler #=-2 (113864,341526,227660) : difference with theory (-2) = 0 CORRECTING DEFECT 47 (vertices=27, convex hull=30, v0=113538) After retessellation of defect 47 (v0=113538), euler #=-1 (113867,341543,227675) : difference with theory (-1) = 0 CORRECTING DEFECT 48 (vertices=20, convex hull=47, v0=114047) After retessellation of defect 48 (v0=114047), euler #=0 (113876,341587,227711) : difference with theory (0) = 0 CORRECTING DEFECT 49 (vertices=23, convex hull=49, v0=114709) After retessellation of defect 49 (v0=114709), euler #=1 (113888,341643,227756) : difference with theory (1) = 0 CORRECTING DEFECT 50 (vertices=28, convex hull=38, v0=115049) After retessellation of defect 50 (v0=115049), euler #=2 (113893,341673,227782) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.11-->9.18) (max @ vno 11425 --> 18595) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.11-->9.18) (max @ vno 11425 --> 18595) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 184 mutations (35.2%), 339 crossovers (64.8%), 239 vertices were eliminated building final representation... 2231 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=113893, nf=227782, ne=341673, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 284 intersecting 001: 26 intersecting terminating search with 0 intersecting topology fixing took 11.8 minutes FSRUNTIME@ mris_fix_topology rh 0.1960 hours 4 threads #VMPC# mris_fix_topology VmPeak 953468 PIDs (4067102 4067106) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 110018 - 330048 + 220032 = 2 --> 0 holes F =2V-4: 220032 = 220036-4 (0) 2E=3F: 660096 = 660096 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 113893 - 341673 + 227782 = 2 --> 0 holes F =2V-4: 227782 = 227786-4 (0) 2E=3F: 683346 = 683346 (0) total defect index = 0 Mon Oct 14 11:56:50 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/defect2seg --s PIB23-310_VYr0_Bay3prisma --cortex freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 defect2seg 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 475639 mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 26 non-cortical segments detected only using segment with 9174 vertices erasing segment 0 (vno[0] = 14409) erasing segment 1 (vno[0] = 16811) erasing segment 2 (vno[0] = 17711) erasing segment 3 (vno[0] = 18494) erasing segment 4 (vno[0] = 19391) erasing segment 5 (vno[0] = 21110) erasing segment 6 (vno[0] = 21198) erasing segment 7 (vno[0] = 21232) erasing segment 9 (vno[0] = 41303) erasing segment 10 (vno[0] = 51992) erasing segment 11 (vno[0] = 62734) erasing segment 12 (vno[0] = 66718) erasing segment 13 (vno[0] = 76631) erasing segment 14 (vno[0] = 78885) erasing segment 15 (vno[0] = 81540) erasing segment 16 (vno[0] = 82380) erasing segment 17 (vno[0] = 83403) erasing segment 18 (vno[0] = 84079) erasing segment 19 (vno[0] = 85676) erasing segment 20 (vno[0] = 85688) erasing segment 21 (vno[0] = 85990) erasing segment 22 (vno[0] = 86510) erasing segment 23 (vno[0] = 86520) erasing segment 24 (vno[0] = 88163) erasing segment 25 (vno[0] = 90319) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz 1000 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 527388 mris_defects_pointset done mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 24 non-cortical segments detected only using segment with 8970 vertices erasing segment 0 (vno[0] = 6537) erasing segment 1 (vno[0] = 7879) erasing segment 2 (vno[0] = 8530) erasing segment 3 (vno[0] = 13830) erasing segment 4 (vno[0] = 13901) erasing segment 5 (vno[0] = 15663) erasing segment 6 (vno[0] = 22328) erasing segment 7 (vno[0] = 24370) erasing segment 8 (vno[0] = 27043) erasing segment 9 (vno[0] = 29534) erasing segment 10 (vno[0] = 29544) erasing segment 12 (vno[0] = 50815) erasing segment 13 (vno[0] = 70005) erasing segment 14 (vno[0] = 83918) erasing segment 15 (vno[0] = 83937) erasing segment 16 (vno[0] = 84721) erasing segment 17 (vno[0] = 85643) erasing segment 18 (vno[0] = 88872) erasing segment 19 (vno[0] = 90721) erasing segment 20 (vno[0] = 92058) erasing segment 21 (vno[0] = 99375) erasing segment 22 (vno[0] = 100061) erasing segment 23 (vno[0] = 102596) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz 2000 1 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 530620 mris_defects_pointset done Started at Mon Oct 14 11:56:50 CDT 2024 Ended at Mon Oct 14 11:57:43 CDT 2024 Defect2seg-Run-Time-Sec 53 Defect2seg-Run-Time-Min 1.06 Defect2seg-Run-Time-Hours 0.01 tkmeditfv PIB23-310_VYr0_Bay3prisma brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2024:10:14:11:56:49 defect2seg N 3 e 53.18 S 1.52 U 51.28 P 99% M 375156 F 59 R 615533 W 0 c 6077 w 1263 I 19512 O 18664 L 94.88 81.54 71.47 @#@FSLOADPOST 2024:10:14:11:57:43 defect2seg N 3 86.32 81.32 71.93 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.710301 remeshing to edge length 0.710301 with 3 iterations avg qual before : 0.889824 after: 0.970646 Removing intersections removing intersecting faces 000: 2 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 110018 nv = 114566 1.04134 Area 229128 0.30193 0.03403 0.035230 0.4801 Corner 687384 60.00000 8.88789 13.881353 151.6772 Edge 343692 0.84314 0.08316 0.141007 1.2686 Hinge 343692 9.83137 10.74836 0.000000 155.0411 mris_remesh done @#@FSTIME 2024:10:14:11:57:43 mris_remesh N 7 e 35.37 S 1.21 U 34.35 P 100% M 690228 F 20 R 892096 W 0 c 3550 w 882 I 2920 O 8064 L 86.32 81.32 71.93 @#@FSLOADPOST 2024:10:14:11:58:18 mris_remesh N 7 74.29 79.22 71.59 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.710689 remeshing to edge length 0.710689 with 3 iterations avg qual before : 0.89093 after: 0.970896 Removing intersections Remeshed surface quality stats nv0 = 113893 nv = 118830 1.04335 Area 237656 0.30211 0.03378 0.082054 0.4549 Corner 712968 60.00000 8.84231 17.382693 143.2815 Edge 356484 0.84333 0.08276 0.477122 1.2434 Hinge 356484 9.67659 10.63101 0.000000 131.1914 mris_remesh done @#@FSTIME 2024:10:14:11:58:18 mris_remesh N 7 e 34.41 S 1.14 U 33.48 P 100% M 669760 F 1 R 869632 W 0 c 3544 w 904 I 0 O 8360 L 74.29 79.22 71.59 @#@FSLOADPOST 2024:10:14:11:58:53 mris_remesh N 7 88.19 82.57 73.02 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2024:10:14:11:58:53 mris_remove_intersection N 2 e 3.39 S 0.28 U 3.12 P 100% M 300156 F 18 R 186301 W 0 c 407 w 386 I 2824 O 8064 L 88.19 82.57 73.02 @#@FSLOADPOST 2024:10:14:11:58:56 mris_remove_intersection N 2 84.17 81.83 72.83 rm -f ../surf/lh.inflated /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2024:10:14:11:58:56 mris_remove_intersection N 2 e 3.14 S 0.24 U 3.17 P 108% M 307608 F 2 R 197122 W 0 c 335 w 287 I 8360 O 8360 L 84.17 81.83 72.83 @#@FSLOADPOST 2024:10:14:11:59:00 mris_remove_intersection N 2 80.00 81.00 72.61 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Mon Oct 14 11:59:00 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 226679 voxels (1.35%) border gray 232711 voxels (1.39%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 100.2 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 80.8 +- 11.9 [30.0 --> 110.0] white_mean = 100.248 +/- 6.77433, gray_mean = 80.8221 +/- 11.8559 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=213 nbins=214 intensity peaks found at WM=102+-6.1, GM=80+-7.0 white_mode = 102, gray_mode = 80 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 68.1 (was 70.000000) setting MAX_BORDER_WHITE to 108.8 (was 105.000000) setting MIN_BORDER_WHITE to 80.0 (was 85.000000) setting MAX_CSF to 56.3 (was 40.000000) setting MAX_GRAY to 95.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40.000000) When placing the white surface white_border_hi = 108.774; white_border_low = 80; white_outside_low = 68.1441; white_inside_hi = 120; white_outside_hi = 108.774; When placing the pial surface pial_border_hi = 68.1441; pial_border_low = 44.4324; pial_outside_low = 10; pial_inside_hi = 95.2257; pial_outside_hi = 62.2162; #VMPC# mris_autodet_gwstats VmPeak 549796 mris_autodet_gwstats done @#@FSTIME 2024:10:14:11:59:00 mris_autodet_gwstats N 8 e 7.00 S 0.21 U 7.43 P 109% M 207028 F 25 R 102687 W 0 c 803 w 122 I 3880 O 8 L 80.00 81.00 72.61 @#@FSLOADPOST 2024:10:14:11:59:07 mris_autodet_gwstats N 8 81.60 81.32 72.76 #-------------------------------------------- #@# AutoDetGWStats rh Mon Oct 14 11:59:07 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 226679 voxels (1.35%) border gray 232711 voxels (1.39%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 100.2 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 80.8 +- 11.9 [30.0 --> 110.0] white_mean = 100.248 +/- 6.77433, gray_mean = 80.8221 +/- 11.8559 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=213 nbins=214 intensity peaks found at WM=103+-5.2, GM=81+-7.0 white_mode = 103, gray_mode = 81 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 69.1 (was 70.000000) setting MAX_BORDER_WHITE to 109.8 (was 105.000000) setting MIN_BORDER_WHITE to 81.0 (was 85.000000) setting MAX_CSF to 57.3 (was 40.000000) setting MAX_GRAY to 96.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 69.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 45.4 (was 40.000000) When placing the white surface white_border_hi = 109.774; white_border_low = 81; white_outside_low = 69.1441; white_inside_hi = 120; white_outside_hi = 109.774; When placing the pial surface pial_border_hi = 69.1441; pial_border_low = 45.4324; pial_outside_low = 10; pial_inside_hi = 96.2257; pial_outside_hi = 63.2162; #VMPC# mris_autodet_gwstats VmPeak 502444 mris_autodet_gwstats done @#@FSTIME 2024:10:14:11:59:07 mris_autodet_gwstats N 8 e 7.24 S 0.18 U 7.18 P 101% M 212276 F 1 R 113378 W 0 c 867 w 131 I 0 O 8 L 81.60 81.32 72.76 @#@FSLOADPOST 2024:10:14:11:59:14 mris_autodet_gwstats N 8 80.08 81.04 72.76 #-------------------------------------------- #@# WhitePreAparc lh Mon Oct 14 11:59:14 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface before ripping with 5 iterations Area 229128 0.26718 0.06565 0.000423 0.5640 Corner 687384 60.00000 9.66063 3.257094 166.6307 Edge 343692 0.78878 0.11895 0.024812 1.3030 Hinge 343692 6.28576 6.79311 0.000000 150.3783 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 MRIfindBrightNonWM(): 371 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8259, nmarked2=4, nripped=8259 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57283: xyz = (-51.8696,2.31681,24.5631) oxyz = (-51.8696,2.31681,24.5631) wxzy = (-51.8696,2.31681,24.5631) pxyz = (0,0,0) CBVO Creating mask 114566 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8259 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8259, nmarked2=4, nripped=8259 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=2 had to be increased for 255 vertices, nripped=8259 mean border=86.7, 547 (547) missing vertices, mean dist 0.3 [1.1 (%31.2)->1.0 (%68.8))] %28 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0650 min Finding expansion regions mean absolute distance = 1.01 +- 1.19 4045 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1795488.0, rms=8.890 001: dt: 0.5000, sse=1000553.7, rms=6.450 (27.443%) 002: dt: 0.5000, sse=611141.4, rms=4.810 (25.435%) 003: dt: 0.5000, sse=427986.6, rms=3.769 (21.634%) 004: dt: 0.5000, sse=343760.4, rms=3.145 (16.563%) 005: dt: 0.5000, sse=300448.6, rms=2.755 (12.393%) 006: dt: 0.5000, sse=277312.7, rms=2.512 (8.831%) 007: dt: 0.5000, sse=263305.3, rms=2.350 (6.421%) 008: dt: 0.5000, sse=258458.0, rms=2.262 (3.754%) 009: dt: 0.5000, sse=248930.4, rms=2.208 (2.404%) rms = 2.1731/2.2078, sse=264409.5/248930.4, time step reduction 1 of 3 to 0.250 0 1 1 010: dt: 0.5000, sse=264409.5, rms=2.173 (1.574%) 011: dt: 0.2500, sse=206656.2, rms=1.627 (25.137%) 012: dt: 0.2500, sse=200173.5, rms=1.544 (5.087%) rms = 1.5280/1.5441, sse=192243.4/200173.5, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=192243.5, rms=1.528 (1.042%) rms = 1.5058/1.5280, sse=190632.0/192243.4, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=190632.0, rms=1.506 (1.452%) maximum number of reductions reached, breaking from loop positioning took 1.4 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8259 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8549, nmarked2=35, nripped=8549 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=1 had to be increased for 285 vertices, nripped=8549 mean border=88.9, 405 (171) missing vertices, mean dist -0.3 [0.7 (%63.3)->0.3 (%36.7))] %47 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0454 min Finding expansion regions mean absolute distance = 0.54 +- 0.88 4557 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=474915.3, rms=3.703 015: dt: 0.5000, sse=327404.5, rms=2.428 (34.437%) 016: dt: 0.5000, sse=286134.6, rms=2.007 (17.342%) 017: dt: 0.5000, sse=269183.8, rms=1.850 (7.814%) rms = 1.8214/1.8499, sse=260119.0/269183.8, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=260119.0, rms=1.821 (1.543%) 019: dt: 0.2500, sse=221458.5, rms=1.338 (26.518%) rms = 1.2509/1.3384, sse=231900.4/221458.5, time step reduction 2 of 3 to 0.125 0 1 0 020: dt: 0.2500, sse=231900.4, rms=1.251 (6.536%) rms = 1.2269/1.2509, sse=210645.9/231900.4, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=210645.9, rms=1.227 (1.918%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8549 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8619, nmarked2=35, nripped=8619 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 375 vertices, nripped=8619 mean border=91.3, 359 (113) missing vertices, mean dist -0.2 [0.4 (%72.2)->0.3 (%27.8))] %71 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0214 min Finding expansion regions mean absolute distance = 0.40 +- 0.52 3558 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=419218.3, rms=3.387 022: dt: 0.5000, sse=282548.4, rms=1.911 (43.586%) 023: dt: 0.5000, sse=250073.6, rms=1.678 (12.167%) rms = 1.6974/1.6781, sse=255028.1/250073.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=226924.4, rms=1.342 (20.020%) 025: dt: 0.2500, sse=224130.5, rms=1.162 (13.403%) rms = 1.1259/1.1622, sse=215072.5/224130.5, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=215072.5, rms=1.126 (3.130%) rms = 1.0987/1.1259, sse=214231.0/215072.5, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=214231.0, rms=1.099 (2.409%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8619 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8668, nmarked2=35, nripped=8668 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 424 vertices, nripped=8668 mean border=92.3, 383 (100) missing vertices, mean dist -0.1 [0.3 (%59.7)->0.2 (%40.3))] %79 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0125 min Finding expansion regions mean absolute distance = 0.29 +- 0.39 2881 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=240736.3, rms=1.612 028: dt: 0.5000, sse=222784.2, rms=1.168 (27.567%) rms = 1.3658/1.1680, sse=230535.8/222784.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=208116.1, rms=0.943 (19.240%) rms = 0.9088/0.9432, sse=214325.8/208116.1, time step reduction 2 of 3 to 0.125 0 1 1 030: dt: 0.2500, sse=214325.8, rms=0.909 (3.648%) rms = 0.8693/0.9088, sse=208487.3/214325.8, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=208487.3, rms=0.869 (4.351%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 2.97 minutes #VMPC# mris_place_surfaces VmPeak 2046716 mris_place_surface done @#@FSTIME 2024:10:14:11:59:15 mris_place_surface N 18 e 188.10 S 5.74 U 308.39 P 167% M 1609960 F 22 R 6553493 W 0 c 34114 w 2190 I 2176 O 8064 L 80.08 81.04 72.76 @#@FSLOADPOST 2024:10:14:12:02:23 mris_place_surface N 18 54.42 73.47 71.70 #-------------------------------------------- #@# WhitePreAparc rh Mon Oct 14 12:02:23 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface before ripping with 5 iterations Area 237656 0.26765 0.06509 0.001410 0.6267 Corner 712968 60.00000 9.58742 4.374291 142.9564 Edge 356484 0.78956 0.11786 0.022869 1.3505 Hinge 356484 6.23645 6.68355 0.000000 151.7714 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 MRIfindBrightNonWM(): 371 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 #FML# MRISripMidline(): nmarked=8397, nmarked2=0, nripped=8397 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59415: xyz = (35.4352,5.89772,-20.2586) oxyz = (35.4352,5.89772,-20.2586) wxzy = (35.4352,5.89772,-20.2586) pxyz = (0,0,0) CBVO Creating mask 118830 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8397 #FML# MRISripMidline(): nmarked=8397, nmarked2=0, nripped=8397 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=2 had to be increased for 156 vertices, nripped=8397 mean border=87.4, 484 (484) missing vertices, mean dist 0.3 [1.2 (%30.9)->0.9 (%69.1))] %31 local maxima, %61 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0714 min Finding expansion regions mean absolute distance = 1.01 +- 1.22 4628 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1731132.8, rms=8.538 001: dt: 0.5000, sse=951002.6, rms=6.131 (28.195%) 002: dt: 0.5000, sse=580196.2, rms=4.552 (25.750%) 003: dt: 0.5000, sse=406284.4, rms=3.568 (21.618%) 004: dt: 0.5000, sse=322642.8, rms=2.945 (17.470%) 005: dt: 0.5000, sse=284932.4, rms=2.548 (13.453%) 006: dt: 0.5000, sse=268194.2, rms=2.304 (9.575%) 007: dt: 0.5000, sse=255826.1, rms=2.154 (6.520%) 008: dt: 0.5000, sse=240275.0, rms=2.066 (4.112%) rms = 2.0192/2.0656, sse=241250.8/240275.0, time step reduction 1 of 3 to 0.250 0 1 1 009: dt: 0.5000, sse=241250.8, rms=2.019 (2.248%) 010: dt: 0.2500, sse=202050.2, rms=1.474 (26.987%) 011: dt: 0.2500, sse=193191.7, rms=1.391 (5.664%) rms = 1.3723/1.3908, sse=188861.8/193191.7, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=188861.8, rms=1.372 (1.329%) rms = 1.3527/1.3723, sse=203563.5/188861.8, time step reduction 3 of 3 to 0.062 0 1 1 013: dt: 0.1250, sse=203563.5, rms=1.353 (1.431%) maximum number of reductions reached, breaking from loop positioning took 1.2 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8397 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8670, nmarked2=0, nripped=8670 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=1 had to be increased for 271 vertices, nripped=8670 mean border=89.5, 316 (139) missing vertices, mean dist -0.3 [0.6 (%63.8)->0.3 (%36.2))] %50 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0408 min Finding expansion regions mean absolute distance = 0.51 +- 0.83 4135 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=492160.2, rms=3.609 014: dt: 0.5000, sse=324368.1, rms=2.354 (34.781%) 015: dt: 0.5000, sse=278934.4, rms=1.918 (18.538%) 016: dt: 0.5000, sse=257184.4, rms=1.752 (8.617%) rms = 1.7180/1.7524, sse=262366.4/257184.4, time step reduction 1 of 3 to 0.250 0 1 1 017: dt: 0.5000, sse=262366.3, rms=1.718 (1.960%) 018: dt: 0.2500, sse=233703.5, rms=1.270 (26.093%) 019: dt: 0.2500, sse=231343.7, rms=1.191 (6.171%) rms = 1.1750/1.1914, sse=228074.3/231343.7, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=228074.3, rms=1.175 (1.374%) rms = 1.1573/1.1750, sse=249329.8/228074.3, time step reduction 3 of 3 to 0.062 0 1 1 021: dt: 0.1250, sse=249329.8, rms=1.157 (1.510%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8670 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8690, nmarked2=0, nripped=8690 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 336 vertices, nripped=8690 mean border=92.0, 296 (90) missing vertices, mean dist -0.3 [0.4 (%73.1)->0.3 (%26.9))] %73 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0306 min Finding expansion regions mean absolute distance = 0.39 +- 0.50 3198 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=469964.8, rms=3.395 022: dt: 0.5000, sse=296049.8, rms=1.920 (43.446%) 023: dt: 0.5000, sse=267758.6, rms=1.584 (17.491%) rms = 1.5878/1.5840, sse=285930.0/267758.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=245575.6, rms=1.277 (19.380%) 025: dt: 0.2500, sse=245035.2, rms=1.109 (13.151%) rms = 1.0742/1.1091, sse=254664.4/245035.2, time step reduction 2 of 3 to 0.125 0 1 1 026: dt: 0.2500, sse=254664.4, rms=1.074 (3.143%) rms = 1.0542/1.0742, sse=233948.0/254664.4, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=233948.0, rms=1.054 (1.860%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8690 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8733, nmarked2=0, nripped=8733 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 390 vertices, nripped=8733 mean border=93.0, 336 (72) missing vertices, mean dist -0.1 [0.3 (%60.2)->0.2 (%39.8))] %80 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0248 min Finding expansion regions mean absolute distance = 0.28 +- 0.39 2684 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=262130.6, rms=1.597 028: dt: 0.5000, sse=245113.5, rms=1.087 (31.945%) rms = 1.2719/1.0869, sse=249596.4/245113.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=242589.9, rms=0.903 (16.940%) rms = 0.8654/0.9028, sse=229043.1/242589.9, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=229043.1, rms=0.865 (4.149%) rms = 0.8385/0.8654, sse=251422.0/229043.1, time step reduction 3 of 3 to 0.062 0 1 1 031: dt: 0.1250, sse=251422.0, rms=0.839 (3.102%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 3.04 minutes #VMPC# mris_place_surfaces VmPeak 2101096 mris_place_surface done @#@FSTIME 2024:10:14:12:02:23 mris_place_surface N 18 e 189.94 S 4.44 U 310.30 P 165% M 1665780 F 3 R 4279095 W 0 c 36183 w 2616 I 8552 O 8360 L 54.42 73.47 71.70 @#@FSLOADPOST 2024:10:14:12:05:33 mris_place_surface N 18 79.90 78.59 74.10 #-------------------------------------------- #@# CortexLabel lh Mon Oct 14 12:05:33 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 12 non-cortical segments detected only using segment with 10176 vertices erasing segment 0 (vno[0] = 17536) erasing segment 1 (vno[0] = 29399) erasing segment 3 (vno[0] = 42690) erasing segment 4 (vno[0] = 53433) erasing segment 5 (vno[0] = 64827) erasing segment 6 (vno[0] = 68816) erasing segment 7 (vno[0] = 70189) erasing segment 8 (vno[0] = 79404) erasing segment 9 (vno[0] = 97173) erasing segment 10 (vno[0] = 104586) erasing segment 11 (vno[0] = 105768) @#@FSTIME 2024:10:14:12:05:33 mri_label2label N 5 e 21.03 S 0.37 U 19.68 P 95% M 319756 F 1 R 180689 W 0 c 2157 w 248 I 0 O 9056 L 79.90 78.59 74.10 @#@FSLOADPOST 2024:10:14:12:05:54 mri_label2label N 5 90.65 81.13 75.03 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Mon Oct 14 12:05:54 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 15 non-cortical segments detected only using segment with 8747 vertices erasing segment 0 (vno[0] = 17536) erasing segment 1 (vno[0] = 29399) erasing segment 3 (vno[0] = 36204) erasing segment 4 (vno[0] = 38502) erasing segment 5 (vno[0] = 39231) erasing segment 6 (vno[0] = 39290) erasing segment 7 (vno[0] = 63748) erasing segment 8 (vno[0] = 64827) erasing segment 9 (vno[0] = 68816) erasing segment 10 (vno[0] = 70189) erasing segment 11 (vno[0] = 79404) erasing segment 12 (vno[0] = 97173) erasing segment 13 (vno[0] = 104586) erasing segment 14 (vno[0] = 105768) @#@FSTIME 2024:10:14:12:05:54 mri_label2label N 5 e 23.12 S 0.28 U 20.79 P 91% M 331568 F 2 R 166072 W 0 c 2487 w 220 I 0 O 9184 L 90.65 81.13 75.03 @#@FSLOADPOST 2024:10:14:12:06:17 mri_label2label N 5 102.32 84.13 76.16 #-------------------------------------------- #@# CortexLabel rh Mon Oct 14 12:06:17 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 11 non-cortical segments detected only using segment with 10075 vertices erasing segment 0 (vno[0] = 12843) erasing segment 2 (vno[0] = 30479) erasing segment 3 (vno[0] = 37298) erasing segment 4 (vno[0] = 54969) erasing segment 5 (vno[0] = 74071) erasing segment 6 (vno[0] = 74123) erasing segment 7 (vno[0] = 74153) erasing segment 8 (vno[0] = 76880) erasing segment 9 (vno[0] = 78133) erasing segment 10 (vno[0] = 106322) @#@FSTIME 2024:10:14:12:06:18 mri_label2label N 5 e 23.72 S 0.37 U 22.18 P 95% M 322024 F 0 R 161239 W 0 c 2506 w 164 I 8360 O 9240 L 102.32 84.13 76.16 @#@FSLOADPOST 2024:10:14:12:06:41 mri_label2label N 5 98.26 84.54 76.51 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Mon Oct 14 12:06:41 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 10 non-cortical segments detected only using segment with 8509 vertices erasing segment 0 (vno[0] = 12843) erasing segment 2 (vno[0] = 30479) erasing segment 3 (vno[0] = 37298) erasing segment 4 (vno[0] = 74071) erasing segment 5 (vno[0] = 74123) erasing segment 6 (vno[0] = 74153) erasing segment 7 (vno[0] = 76880) erasing segment 8 (vno[0] = 78133) erasing segment 9 (vno[0] = 106322) @#@FSTIME 2024:10:14:12:06:41 mri_label2label N 5 e 22.37 S 0.27 U 21.52 P 97% M 317648 F 2 R 167968 W 0 c 2327 w 112 I 0 O 9352 L 98.26 84.54 76.51 @#@FSLOADPOST 2024:10:14:12:07:04 mri_label2label N 5 93.25 84.53 76.69 #-------------------------------------------- #@# Smooth2 lh Mon Oct 14 12:07:04 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Mon Oct 14 12:07:04 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 987888 of (987888 987892) to complete... Waiting for PID 987892 of (987888 987892) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (987888 987892) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Mon Oct 14 12:07:09 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Mon Oct 14 12:07:09 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 994572 of (994572 994738) to complete... Waiting for PID 994738 of (994572 994738) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.7 mm, total surface area = 71086 mm^2 step 000: RMS=0.169 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 39.281863 mris_inflate stimesec 0.381989 mris_inflate ru_maxrss 178596 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 192901 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 352 mris_inflate ru_oublock 8992 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2236 mris_inflate ru_nivcsw 4471 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 47.1 mm, total surface area = 72856 mm^2 step 000: RMS=0.167 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 40.633856 mris_inflate stimesec 1.693733 mris_inflate ru_maxrss 184232 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 656387 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8456 mris_inflate ru_oublock 9328 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3099 mris_inflate ru_nivcsw 4565 PIDs (994572 994738) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Mon Oct 14 12:07:31 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature -w -seed 1234 lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Mon Oct 14 12:07:32 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf reconbatchjobs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 1020196 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020200 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020267 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020335 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020340 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020345 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020483 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020552 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020556 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020559 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020566 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... Waiting for PID 1020570 of (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 23.097*4pi (290.240) --> -22 handles ICI = 156.7, FI = 1325.6, variation=21640.338 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 123 vertices thresholded to be in k1 ~ [-1.94 0.65], k2 ~ [-0.22 0.21] total integrated curvature = 0.474*4pi (5.956) --> 1 handles ICI = 1.4, FI = 8.5, variation=148.627 96 vertices thresholded to be in [-0.14 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 93 vertices thresholded to be in [-0.65 0.23] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.019, std = 0.026 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 19.488*4pi (244.894) --> -18 handles ICI = 150.4, FI = 1312.9, variation=21321.204 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 141 vertices thresholded to be in k1 ~ [-3.40 0.55], k2 ~ [-0.26 0.15] total integrated curvature = 0.480*4pi (6.028) --> 1 handles ICI = 1.5, FI = 10.4, variation=172.654 135 vertices thresholded to be in [-0.05 0.05] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 97 vertices thresholded to be in [-1.09 0.25] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.020, std = 0.034 done. PIDs (1020196 1020200 1020267 1020335 1020340 1020345 1020483 1020552 1020556 1020559 1020566 1020570) completed and logs appended. #-------------------------------------------- #@# Sphere lh Mon Oct 14 12:08:31 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Mon Oct 14 12:08:31 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 1091581 of (1091581 1091584) to complete... Waiting for PID 1091584 of (1091581 1091584) to complete... mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.315... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.31 pass 1: epoch 2 of 3 starting distance error %19.26 unfolding complete - removing small folds... starting distance error %19.19 removing remaining folds... final distance error %19.23 MRISunfold() return, current seed 1234 -01: dt=0.0000, 28 negative triangles VmPeak 773736 213: dt=0.9900, 28 negative triangles 214: dt=0.9900, 11 negative triangles 215: dt=0.9900, 8 negative triangles 216: dt=0.9900, 13 negative triangles 217: dt=0.9900, 7 negative triangles 218: dt=0.9900, 8 negative triangles 219: dt=0.9900, 5 negative triangles 220: dt=0.9900, 6 negative triangles 221: dt=0.9900, 6 negative triangles 222: dt=0.9900, 5 negative triangles 223: dt=0.9900, 6 negative triangles 224: dt=0.9900, 2 negative triangles 225: dt=0.9900, 2 negative triangles 226: dt=0.9900, 2 negative triangles 227: dt=0.9900, 2 negative triangles 228: dt=0.9900, 4 negative triangles 229: dt=0.9900, 2 negative triangles 230: dt=0.9900, 1 negative triangles 231: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1445 hours FSRUNTIME@ mris_sphere 0.1445 hours 4 threads #VMPC# mris_sphere VmPeak 773736 mris_sphere done mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.305... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.14 pass 1: epoch 2 of 3 starting distance error %19.11 unfolding complete - removing small folds... starting distance error %19.07 removing remaining folds... final distance error %19.11 MRISunfold() return, current seed 1234 -01: dt=0.0000, 14 negative triangles VmPeak 777144 169: dt=0.9900, 14 negative triangles 170: dt=0.9900, 4 negative triangles 171: dt=0.9900, 2 negative triangles 172: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1198 hours FSRUNTIME@ mris_sphere 0.1198 hours 4 threads #VMPC# mris_sphere VmPeak 777144 mris_sphere done PIDs (1091581 1091584) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Mon Oct 14 12:17:12 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Mon Oct 14 12:17:12 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 1615613 of (1615613 1615617) to complete... Waiting for PID 1615617 of (1615613 1615617) to complete... mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts cmdline mris_register -curv ../surf/lh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from ../surf/lh.sphere... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.289 curvature mean = 0.041, std = 0.820 curvature mean = 0.013, std = 0.886 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (9.50, -6.50, 0.00) sse = 177666.9, elapsed since starting=0.1675 min MRISrigidBodyAlignGlobal() done 0.17 min curvature mean = 0.044, std = 0.848 curvature mean = 0.005, std = 0.959 curvature mean = 0.043, std = 0.861 curvature mean = 0.002, std = 0.984 curvature mean = 0.043, std = 0.865 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.023, std = 0.269 curvature mean = 0.045, std = 0.252 curvature mean = 0.056, std = 0.382 curvature mean = 0.038, std = 0.312 curvature mean = 0.028, std = 0.568 curvature mean = 0.037, std = 0.340 curvature mean = 0.012, std = 0.707 curvature mean = 0.037, std = 0.353 curvature mean = 0.003, std = 0.816 MRISregister() return, current seed 0 -01: dt=0.0000, 18 negative triangles VmPeak 773772 110: dt=0.9900, 18 negative triangles 111: dt=0.9900, 17 negative triangles 112: dt=0.9900, 21 negative triangles 113: dt=0.9900, 15 negative triangles 114: dt=0.9900, 16 negative triangles 115: dt=0.9900, 13 negative triangles 116: dt=0.9900, 9 negative triangles 117: dt=0.9900, 11 negative triangles 118: dt=0.9900, 8 negative triangles 119: dt=0.9900, 11 negative triangles 120: dt=0.9900, 8 negative triangles 121: dt=0.9900, 11 negative triangles 122: dt=0.9900, 10 negative triangles 123: dt=0.9900, 9 negative triangles 124: dt=0.9900, 2 negative triangles 125: dt=0.9900, 4 negative triangles 126: dt=0.9900, 6 negative triangles 127: dt=0.9900, 1 negative triangles 128: dt=0.9900, 1 negative triangles 129: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.10 hours #VMPC# mris_register VmPeak 773772 FSRUNTIME@ mris_register 0.0964 hours 4 threads mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts cmdline mris_register -curv ../surf/rh.sphere /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from ../surf/rh.sphere... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host=chopi, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.250 curvature mean = 0.041, std = 0.818 curvature mean = 0.016, std = 0.881 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (9.00, -6.50, 2.00) sse = 235440.3, elapsed since starting=0.1782 min MRISrigidBodyAlignGlobal() done 0.18 min curvature mean = 0.033, std = 0.846 curvature mean = 0.006, std = 0.957 curvature mean = 0.032, std = 0.858 curvature mean = 0.002, std = 0.983 curvature mean = 0.031, std = 0.862 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.023, std = 0.269 curvature mean = 0.039, std = 0.246 curvature mean = 0.061, std = 0.388 curvature mean = 0.033, std = 0.307 curvature mean = 0.028, std = 0.575 curvature mean = 0.031, std = 0.334 curvature mean = 0.012, std = 0.716 curvature mean = 0.031, std = 0.347 curvature mean = 0.002, std = 0.825 MRISregister() return, current seed 0 -01: dt=0.0000, 5 negative triangles VmPeak 712304 110: dt=0.9900, 5 negative triangles 111: dt=0.9900, 4 negative triangles 112: dt=0.9900, 6 negative triangles 113: dt=0.9900, 8 negative triangles 114: dt=0.9900, 6 negative triangles 115: dt=0.9900, 4 negative triangles 116: dt=0.9900, 6 negative triangles 117: dt=0.9900, 6 negative triangles 118: dt=0.9900, 5 negative triangles 119: dt=0.9900, 3 negative triangles 120: dt=0.9900, 4 negative triangles 121: dt=0.9900, 4 negative triangles 122: dt=0.9900, 3 negative triangles 123: dt=0.9900, 1 negative triangles 124: dt=0.9900, 3 negative triangles 125: dt=0.9900, 1 negative triangles 126: dt=0.9900, 3 negative triangles 127: dt=0.9900, 1 negative triangles 128: dt=0.9900, 3 negative triangles 129: dt=0.9900, 5 negative triangles 130: dt=0.9900, 3 negative triangles 131: dt=0.9900, 1 negative triangles 132: dt=0.9900, 1 negative triangles 133: dt=0.9405, 3 negative triangles 134: dt=0.9405, 1 negative triangles 135: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.11 hours #VMPC# mris_register VmPeak 712304 FSRUNTIME@ mris_register 0.1103 hours 4 threads PIDs (1615613 1615617) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Mon Oct 14 12:23:49 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Mon Oct 14 12:23:49 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 2024477 of (2024477 2024481) to complete... Waiting for PID 2024481 of (2024477 2024481) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (2024477 2024481) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Mon Oct 14 12:23:51 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Mon Oct 14 12:23:51 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 2024579 of (2024579 2024582) to complete... Waiting for PID 2024582 of (2024579 2024582) to complete... mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (2024579 2024582) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Mon Oct 14 12:23:52 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Mon Oct 14 12:23:52 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 2025938 of (2025938 2025941) to complete... Waiting for PID 2025941 of (2025938 2025941) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1159 labels changed using aseg relabeling using gibbs priors... 000: 2616 changed, 114566 examined... 001: 603 changed, 11491 examined... 002: 137 changed, 3449 examined... 003: 38 changed, 891 examined... 004: 15 changed, 242 examined... 005: 6 changed, 89 examined... 006: 1 changed, 36 examined... 007: 0 changed, 7 examined... 195 labels changed using aseg 000: 82 total segments, 37 labels (264 vertices) changed 001: 46 total segments, 1 labels (1 vertices) changed 002: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1660 vertices marked for relabeling... 1660 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 15 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1265 labels changed using aseg relabeling using gibbs priors... 000: 2399 changed, 118830 examined... 001: 536 changed, 10807 examined... 002: 113 changed, 3148 examined... 003: 39 changed, 697 examined... 004: 13 changed, 236 examined... 005: 5 changed, 81 examined... 006: 5 changed, 34 examined... 007: 3 changed, 29 examined... 008: 4 changed, 20 examined... 009: 4 changed, 16 examined... 010: 2 changed, 16 examined... 011: 4 changed, 14 examined... 012: 3 changed, 22 examined... 013: 2 changed, 15 examined... 014: 0 changed, 10 examined... 216 labels changed using aseg 000: 76 total segments, 25 labels (106 vertices) changed 001: 51 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1286 vertices marked for relabeling... 1286 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 15 seconds. PIDs (2025938 2025941) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Mon Oct 14 12:24:07 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 229128 0.34374 0.13007 0.000419 1.9278 Corner 687384 60.00000 15.10488 0.511036 178.1723 Edge 343692 0.90418 0.21587 0.010652 3.1648 Hinge 343692 11.77350 13.07546 0.000000 179.9765 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 MRIfindBrightNonWM(): 371 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label MRISripNotLabel() ripped 10408/114566 vertices (104158 unripped) Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 418 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57283: xyz = (-52.0295,2.33089,24.5719) oxyz = (-52.0295,2.33089,24.5719) wxzy = (-52.0295,2.33089,24.5719) pxyz = (0,0,0) CBVO Creating mask 114566 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=2 had to be increased for 254 vertices, nripped=10826 mean border=86.7, 1014 (1014) missing vertices, mean dist 0.4 [2.4 (%11.7)->0.8 (%88.3))] %27 local maxima, %63 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0616 min Finding expansion regions mean absolute distance = 0.95 +- 1.11 3490 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1082156.1, rms=6.676 001: dt: 0.5000, sse=495130.9, rms=4.025 (39.720%) 002: dt: 0.5000, sse=317699.9, rms=2.736 (32.019%) 003: dt: 0.5000, sse=267654.1, rms=2.257 (17.517%) 004: dt: 0.5000, sse=250808.2, rms=2.045 (9.395%) 005: dt: 0.5000, sse=248462.7, rms=1.993 (2.507%) rms = 1.9377/1.9934, sse=249558.2/248462.7, time step reduction 1 of 3 to 0.250 0 1 0 006: dt: 0.5000, sse=249558.2, rms=1.938 (2.793%) 007: dt: 0.2500, sse=216879.2, rms=1.536 (20.723%) 008: dt: 0.2500, sse=213314.7, rms=1.473 (4.126%) rms = 1.4615/1.4728, sse=213813.3/213314.7, time step reduction 2 of 3 to 0.125 0 1 1 009: dt: 0.2500, sse=213813.3, rms=1.462 (0.766%) rms = 1.4494/1.4615, sse=214514.0/213813.3, time step reduction 3 of 3 to 0.062 0 1 1 010: dt: 0.1250, sse=214514.0, rms=1.449 (0.827%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=1 had to be increased for 240 vertices, nripped=10826 mean border=88.7, 446 (319) missing vertices, mean dist -0.3 [0.7 (%60.2)->0.3 (%39.8))] %45 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0467 min Finding expansion regions mean absolute distance = 0.53 +- 0.88 4309 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=437666.9, rms=3.527 011: dt: 0.5000, sse=297376.1, rms=2.408 (31.721%) 012: dt: 0.5000, sse=267130.2, rms=2.057 (14.605%) 013: dt: 0.5000, sse=257469.5, rms=1.947 (5.333%) rms = 1.9393/1.9469, sse=255442.1/257469.5, time step reduction 1 of 3 to 0.250 0 0 1 014: dt: 0.5000, sse=255442.1, rms=1.939 (0.387%) 015: dt: 0.2500, sse=229660.3, rms=1.562 (19.435%) 016: dt: 0.2500, sse=227456.5, rms=1.504 (3.740%) rms = 1.4901/1.5040, sse=224751.4/227456.5, time step reduction 2 of 3 to 0.125 0 0 1 017: dt: 0.2500, sse=224751.4, rms=1.490 (0.921%) rms = 1.4734/1.4901, sse=223707.2/224751.4, time step reduction 3 of 3 to 0.062 0 0 1 018: dt: 0.1250, sse=223707.2, rms=1.473 (1.125%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 261 vertices, nripped=10826 mean border=91.2, 417 (224) missing vertices, mean dist -0.3 [0.5 (%72.0)->0.3 (%28.0))] %70 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0265 min Finding expansion regions mean absolute distance = 0.40 +- 0.51 3506 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=440764.6, rms=3.577 019: dt: 0.5000, sse=279783.7, rms=2.211 (38.200%) 020: dt: 0.5000, sse=258699.3, rms=1.979 (10.467%) rms = 1.9556/1.9793, sse=257559.3/258699.3, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=257559.3, rms=1.956 (1.197%) 022: dt: 0.2500, sse=227209.7, rms=1.550 (20.718%) 023: dt: 0.2500, sse=221852.0, rms=1.454 (6.213%) rms = 1.4167/1.4541, sse=218531.3/221852.0, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=218531.3, rms=1.417 (2.572%) rms = 1.3827/1.4167, sse=217130.4/218531.3, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=217130.4, rms=1.383 (2.396%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 299 vertices, nripped=10826 mean border=92.2, 454 (188) missing vertices, mean dist -0.1 [0.3 (%59.3)->0.2 (%40.7))] %78 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0209 min Finding expansion regions mean absolute distance = 0.28 +- 0.39 2610 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=244605.7, rms=1.845 026: dt: 0.5000, sse=221846.6, rms=1.401 (24.057%) rms = 1.5517/1.4010, sse=229245.7/221846.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=212529.9, rms=1.245 (11.106%) rms = 1.2000/1.2454, sse=208123.3/212529.9, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=208123.3, rms=1.200 (3.645%) rms = 1.1745/1.2000, sse=208465.1/208123.3, time step reduction 3 of 3 to 0.062 0 1 1 029: dt: 0.1250, sse=208465.1, rms=1.174 (2.127%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 2.65 minutes #VMPC# mris_place_surfaces VmPeak 2014136 mris_place_surface done @#@FSTIME 2024:10:14:12:24:07 mris_place_surface N 25 e 168.29 S 2.63 U 286.64 P 171% M 1589608 F 3 R 1819586 W 0 c 30481 w 2152 I 368 O 8064 L 64.70 78.72 86.64 @#@FSLOADPOST 2024:10:14:12:26:56 mris_place_surface N 25 60.99 71.47 82.59 #-------------------------------------------- #@# WhiteSurfs rh Mon Oct 14 12:26:56 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 237656 0.33784 0.12575 0.001522 2.4832 Corner 712968 60.00000 15.09914 0.467207 178.2752 Edge 356484 0.89591 0.20906 0.013162 3.2739 Hinge 356484 11.37556 12.68166 0.000000 179.9197 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 MRIfindBrightNonWM(): 371 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label MRISripNotLabel() ripped 10394/118830 vertices (108436 unripped) Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 277 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59415: xyz = (35.898,6.29272,-19.656) oxyz = (35.898,6.29272,-19.656) wxzy = (35.898,6.29272,-19.656) pxyz = (0,0,0) CBVO Creating mask 118830 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=2 had to be increased for 249 vertices, nripped=10671 mean border=87.4, 835 (835) missing vertices, mean dist 0.4 [2.4 (%11.5)->0.8 (%88.5))] %30 local maxima, %61 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0794 min Finding expansion regions mean absolute distance = 0.96 +- 1.12 3702 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1133635.8, rms=6.683 001: dt: 0.5000, sse=516616.0, rms=4.037 (39.589%) 002: dt: 0.5000, sse=321322.8, rms=2.655 (34.238%) 003: dt: 0.5000, sse=265671.1, rms=2.108 (20.594%) 004: dt: 0.5000, sse=242846.1, rms=1.854 (12.036%) 005: dt: 0.5000, sse=238909.2, rms=1.800 (2.915%) 006: dt: 0.5000, sse=236519.0, rms=1.726 (4.118%) rms = 1.7573/1.7262, sse=237373.9/236519.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 007: dt: 0.2500, sse=215534.0, rms=1.424 (17.485%) 008: dt: 0.2500, sse=208166.0, rms=1.286 (9.747%) rms = 1.2573/1.2855, sse=206952.7/208166.0, time step reduction 2 of 3 to 0.125 0 0 1 009: dt: 0.2500, sse=206952.7, rms=1.257 (2.200%) rms = 1.2446/1.2573, sse=205956.5/206952.7, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=205956.5, rms=1.245 (1.008%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=1 had to be increased for 227 vertices, nripped=10671 mean border=89.4, 402 (289) missing vertices, mean dist -0.3 [0.7 (%60.9)->0.3 (%39.1))] %48 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0554 min Finding expansion regions mean absolute distance = 0.52 +- 0.86 4198 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=420560.2, rms=3.318 011: dt: 0.5000, sse=279589.2, rms=2.125 (35.962%) 012: dt: 0.5000, sse=243047.5, rms=1.698 (20.087%) 013: dt: 0.5000, sse=233424.4, rms=1.566 (7.803%) rms = 1.5478/1.5657, sse=232179.6/233424.4, time step reduction 1 of 3 to 0.250 0 0 1 014: dt: 0.5000, sse=232179.6, rms=1.548 (1.145%) 015: dt: 0.2500, sse=209380.5, rms=1.129 (27.043%) 016: dt: 0.2500, sse=206822.9, rms=1.066 (5.634%) rms = 1.0615/1.0656, sse=206654.1/206822.9, time step reduction 2 of 3 to 0.125 0 0 1 017: dt: 0.2500, sse=206654.1, rms=1.061 (0.383%) rms = 1.0501/1.0615, sse=207033.7/206654.1, time step reduction 3 of 3 to 0.062 0 1 1 018: dt: 0.1250, sse=207033.7, rms=1.050 (1.070%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 285 vertices, nripped=10671 mean border=91.9, 387 (216) missing vertices, mean dist -0.3 [0.5 (%72.8)->0.3 (%27.2))] %72 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0365 min Finding expansion regions mean absolute distance = 0.40 +- 0.51 3411 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=424848.9, rms=3.373 019: dt: 0.5000, sse=256725.5, rms=1.871 (44.519%) 020: dt: 0.5000, sse=230287.0, rms=1.502 (19.733%) rms = 1.4958/1.5019, sse=230101.5/230287.0, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=230101.5, rms=1.496 (0.409%) 022: dt: 0.2500, sse=205046.8, rms=1.047 (30.011%) 023: dt: 0.2500, sse=202241.5, rms=0.984 (6.028%) rms = 0.9847/0.9838, sse=202746.4/202241.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.9769/0.9838, sse=201842.5/202241.5, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=201842.5, rms=0.977 (0.698%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 342 vertices, nripped=10671 mean border=92.9, 380 (172) missing vertices, mean dist -0.1 [0.3 (%59.7)->0.2 (%40.3))] %79 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0233 min Finding expansion regions mean absolute distance = 0.28 +- 0.39 3134 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=228953.3, rms=1.541 025: dt: 0.5000, sse=209028.7, rms=1.053 (31.690%) rms = 1.2623/1.0530, sse=219688.6/209028.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=200683.5, rms=0.845 (19.734%) rms = 0.8021/0.8452, sse=199609.4/200683.4, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=199609.4, rms=0.802 (5.092%) rms = 0.7806/0.8021, sse=195918.6/199609.4, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=195918.6, rms=0.781 (2.686%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 3.30 minutes #VMPC# mris_place_surfaces VmPeak 2096312 mris_place_surface done @#@FSTIME 2024:10:14:12:26:56 mris_place_surface N 25 e 208.81 S 5.60 U 333.51 P 162% M 1673596 F 1 R 4906159 W 0 c 39509 w 2581 I 0 O 8360 L 60.99 71.47 82.59 @#@FSLOADPOST 2024:10:14:12:30:25 mris_place_surface N 25 76.12 72.93 80.90 #-------------------------------------------- #@# T1PialSurf lh Mon Oct 14 12:30:25 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 229128 0.34779 0.14570 0.000902 2.4308 Corner 687384 60.00000 16.53995 0.516989 178.7201 Edge 343692 0.91149 0.23822 0.026064 3.5297 Hinge 343692 11.89190 13.24070 0.000000 179.9765 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 MRIfindBrightNonWM(): 371 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 69.829 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 9000/114566 vertices (105566 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57283: xyz = (-52.0615,2.22535,24.8745) oxyz = (-52.0615,2.22535,24.8745) wxzy = (-52.0615,2.22535,24.8745) pxyz = (-52.0615,2.22535,24.8745) CBVO Creating mask 114566 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.2256700; border_hi = 68.1441420; border_low = 44.4324190; outside_low = 10.0000000; outside_hi = 62.2162090; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=2 had to be increased for 305 vertices, nripped=9000 mean border=63.2, 962 (962) missing vertices, mean dist 2.3 [1.7 (%0.1)->2.6 (%99.9))] %38 local maxima, %41 large gradients and %12 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0831 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=18437542.0, rms=29.552 001: dt: 0.5000, sse=14423143.0, rms=26.104 (11.667%) 002: dt: 0.5000, sse=11309838.0, rms=23.078 (11.595%) 003: dt: 0.5000, sse=9009195.0, rms=20.555 (10.929%) 004: dt: 0.5000, sse=7311124.5, rms=18.473 (10.130%) 005: dt: 0.5000, sse=5968809.5, rms=16.643 (9.906%) 006: dt: 0.5000, sse=4791435.5, rms=14.854 (10.753%) 007: dt: 0.5000, sse=3775492.8, rms=13.114 (11.713%) 008: dt: 0.5000, sse=2916723.2, rms=11.438 (12.780%) 009: dt: 0.5000, sse=2244607.5, rms=9.929 (13.188%) 010: dt: 0.5000, sse=1758867.9, rms=8.676 (12.622%) 011: dt: 0.5000, sse=1435001.8, rms=7.727 (10.943%) 012: dt: 0.5000, sse=1215985.4, rms=7.011 (9.266%) 013: dt: 0.5000, sse=1075416.2, rms=6.509 (7.161%) 014: dt: 0.5000, sse=976289.2, rms=6.129 (5.831%) 015: dt: 0.5000, sse=912228.1, rms=5.869 (4.241%) 016: dt: 0.5000, sse=863002.6, rms=5.661 (3.540%) 017: dt: 0.5000, sse=825117.2, rms=5.495 (2.935%) 018: dt: 0.5000, sse=796430.6, rms=5.366 (2.354%) 019: dt: 0.5000, sse=775426.9, rms=5.269 (1.812%) 020: dt: 0.5000, sse=757143.8, rms=5.183 (1.629%) 021: dt: 0.5000, sse=743864.7, rms=5.119 (1.231%) 022: dt: 0.5000, sse=731706.2, rms=5.060 (1.149%) rms = 5.0259/5.0603, sse=724838.6/731706.3, time step reduction 1 of 3 to 0.250 0 0 1 023: dt: 0.5000, sse=724838.6, rms=5.026 (0.680%) 024: dt: 0.2500, sse=494389.7, rms=3.748 (25.430%) 025: dt: 0.2500, sse=444274.0, rms=3.411 (8.988%) 026: dt: 0.2500, sse=432546.8, rms=3.326 (2.474%) rms = 3.2815/3.3265, sse=426298.1/432546.8, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=426298.1, rms=3.282 (1.352%) 028: dt: 0.1250, sse=398487.7, rms=3.069 (6.475%) rms = 3.0370/3.0690, sse=394416.8/398487.7, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=394416.8, rms=3.037 (1.043%) maximum number of reductions reached, breaking from loop positioning took 2.2 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.2256700; border_hi = 68.1441420; border_low = 44.4324190; outside_low = 10.0000000; outside_hi = 62.2162090; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=1 had to be increased for 2414 vertices, nripped=9000 mean border=60.1, 614 (63) missing vertices, mean dist 0.2 [0.1 (%32.9)->0.4 (%67.1))] %59 local maxima, %24 large gradients and % 9 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0212 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=864368.7, rms=5.406 030: dt: 0.5000, sse=752352.8, rms=4.884 (9.647%) rms = 4.8962/4.8841, sse=750566.7/752352.7, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 031: dt: 0.2500, sse=568267.8, rms=3.888 (20.385%) 032: dt: 0.2500, sse=501896.9, rms=3.465 (10.884%) 033: dt: 0.2500, sse=485695.0, rms=3.352 (3.258%) 034: dt: 0.2500, sse=477907.3, rms=3.298 (1.628%) rms = 3.2720/3.2978, sse=474204.8/477907.3, time step reduction 2 of 3 to 0.125 0 0 1 035: dt: 0.2500, sse=474204.8, rms=3.272 (0.782%) 036: dt: 0.1250, sse=450444.6, rms=3.092 (5.488%) rms = 3.0528/3.0924, sse=445293.4/450444.6, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=445293.4, rms=3.053 (1.280%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.2256700; border_hi = 68.1441420; border_low = 44.4324190; outside_low = 10.0000000; outside_hi = 62.2162090; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 2571 vertices, nripped=9000 mean border=58.4, 792 (39) missing vertices, mean dist 0.1 [0.1 (%35.8)->0.3 (%64.2))] %69 local maxima, %14 large gradients and % 8 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0149 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=550378.1, rms=3.765 rms = 4.6870/3.7649, sse=715572.9/550378.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 038: dt: 0.2500, sse=470084.9, rms=3.216 (14.577%) 039: dt: 0.2500, sse=452981.8, rms=3.086 (4.035%) rms = 3.0620/3.0863, sse=449340.7/452981.8, time step reduction 2 of 3 to 0.125 0 0 1 040: dt: 0.2500, sse=449340.7, rms=3.062 (0.790%) 041: dt: 0.1250, sse=435169.8, rms=2.949 (3.706%) rms = 2.9214/2.9485, sse=431695.2/435169.9, time step reduction 3 of 3 to 0.062 0 0 1 042: dt: 0.1250, sse=431695.2, rms=2.921 (0.918%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.2256700; border_hi = 68.1441420; border_low = 44.4324190; outside_low = 10.0000000; outside_hi = 62.2162090; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 2248 vertices, nripped=9000 mean border=57.7, 1433 (34) missing vertices, mean dist 0.0 [0.2 (%44.5)->0.2 (%55.5))] %71 local maxima, %11 large gradients and % 8 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0100 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=450593.7, rms=3.076 rms = 3.7812/3.0755, sse=551710.2/450593.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 043: dt: 0.2500, sse=428512.5, rms=2.899 (5.723%) rms = 2.8609/2.8995, sse=423213.6/428512.5, time step reduction 2 of 3 to 0.125 0 0 1 044: dt: 0.2500, sse=423213.6, rms=2.861 (1.331%) 045: dt: 0.1250, sse=416302.6, rms=2.803 (2.030%) rms = 2.7716/2.8028, sse=412383.6/416302.6, time step reduction 3 of 3 to 0.062 0 0 1 046: dt: 0.1250, sse=412383.6, rms=2.772 (1.114%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 8 intersecting step 1 with no progress (num=11, old_num=8) 001: 11 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 3.79 minutes #VMPC# mris_place_surfaces VmPeak 1463220 mris_place_surface done @#@FSTIME 2024:10:14:12:30:25 mris_place_surface N 28 e 238.47 S 3.16 U 414.94 P 175% M 1026676 F 1 R 2400784 W 0 c 46874 w 2856 I 9184 O 8064 L 76.12 72.93 80.90 @#@FSLOADPOST 2024:10:14:12:34:23 mris_place_surface N 28 58.44 68.87 77.78 #-------------------------------------------- #@# T1PialSurf rh Mon Oct 14 12:34:23 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 237656 0.34148 0.14152 0.000418 2.9781 Corner 712968 60.00000 16.62719 0.172661 179.5496 Edge 356484 0.90267 0.23099 0.018733 4.0220 Hinge 356484 11.56079 13.08780 0.000000 179.9863 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 MRIfindBrightNonWM(): 371 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 70.829 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 9056/118830 vertices (109774 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59415: xyz = (35.898,6.29272,-19.656) oxyz = (35.898,6.29272,-19.656) wxzy = (35.898,6.29272,-19.656) pxyz = (35.898,6.29272,-19.656) CBVO Creating mask 118830 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2256700; border_hi = 69.1441420; border_low = 45.4324190; outside_low = 10.0000000; outside_hi = 63.2162090; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=2 had to be increased for 287 vertices, nripped=9056 mean border=64.3, 812 (812) missing vertices, mean dist 2.2 [1.0 (%0.0)->2.7 (%100.0))] %37 local maxima, %40 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0643 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=18787016.0, rms=29.229 001: dt: 0.5000, sse=14717087.0, rms=25.837 (11.604%) 002: dt: 0.5000, sse=11564695.0, rms=22.866 (11.499%) 003: dt: 0.5000, sse=9239270.0, rms=20.398 (10.794%) 004: dt: 0.5000, sse=7520923.0, rms=18.361 (9.985%) 005: dt: 0.5000, sse=6168518.5, rms=16.582 (9.687%) 006: dt: 0.5000, sse=4983826.0, rms=14.850 (10.448%) 007: dt: 0.5000, sse=3946070.2, rms=13.145 (11.478%) 008: dt: 0.5000, sse=3052388.2, rms=11.475 (12.705%) 009: dt: 0.5000, sse=2321998.8, rms=9.902 (13.706%) 010: dt: 0.5000, sse=1778953.1, rms=8.546 (13.698%) 011: dt: 0.5000, sse=1423644.5, rms=7.525 (11.945%) 012: dt: 0.5000, sse=1209120.5, rms=6.834 (9.188%) 013: dt: 0.5000, sse=1071414.5, rms=6.349 (7.097%) 014: dt: 0.5000, sse=978952.7, rms=6.000 (5.495%) 015: dt: 0.5000, sse=910268.8, rms=5.726 (4.563%) 016: dt: 0.5000, sse=860339.5, rms=5.518 (3.634%) 017: dt: 0.5000, sse=817261.3, rms=5.332 (3.378%) 018: dt: 0.5000, sse=787713.1, rms=5.199 (2.487%) 019: dt: 0.5000, sse=761192.2, rms=5.077 (2.345%) 020: dt: 0.5000, sse=744457.8, rms=4.998 (1.555%) 021: dt: 0.5000, sse=728664.1, rms=4.923 (1.506%) rms = 4.8737/4.9229, sse=718722.1/728664.1, time step reduction 1 of 3 to 0.250 0 0 1 022: dt: 0.5000, sse=718722.1, rms=4.874 (0.999%) 023: dt: 0.2500, sse=496260.9, rms=3.654 (25.026%) 024: dt: 0.2500, sse=448017.5, rms=3.334 (8.750%) 025: dt: 0.2500, sse=438634.3, rms=3.267 (2.009%) 026: dt: 0.2500, sse=430729.0, rms=3.211 (1.724%) rms = 3.1797/3.2110, sse=426452.8/430729.0, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=426452.8, rms=3.180 (0.973%) 028: dt: 0.1250, sse=398678.5, rms=2.969 (6.615%) rms = 2.9332/2.9694, sse=394069.6/398678.5, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=394069.6, rms=2.933 (1.219%) maximum number of reductions reached, breaking from loop positioning took 2.4 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2256700; border_hi = 69.1441420; border_low = 45.4324190; outside_low = 10.0000000; outside_hi = 63.2162090; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=1 had to be increased for 3218 vertices, nripped=9056 mean border=61.4, 817 (72) missing vertices, mean dist 0.2 [0.1 (%33.9)->0.4 (%66.1))] %55 local maxima, %24 large gradients and %12 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0291 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=820534.8, rms=5.076 030: dt: 0.5000, sse=737247.8, rms=4.682 (7.760%) 031: dt: 0.5000, sse=717442.6, rms=4.604 (1.654%) rms = 4.9025/4.6043, sse=781061.1/717442.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=531266.6, rms=3.550 (22.889%) 033: dt: 0.2500, sse=478304.3, rms=3.183 (10.345%) 034: dt: 0.2500, sse=464243.0, rms=3.081 (3.211%) rms = 3.0405/3.0809, sse=458915.2/464243.0, time step reduction 2 of 3 to 0.125 0 0 1 035: dt: 0.2500, sse=458915.2, rms=3.041 (1.311%) 036: dt: 0.1250, sse=433396.1, rms=2.839 (6.622%) rms = 2.7982/2.8392, sse=428370.1/433396.1, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=428370.1, rms=2.798 (1.442%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2256700; border_hi = 69.1441420; border_low = 45.4324190; outside_low = 10.0000000; outside_hi = 63.2162090; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 3522 vertices, nripped=9056 mean border=60.0, 962 (32) missing vertices, mean dist 0.1 [0.2 (%37.1)->0.3 (%62.9))] %66 local maxima, %14 large gradients and %12 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0217 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=522601.9, rms=3.462 rms = 4.3711/3.4616, sse=679268.0/522601.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 038: dt: 0.2500, sse=452914.9, rms=2.964 (14.376%) 039: dt: 0.2500, sse=439268.9, rms=2.857 (3.616%) rms = 2.8595/2.8568, sse=439092.0/439268.9, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 2.8126/2.8568, sse=433845.1/439268.9, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=433845.1, rms=2.813 (1.545%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 96.2256700; border_hi = 69.1441420; border_low = 45.4324190; outside_low = 10.0000000; outside_hi = 63.2162090; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 2963 vertices, nripped=9056 mean border=59.4, 1792 (27) missing vertices, mean dist 0.0 [0.2 (%46.5)->0.2 (%53.5))] %68 local maxima, %12 large gradients and %12 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0146 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=445195.0, rms=2.908 rms = 3.5583/2.9078, sse=535581.5/445195.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 041: dt: 0.2500, sse=423193.0, rms=2.729 (6.153%) rms = 2.6888/2.7289, sse=417792.9/423193.0, time step reduction 2 of 3 to 0.125 0 0 1 042: dt: 0.2500, sse=417792.8, rms=2.689 (1.470%) 043: dt: 0.1250, sse=408577.2, rms=2.609 (2.967%) rms = 2.5758/2.6090, sse=404562.4/408577.3, time step reduction 3 of 3 to 0.062 0 0 1 044: dt: 0.1250, sse=404562.4, rms=2.576 (1.273%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Pinning medial wall to white surface removing intersecting faces 000: 2 intersecting step 1 with no progress (num=17, old_num=2) 001: 17 intersecting step 2 with no progress (num=24, old_num=17) 002: 24 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 4.20 minutes #VMPC# mris_place_surfaces VmPeak 1478124 mris_place_surface done @#@FSTIME 2024:10:14:12:34:24 mris_place_surface N 28 e 263.17 S 3.66 U 440.16 P 168% M 1042704 F 1 R 3044359 W 0 c 52210 w 2410 I 17712 O 8360 L 58.44 68.87 77.78 @#@FSLOADPOST 2024:10:14:12:38:47 mris_place_surface N 28 94.44 79.86 79.73 #@# white curv lh Mon Oct 14 12:38:47 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2024:10:14:12:38:48 mris_place_surface N 5 e 3.36 S 0.22 U 3.03 P 97% M 158200 F 3 R 63428 W 0 c 448 w 150 I 0 O 896 L 94.44 79.86 79.73 @#@FSLOADPOST 2024:10:14:12:38:51 mris_place_surface N 5 91.68 79.53 79.63 #@# white area lh Mon Oct 14 12:38:51 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2024:10:14:12:38:51 mris_place_surface N 3 e 1.29 S 0.11 U 1.47 P 122% M 158244 F 1 R 42568 W 0 c 228 w 119 I 96 O 896 L 91.68 79.53 79.63 @#@FSLOADPOST 2024:10:14:12:38:53 mris_place_surface N 3 91.68 79.53 79.63 #@# pial curv lh Mon Oct 14 12:38:53 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2024:10:14:12:38:53 mris_place_surface N 5 e 2.78 S 0.12 U 3.04 P 114% M 158312 F 1 R 44581 W 0 c 674 w 123 I 96 O 896 L 91.68 79.53 79.63 @#@FSLOADPOST 2024:10:14:12:38:56 mris_place_surface N 5 91.68 79.53 79.63 #@# pial area lh Mon Oct 14 12:38:56 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2024:10:14:12:38:56 mris_place_surface N 3 e 1.23 S 0.12 U 1.37 P 121% M 158468 F 3 R 42643 W 0 c 167 w 91 I 96 O 896 L 91.68 79.53 79.63 @#@FSLOADPOST 2024:10:14:12:38:57 mris_place_surface N 3 92.43 79.88 79.74 #@# thickness lh Mon Oct 14 12:38:57 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 114566 vertices processed 25000 of 114566 vertices processed 50000 of 114566 vertices processed 75000 of 114566 vertices processed 100000 of 114566 vertices processed 0 of 114566 vertices processed 25000 of 114566 vertices processed 50000 of 114566 vertices processed 75000 of 114566 vertices processed 100000 of 114566 vertices processed thickness calculation complete, 116:1329 truncations. 60788 vertices at 0 distance 94982 vertices at 1 distance 49903 vertices at 2 distance 15853 vertices at 3 distance 4819 vertices at 4 distance 1561 vertices at 5 distance 563 vertices at 6 distance 249 vertices at 7 distance 122 vertices at 8 distance 80 vertices at 9 distance 53 vertices at 10 distance 50 vertices at 11 distance 24 vertices at 12 distance 30 vertices at 13 distance 17 vertices at 14 distance 7 vertices at 15 distance 4 vertices at 16 distance 5 vertices at 17 distance 3 vertices at 18 distance 5 vertices at 19 distance 14 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2024:10:14:12:38:57 mris_place_surface N 6 e 43.20 S 0.32 U 37.77 P 88% M 158440 F 1 R 187480 W 0 c 4229 w 90 I 96 O 896 L 92.43 79.88 79.74 @#@FSLOADPOST 2024:10:14:12:39:40 mris_place_surface N 6 86.14 79.81 79.72 #@# area and vertex vol lh Mon Oct 14 12:39:40 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume PIB23-310_VYr0_Bay3prisma lh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Total face volume 208577 Total vertex volume 208333 (mask=0) #@# PIB23-310_VYr0_Bay3prisma lh 208333 vertexvol Done @#@FSTIME 2024:10:14:12:39:41 vertexvol N 4 e 2.71 S 0.29 U 2.84 P 115% M 263224 F 8 R 128945 W 0 c 488 w 329 I 912 O 2688 L 86.14 79.81 79.72 @#@FSLOADPOST 2024:10:14:12:39:43 vertexvol N 4 98.30 82.44 80.57 #@# white curv rh Mon Oct 14 12:39:43 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2024:10:14:12:39:44 mris_place_surface N 5 e 2.40 S 0.14 U 2.53 P 111% M 163704 F 1 R 46189 W 0 c 479 w 106 I 0 O 936 L 98.30 82.44 80.57 @#@FSLOADPOST 2024:10:14:12:39:46 mris_place_surface N 5 98.30 82.44 80.57 #@# white area rh Mon Oct 14 12:39:46 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2024:10:14:12:39:46 mris_place_surface N 3 e 1.15 S 0.14 U 1.23 P 119% M 163812 F 1 R 44144 W 0 c 167 w 113 I 96 O 936 L 96.04 82.23 80.52 @#@FSLOADPOST 2024:10:14:12:39:47 mris_place_surface N 3 96.04 82.23 80.52 #@# pial curv rh Mon Oct 14 12:39:47 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2024:10:14:12:39:48 mris_place_surface N 5 e 2.43 S 0.13 U 2.53 P 109% M 163896 F 1 R 44201 W 0 c 311 w 136 I 8456 O 936 L 96.04 82.23 80.52 @#@FSLOADPOST 2024:10:14:12:39:50 mris_place_surface N 5 96.04 82.23 80.52 #@# pial area rh Mon Oct 14 12:39:50 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2024:10:14:12:39:50 mris_place_surface N 3 e 1.03 S 0.09 U 1.43 P 148% M 163812 F 2 R 44223 W 0 c 181 w 149 I 96 O 936 L 96.04 82.23 80.52 @#@FSLOADPOST 2024:10:14:12:39:51 mris_place_surface N 3 98.44 82.96 80.76 #@# thickness rh Mon Oct 14 12:39:51 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 118830 vertices processed 25000 of 118830 vertices processed 50000 of 118830 vertices processed 75000 of 118830 vertices processed 100000 of 118830 vertices processed 0 of 118830 vertices processed 25000 of 118830 vertices processed 50000 of 118830 vertices processed 75000 of 118830 vertices processed 100000 of 118830 vertices processed thickness calculation complete, 108:1531 truncations. 61700 vertices at 0 distance 96825 vertices at 1 distance 53128 vertices at 2 distance 17355 vertices at 3 distance 5441 vertices at 4 distance 1764 vertices at 5 distance 727 vertices at 6 distance 317 vertices at 7 distance 145 vertices at 8 distance 82 vertices at 9 distance 57 vertices at 10 distance 37 vertices at 11 distance 28 vertices at 12 distance 21 vertices at 13 distance 13 vertices at 14 distance 7 vertices at 15 distance 1 vertices at 16 distance 3 vertices at 17 distance 1 vertices at 18 distance 4 vertices at 19 distance 4 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2024:10:14:12:39:51 mris_place_surface N 6 e 48.85 S 0.46 U 42.98 P 88% M 164140 F 1 R 252666 W 0 c 5101 w 111 I 96 O 936 L 98.44 82.96 80.76 @#@FSLOADPOST 2024:10:14:12:40:40 mris_place_surface N 6 90.80 82.57 80.70 #@# area and vertex vol rh Mon Oct 14 12:40:40 CDT 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume PIB23-310_VYr0_Bay3prisma rh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Total face volume 217158 Total vertex volume 216888 (mask=0) #@# PIB23-310_VYr0_Bay3prisma rh 216888 vertexvol Done @#@FSTIME 2024:10:14:12:40:40 vertexvol N 4 e 2.74 S 0.27 U 2.74 P 110% M 272704 F 1 R 118689 W 0 c 364 w 305 I 192 O 2808 L 90.80 82.57 80.70 @#@FSLOADPOST 2024:10:14:12:40:43 vertexvol N 4 87.93 82.11 80.56 #----------------------------------------- #@# Curvature Stats lh Mon Oct 14 12:40:43 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PIB23-310_VYr0_Bay3prisma lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ PIB23-310_VYr0_Bay3prisma/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 219 ] Gb_filter = 0 WARN: S lookup min: -0.037145 WARN: S explicit min: 0.000000 vertex = 785 @#@FSTIME 2024:10:14:12:40:43 mris_curvature_stats N 11 e 5.44 S 0.24 U 4.77 P 92% M 158108 F 4 R 94072 W 0 c 717 w 328 I 952 O 7208 L 87.93 82.11 80.56 @#@FSLOADPOST 2024:10:14:12:40:49 mris_curvature_stats N 11 85.93 81.79 80.47 #----------------------------------------- #@# Curvature Stats rh Mon Oct 14 12:40:49 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PIB23-310_VYr0_Bay3prisma rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ PIB23-310_VYr0_Bay3prisma/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 212 ] Gb_filter = 0 WARN: S lookup min: -0.106930 WARN: S explicit min: 0.000000 vertex = 910 @#@FSTIME 2024:10:14:12:40:49 mris_curvature_stats N 11 e 5.02 S 0.22 U 4.55 P 95% M 164008 F 1 R 77001 W 0 c 698 w 310 I 768 O 7528 L 85.93 81.79 80.47 @#@FSLOADPOST 2024:10:14:12:40:54 mris_curvature_stats N 11 83.62 81.38 80.34 #-------------------------------------------- #@# Cortical ribbon mask Mon Oct 14 12:40:54 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon PIB23-310_VYr0_Bay3prisma SUBJECTS_DIR is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing loading input data... Running hemis serially Processing left hemi computing distance to left white surface computing distance to left pial surface Processing right hemi computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 65 writing volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz mris_volmask took 6.28 minutes writing ribbon files @#@FSTIME 2024:10:14:12:40:54 mris_volmask N 12 e 376.84 S 2.58 U 348.49 P 93% M 910016 F 8 R 2477546 W 0 c 37530 w 368 I 864 O 816 L 83.62 81.38 80.34 @#@FSLOADPOST 2024:10:14:12:47:11 mris_volmask N 12 55.96 71.56 76.94 #----------------------------------------- #@# Cortical Parc 2 lh Mon Oct 14 12:47:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Mon Oct 14 12:47:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 3360085 of (3360085 3360089) to complete... Waiting for PID 3360089 of (3360085 3360089) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 3.0 using min determinant for regularization = 0.088 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 492 labels changed using aseg relabeling using gibbs priors... 000: 7307 changed, 114566 examined... 001: 1709 changed, 28708 examined... 002: 499 changed, 9100 examined... 003: 208 changed, 2909 examined... 004: 93 changed, 1191 examined... 005: 54 changed, 552 examined... 006: 22 changed, 299 examined... 007: 10 changed, 127 examined... 008: 6 changed, 58 examined... 009: 5 changed, 35 examined... 010: 4 changed, 23 examined... 011: 3 changed, 18 examined... 012: 4 changed, 18 examined... 013: 1 changed, 23 examined... 014: 0 changed, 7 examined... 116 labels changed using aseg 000: 198 total segments, 113 labels (1181 vertices) changed 001: 88 total segments, 5 labels (150 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 22 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1167 vertices marked for relabeling... 1167 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 18 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.021 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 756 labels changed using aseg relabeling using gibbs priors... 000: 7953 changed, 118830 examined... 001: 1815 changed, 30976 examined... 002: 557 changed, 9754 examined... 003: 227 changed, 3263 examined... 004: 116 changed, 1304 examined... 005: 65 changed, 644 examined... 006: 44 changed, 384 examined... 007: 14 changed, 245 examined... 008: 7 changed, 96 examined... 009: 6 changed, 44 examined... 010: 5 changed, 37 examined... 011: 1 changed, 26 examined... 012: 0 changed, 9 examined... 81 labels changed using aseg 000: 214 total segments, 129 labels (1563 vertices) changed 001: 88 total segments, 5 labels (34 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 31 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 959 vertices marked for relabeling... 959 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. PIDs (3360085 3360089) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Mon Oct 14 12:47:29 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Mon Oct 14 12:47:29 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 3366969 of (3366969 3366976) to complete... Waiting for PID 3366976 of (3366969 3366976) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma lh ../surf/lh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1513 labels changed using aseg relabeling using gibbs priors... 000: 1693 changed, 114566 examined... 001: 369 changed, 8186 examined... 002: 103 changed, 2161 examined... 003: 53 changed, 592 examined... 004: 29 changed, 292 examined... 005: 22 changed, 168 examined... 006: 20 changed, 102 examined... 007: 20 changed, 98 examined... 008: 18 changed, 93 examined... 009: 13 changed, 78 examined... 010: 10 changed, 68 examined... 011: 4 changed, 49 examined... 012: 7 changed, 23 examined... 013: 7 changed, 33 examined... 014: 3 changed, 28 examined... 015: 2 changed, 15 examined... 016: 3 changed, 12 examined... 017: 4 changed, 15 examined... 018: 3 changed, 22 examined... 019: 3 changed, 15 examined... 020: 2 changed, 18 examined... 021: 0 changed, 13 examined... 407 labels changed using aseg 000: 48 total segments, 15 labels (82 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 8 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 606 vertices marked for relabeling... 606 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB23-310_VYr0_Bay3prisma rh ../surf/rh.sphere.reg /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline 7.3.2 7.3.2 reading atlas from /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1712 labels changed using aseg relabeling using gibbs priors... 000: 1727 changed, 118830 examined... 001: 428 changed, 8163 examined... 002: 117 changed, 2398 examined... 003: 64 changed, 671 examined... 004: 42 changed, 362 examined... 005: 18 changed, 226 examined... 006: 15 changed, 102 examined... 007: 11 changed, 84 examined... 008: 5 changed, 58 examined... 009: 3 changed, 30 examined... 010: 6 changed, 20 examined... 011: 4 changed, 30 examined... 012: 1 changed, 26 examined... 013: 0 changed, 7 examined... 314 labels changed using aseg 000: 47 total segments, 14 labels (125 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 555 vertices marked for relabeling... 555 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. PIDs (3366969 3366976) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Mon Oct 14 12:47:42 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts pctsurfcon --s PIB23-310_VYr0_Bay3prisma --lh-only #----------------------------------------- #@# WM/GM Contrast rh Mon Oct 14 12:47:42 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts pctsurfcon --s PIB23-310_VYr0_Bay3prisma --rh-only Waiting for PID 3372251 of (3372251 3372254) to complete... Waiting for PID 3372254 of (3372251 3372254) to complete... pctsurfcon --s PIB23-310_VYr0_Bay3prisma --lh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/pctsurfcon.log Mon Oct 14 12:47:42 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/pctsurfcon pctsurfcon 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372251/lh.wm.mgh --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 74445 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372251/lh.wm.mgh Dim: 114566 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372251/lh.gm.mgh --projfrac 0.3 --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 88144 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372251/lh.gm.mgh Dim: 114566 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372251/lh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372251/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/lh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/lh.w-g.pct.stats --snr sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Seg base 1000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.w-g.pct.mgh Vertex Area is 0.695572 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s PIB23-310_VYr0_Bay3prisma --rh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts/pctsurfcon.log Mon Oct 14 12:47:42 CDT 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/pctsurfcon pctsurfcon 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372254/rh.wm.mgh --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 76342 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372254/rh.wm.mgh Dim: 118830 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372254/rh.gm.mgh --projfrac 0.3 --regheader PIB23-310_VYr0_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06311 0.99203 0.10904 0.00003; -0.99800 -0.06314 -0.00323 -0.00004; 0.00368 -0.10903 0.99403 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 90963 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372254/rh.gm.mgh Dim: 118830 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372254/rh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/tmp.pctsurfcon.3372254/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/rh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB23-310_VYr0_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/stats/rh.w-g.pct.stats --snr sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Seg base 2000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.w-g.pct.mgh Vertex Area is 0.682942 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (3372251 3372254) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Mon Oct 14 12:47:49 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2397 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2463 voxels changed to hypointensity... 4627 hypointense voxels neighboring cortex changed @#@FSTIME 2024:10:14:12:47:49 mri_relabel_hypointensities N 3 e 22.18 S 0.89 U 21.76 P 102% M 453424 F 12 R 562244 W 0 c 2384 w 171 I 1824 O 672 L 53.43 69.24 75.95 @#@FSLOADPOST 2024:10:14:12:48:11 mri_relabel_hypointensities N 3 48.88 67.19 75.13 #----------------------------------------- #@# APas-to-ASeg Mon Oct 14 12:48:11 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz --threads 4 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aseg.mgz 72 avail.processors, using 4 Loading aseg.presurf.hypos.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/ribbon.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Done loading 64 128 0 192 193 1 65 194 2 66 195 3 196 4 67 5 197 6 68 7 69 198 8 70 9 199 129 10 200 11 71 201 12 202 13 72 203 14 204 15 205 16 130 206 73 17 207 18 208 19 209 74 210 20 211 21 131 212 22 213 75 23 214 24 215 25 76 26 216 132 217 27 77 28 218 29 219 30 220 78 31 221 133 32 222 79 33 34 223 35 80 134 224 36 37 225 81 38 226 135 39 227 82 40 228 41 229 42 230 136 83 43 231 44 232 45 233 84 46 234 137 47 235 48 236 85 237 49 138 238 50 51 239 86 240 52 139 53 241 54 242 55 87 243 56 140 57 244 58 59 88 245 141 60 246 61 62 247 89 142 63 248 249 250 143 90 251 252 253 144 254 91 255 145 92 146 93 147 148 94 149 95 150 96 151 97 152 98 153 99 154 100 155 101 156 102 157 103 158 159 104 105 160 106 161 107 162 108 163 109 164 110 165 111 166 112 113 167 114 168 169 115 170 116 171 172 117 173 174 118 175 176 177 119 178 179 120 180 181 121 182 183 184 122 185 186 187 123 188 189 190 191 124 125 126 127 nrelabeled = 107666 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 998108 mri_surf2volseg done @#@FSTIME 2024:10:14:12:48:11 mri_surf2volseg N 20 e 10.26 S 1.34 U 15.48 P 163% M 811960 F 4 R 435408 W 0 c 1942 w 6624 I 352 O 704 L 48.88 67.19 75.13 @#@FSLOADPOST 2024:10:14:12:48:21 mri_surf2volseg N 20 47.90 66.37 74.78 mri_brainvol_stats PIB23-310_VYr0_Bay3prisma ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1607897.0 #CBVS2 BrainSegVol 1083774.0 #CBVS2 BrainSegVolNotVent 960291.0 #CBVS2 SupraTentVol 958341.0 #CBVS2 SupraTentVolNotVent 834858.0 #CBVS2 lhCtxGM 208437.3 #CBVS2 rhCtxGM 217095.1 #CBVS2 lhCerebralWM 180403.5 #CBVS2 rhCerebralWM 180562.5 #CBVS2 SubCortGMVol 49450.0 #CBVS2 CerebellumVol 125433.0 #CBVS2 CerebellumGMVol 100644.0 #CBVS2 VentChorVol 115326.0 #CBVS2 3rd4th5thCSF 8157.0 #CBVS2 AllCSF 123483.0 #CBVS2 CCVol 3869.0 @#@FSTIME 2024:10:14:12:48:21 mri_brainvol_stats N 1 e 5.05 S 0.55 U 7.13 P 152% M 212900 F 27 R 221819 W 0 c 939 w 312 I 4200 O 8 L 47.90 66.37 74.78 @#@FSLOADPOST 2024:10:14:12:48:26 mri_brainvol_stats N 1 52.79 67.08 74.96 #----------------------------------------- #@# AParc-to-ASeg aparc Mon Oct 14 12:48:26 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10408 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10394 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Done loading 64 128 192 0 193 1 2 194 3 195 4 196 5 197 6 198 7 199 8 200 9 201 10 202 65 11 203 12 204 13 205 14 206 15 207 16 208 17 209 18 210 19 211 20 212 21 213 22 214 23 215 24 66 216 25 26 217 27 218 28 219 29 220 30 221 31 222 32 223 33 224 34 35 225 36 226 37 227 38 228 39 229 40 230 41 231 42 232 43 67 233 44 234 45 235 46 47 236 48 237 49 238 50 239 51 240 52 241 53 242 54 243 55 244 56 245 57 246 58 247 59 248 60 249 61 250 251 252 62 253 254 255 68 63 69 129 70 71 130 72 73 131 74 132 75 76 133 77 134 78 135 79 136 80 137 81 82 138 83 139 84 140 85 141 142 86 143 87 144 88 145 89 146 147 90 148 91 149 150 92 151 93 152 94 153 95 154 155 96 156 157 97 158 98 159 160 99 161 100 162 163 101 164 102 165 103 166 104 167 105 168 106 169 107 170 108 171 109 172 110 173 111 174 112 175 113 176 114 177 178 115 179 116 180 181 117 182 118 183 184 185 119 186 187 188 189 190 191 120 121 122 123 124 125 126 127 nrelabeled = 424428 ndotcheck = 12867 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 982140 mri_surf2volseg done @#@FSTIME 2024:10:14:12:48:27 mri_surf2volseg N 25 e 63.78 S 1.24 U 114.15 P 180% M 797064 F 2 R 990086 W 0 c 11272 w 4982 I 256 O 800 L 57.61 67.84 75.17 @#@FSLOADPOST 2024:10:14:12:49:30 mri_surf2volseg N 25 39.89 61.11 72.40 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Mon Oct 14 12:49:30 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc.a2009s+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10408 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.a2009s.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10394 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.a2009s.annot Done loading 0 64 128 192 193 1 2 194 3 195 4 196 5 197 6 198 7 199 8 200 9 201 10 202 11 203 65 12 204 13 205 14 206 15 207 16 208 17 209 18 210 211 19 212 20 213 214 21 215 22 216 23 217 66 24 218 219 25 220 26 221 27 222 28 223 224 29 225 30 226 227 31 228 32 229 33 230 231 34 232 35 233 36 234 235 37 236 38 237 39 238 40 67 239 41 240 241 42 242 43 243 44 244 245 45 246 46 247 248 47 249 48 250 49 251 50 252 253 51 254 52 255 53 54 55 56 57 58 59 60 61 68 62 63 129 69 70 71 130 72 131 73 74 132 75 133 76 77 134 78 135 79 136 80 137 81 138 82 83 139 84 140 141 85 142 86 143 87 144 145 88 146 89 147 90 148 149 91 150 92 151 93 152 153 94 154 95 155 156 96 157 97 158 159 98 160 161 99 162 100 163 101 164 102 165 166 103 104 167 168 105 169 106 170 107 171 108 172 109 173 110 174 111 175 112 176 113 177 178 114 179 115 180 116 181 182 117 183 184 185 118 186 187 188 189 190 191 119 120 121 122 123 124 125 126 127 nrelabeled = 424428 ndotcheck = 12867 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 982172 mri_surf2volseg done @#@FSTIME 2024:10:14:12:49:31 mri_surf2volseg N 25 e 63.84 S 1.38 U 112.74 P 178% M 797228 F 1 R 802269 W 0 c 11316 w 8502 I 0 O 864 L 39.89 61.11 72.40 @#@FSLOADPOST 2024:10:14:12:50:34 mri_surf2volseg N 25 34.58 56.08 69.95 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Mon Oct 14 12:50:34 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol aparc.DKTatlas+aseg.mgz 72 avail.processors, using 4 Loading aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10408 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.DKTatlas.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10394 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.DKTatlas.annot Done loading 0 192 64 128 1 193 2 194 3 195 4 196 5 197 6 198 7 199 200 8 201 9 10 202 65 203 11 204 12 13 205 14 206 15 207 16 208 17 209 18 210 19 211 20 212 21 213 22 214 23 215 24 216 25 217 26 66 218 27 219 28 220 29 221 30 222 31 223 32 224 33 225 34 226 35 227 36 228 37 229 38 230 39 231 40 232 41 233 42 234 43 67 235 44 236 45 237 46 238 47 239 48 240 49 241 50 242 51 243 52 53 244 54 245 55 246 56 247 57 248 58 249 59 250 60 251 252 61 253 254 255 62 68 63 129 69 70 71 130 72 73 131 74 132 75 133 76 77 134 78 135 79 136 80 81 137 82 138 83 139 84 140 141 85 142 86 143 87 144 145 88 146 89 147 90 148 91 149 150 92 151 93 152 94 153 95 154 155 96 156 97 157 158 98 159 99 160 161 100 162 101 163 102 164 103 165 104 166 105 167 106 168 107 108 169 109 170 110 171 111 172 112 173 113 174 114 175 176 115 177 116 178 179 117 180 118 181 119 182 183 120 184 185 186 121 187 188 189 190 191 122 123 124 125 126 127 nrelabeled = 424428 ndotcheck = 12867 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 982144 mri_surf2volseg done @#@FSTIME 2024:10:14:12:50:35 mri_surf2volseg N 25 e 70.32 S 1.40 U 124.34 P 178% M 796804 F 1 R 1121260 W 0 c 13608 w 3718 I 0 O 792 L 34.58 56.08 69.95 @#@FSLOADPOST 2024:10:14:12:51:45 mri_surf2volseg N 25 36.83 52.53 67.72 #----------------------------------------- #@# WMParc Mon Oct 14 12:51:45 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 4 --lh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot 3000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot 4000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing outvol wmparc.mgz 72 avail.processors, using 4 Loading aparc+aseg.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10408 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10394 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.aparc.annot Done loading 192 64 0 128 193 65 1 194 2 66 195 3 196 4 197 5 198 6 67 199 7 200 8 201 68 9 202 203 10 204 11 205 12 13 206 69 14 15 207 16 208 17 209 18 210 19 211 20 212 70 21 213 22 214 23 215 24 216 25 217 26 218 27 71 219 28 220 29 30 221 31 222 32 223 33 224 34 225 35 226 36 72 227 37 129 228 38 39 229 40 230 41 231 42 232 43 233 44 234 45 235 46 236 47 237 48 238 49 239 50 240 51 241 52 73 242 53 243 54 244 55 245 56 246 57 247 58 248 59 249 60 130 250 61 62 251 63 252 253 254 74 255 131 75 76 132 77 133 78 134 79 135 80 136 81 137 82 138 83 139 84 85 140 86 87 141 88 142 89 90 143 91 92 144 93 145 94 146 95 147 148 96 97 149 150 98 99 151 100 152 101 153 102 154 103 155 156 104 157 105 158 106 159 160 107 161 108 162 109 163 164 110 165 111 166 112 167 168 113 169 170 114 171 115 172 173 116 174 117 175 118 176 119 177 178 120 179 121 180 181 122 182 183 123 184 185 186 187 188 189 190 191 124 125 126 127 nrelabeled = 357097 ndotcheck = 4749 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 982092 mri_surf2volseg done @#@FSTIME 2024:10:14:12:51:45 mri_surf2volseg N 25 e 28.67 S 1.45 U 49.96 P 179% M 797028 F 0 R 787059 W 0 c 5367 w 2245 I 0 O 880 L 36.83 52.53 67.72 @#@FSLOADPOST 2024:10:14:12:52:14 mri_surf2volseg N 25 40.81 52.12 67.11 mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject PIB23-310_VYr0_Bay3prisma --surf-wm-vol --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 7.3.2 cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject PIB23-310_VYr0_Bay3prisma --surf-wm-vol --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/WMParcStatsLUT.txt --etiv sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2024:10:14:12:52:14 mri_segstats N 24 e 270.35 S 1.03 U 530.22 P 196% M 239732 F 0 R 1492029 W 0 c 51905 w 87 I 1392 O 24 L 40.81 52.12 67.11 @#@FSLOADPOST 2024:10:14:12:56:44 mri_segstats N 24 56.37 54.43 64.09 #----------------------------------------- #@# Parcellation Stats lh Mon Oct 14 12:56:44 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh pial #----------------------------------------- #@# Parcellation Stats rh Mon Oct 14 12:56:45 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh pial Waiting for PID 3581149 of (3581149 3581153 3581156 3581160) to complete... Waiting for PID 3581153 of (3581149 3581153 3581156 3581160) to complete... Waiting for PID 3581156 of (3581149 3581153 3581156 3581160) to complete... Waiting for PID 3581160 of (3581149 3581153 3581156 3581160) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208577 Total vertex volume 208333 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1241 841 2034 2.436 0.515 0.084 0.017 5 0.9 bankssts 777 588 1986 3.073 0.706 0.161 0.045 19 1.7 caudalanteriorcingulate 2683 1977 5709 2.531 0.489 0.122 0.031 27 3.6 caudalmiddlefrontal 1829 1202 2532 1.975 0.497 0.145 0.039 26 2.9 cuneus 597 398 1226 2.326 0.917 0.126 0.043 7 1.0 entorhinal 3688 2690 8373 2.623 0.642 0.128 0.030 45 4.4 fusiform 5274 3836 10973 2.530 0.565 0.133 0.035 71 7.3 inferiorparietal 3640 2805 9208 2.662 0.710 0.134 0.032 50 5.0 inferiortemporal 1205 792 1636 2.146 0.751 0.123 0.031 18 1.7 isthmuscingulate 5860 3932 9761 2.283 0.517 0.134 0.031 68 7.6 lateraloccipital 2945 2141 6586 2.675 0.755 0.137 0.037 36 4.5 lateralorbitofrontal 4195 2802 6237 2.044 0.548 0.128 0.033 53 5.6 lingual 2521 1831 4929 2.353 0.872 0.143 0.036 40 3.7 medialorbitofrontal 4045 2803 9082 2.680 0.618 0.116 0.027 50 4.5 middletemporal 1177 732 2130 2.434 0.635 0.083 0.021 7 0.8 parahippocampal 1877 1177 3266 2.535 0.544 0.093 0.022 11 1.7 paracentral 1939 1325 3683 2.471 0.504 0.107 0.025 16 2.0 parsopercularis 683 537 1956 2.751 0.621 0.147 0.035 10 1.0 parsorbitalis 1556 1139 3125 2.380 0.576 0.118 0.026 16 1.6 parstriangularis 1975 1317 2074 1.646 0.464 0.127 0.035 19 2.9 pericalcarine 5818 3862 8832 2.060 0.598 0.107 0.026 52 6.0 postcentral 1165 844 2366 2.689 0.591 0.138 0.034 24 1.7 posteriorcingulate 6931 4769 12891 2.497 0.564 0.119 0.032 66 9.4 precentral 4092 2962 8163 2.576 0.545 0.139 0.034 53 5.6 precuneus 1185 903 2601 2.552 1.046 0.154 0.054 25 2.6 rostralanteriorcingulate 5702 4347 13265 2.478 0.632 0.132 0.032 84 7.5 rostralmiddlefrontal 7465 5687 18548 2.651 0.665 0.132 0.038 110 11.5 superiorfrontal 6220 4392 12131 2.501 0.499 0.123 0.029 69 7.4 superiorparietal 5961 3906 11632 2.581 0.618 0.094 0.021 48 5.3 superiortemporal 5062 3628 9525 2.373 0.522 0.124 0.029 55 5.9 supramarginal 279 229 1258 3.138 0.821 0.160 0.056 8 0.7 frontalpole 568 442 2720 3.303 0.850 0.146 0.063 10 1.2 temporalpole 733 389 940 2.184 0.541 0.092 0.028 5 0.8 transversetemporal 3270 2202 6955 2.954 0.940 0.121 0.038 31 5.2 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208577 Total vertex volume 208333 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1241 781 2034 2.436 0.515 0.089 0.018 8 0.8 bankssts 777 749 1986 3.073 0.706 0.168 0.049 12 1.2 caudalanteriorcingulate 2683 2441 5709 2.531 0.489 0.144 0.028 35 3.0 caudalmiddlefrontal 1829 1460 2532 1.975 0.497 0.139 0.039 54 2.6 cuneus 597 657 1226 2.326 0.917 0.215 0.067 15 2.0 entorhinal 3688 3499 8373 2.623 0.642 0.153 0.034 50 5.3 fusiform 5274 4753 10973 2.530 0.565 0.147 0.033 69 6.5 inferiorparietal 3640 3758 9208 2.662 0.710 0.162 0.033 53 5.2 inferiortemporal 1205 846 1636 2.146 0.751 0.133 0.042 17 1.9 isthmuscingulate 5860 4645 9761 2.283 0.517 0.136 0.032 155 7.1 lateraloccipital 2945 2640 6586 2.675 0.755 0.160 0.037 591 4.3 lateralorbitofrontal 4195 3459 6237 2.044 0.548 0.136 0.032 60 5.4 lingual 2521 2245 4929 2.353 0.872 0.153 0.040 42 3.6 medialorbitofrontal 4045 3792 9082 2.680 0.618 0.141 0.028 43 4.8 middletemporal 1177 1053 2130 2.434 0.635 0.133 0.031 12 1.6 parahippocampal 1877 1431 3266 2.535 0.544 0.117 0.025 21 2.1 paracentral 1939 1597 3683 2.471 0.504 0.128 0.022 19 1.7 parsopercularis 683 853 1956 2.751 0.621 0.186 0.037 8 1.1 parsorbitalis 1556 1430 3125 2.380 0.576 0.143 0.025 15 1.5 parstriangularis 1975 1215 2074 1.646 0.464 0.114 0.028 21 2.2 pericalcarine 5818 4753 8832 2.060 0.598 0.116 0.020 44 4.8 postcentral 1165 989 2366 2.689 0.591 0.153 0.048 26 2.1 posteriorcingulate 6931 5454 12891 2.497 0.564 0.114 0.022 55 6.1 precentral 4092 3353 8163 2.576 0.545 0.149 0.063 86 6.0 precuneus 1185 1150 2601 2.552 1.046 0.178 0.048 33 2.3 rostralanteriorcingulate 5702 5889 13265 2.478 0.632 0.163 0.030 73 7.2 rostralmiddlefrontal 7465 7784 18548 2.651 0.665 0.163 0.036 123 10.2 superiorfrontal 6220 5298 12131 2.501 0.499 0.136 0.028 77 7.2 superiorparietal 5961 4988 11632 2.581 0.618 0.113 0.021 44 4.9 superiortemporal 5062 4321 9525 2.373 0.522 0.137 0.027 51 5.5 supramarginal 279 568 1258 3.138 0.821 0.284 0.045 5 0.5 frontalpole 568 1053 2720 3.303 0.850 0.270 0.054 8 1.8 temporalpole 733 492 940 2.184 0.541 0.085 0.014 3 0.4 transversetemporal 3270 2387 6955 2.954 0.940 0.149 0.047 71 5.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 217158 Total vertex volume 216888 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1216 812 1996 2.543 0.542 0.080 0.016 5 0.8 bankssts 816 568 1455 2.664 0.710 0.121 0.028 13 1.1 caudalanteriorcingulate 2881 2060 5974 2.538 0.524 0.123 0.029 30 3.4 caudalmiddlefrontal 2241 1445 3248 2.036 0.466 0.139 0.033 31 3.0 cuneus 715 495 1942 2.948 0.768 0.127 0.037 9 1.0 entorhinal 3839 2754 8197 2.570 0.648 0.124 0.027 47 4.3 fusiform 6951 4904 14122 2.575 0.523 0.124 0.030 82 8.6 inferiorparietal 3988 2896 9873 2.807 0.661 0.135 0.035 63 5.2 inferiortemporal 873 539 1219 2.120 0.746 0.115 0.027 9 1.0 isthmuscingulate 6370 4230 10333 2.283 0.576 0.128 0.029 70 7.8 lateraloccipital 3022 2194 6698 2.662 0.759 0.143 0.041 44 5.2 lateralorbitofrontal 4754 3170 7041 2.053 0.564 0.127 0.033 61 6.2 lingual 2562 1818 5084 2.342 0.747 0.134 0.041 44 4.1 medialorbitofrontal 4524 3109 10643 2.802 0.598 0.110 0.026 48 4.7 middletemporal 1033 654 2040 2.647 0.756 0.096 0.022 9 0.8 parahippocampal 2097 1316 3498 2.533 0.507 0.107 0.025 18 2.0 paracentral 1531 1141 3617 2.677 0.561 0.130 0.034 18 2.1 parsopercularis 860 675 2545 2.727 0.669 0.145 0.040 14 1.4 parsorbitalis 1680 1215 3456 2.396 0.620 0.115 0.039 39 1.9 parstriangularis 2235 1453 2409 1.768 0.497 0.127 0.036 26 3.1 pericalcarine 6248 3919 9104 2.117 0.577 0.095 0.021 48 5.6 postcentral 930 639 1847 2.665 0.604 0.125 0.029 14 1.2 posteriorcingulate 6388 4251 12246 2.693 0.555 0.109 0.026 48 7.1 precentral 4716 3417 9229 2.508 0.515 0.123 0.028 49 5.5 precuneus 696 473 1957 2.860 0.923 0.124 0.039 12 1.1 rostralanteriorcingulate 5559 4263 13855 2.525 0.752 0.137 0.035 86 8.4 rostralmiddlefrontal 8029 6038 19860 2.616 0.705 0.134 0.037 111 12.9 superiorfrontal 6131 4190 11725 2.563 0.423 0.119 0.027 68 6.4 superiorparietal 5844 3586 10798 2.559 0.686 0.081 0.017 37 3.8 superiortemporal 4833 3336 9199 2.527 0.539 0.116 0.025 47 5.0 supramarginal 387 314 1556 3.082 0.761 0.177 0.051 10 0.9 frontalpole 577 416 2400 3.660 0.799 0.147 0.050 9 1.2 temporalpole 634 325 890 2.365 0.477 0.112 0.033 7 0.7 transversetemporal 3276 2248 6833 2.890 0.854 0.114 0.034 33 4.3 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PIB23-310_VYr0_Bay3prisma rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 217158 Total vertex volume 216888 (mask=0) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1216 731 1996 2.543 0.542 0.083 0.017 7 0.8 bankssts 816 561 1455 2.664 0.710 0.136 0.047 31 0.8 caudalanteriorcingulate 2881 2543 5974 2.538 0.524 0.132 0.024 31 2.6 caudalmiddlefrontal 2241 1805 3248 2.036 0.466 0.147 0.037 158 3.1 cuneus 715 855 1942 2.948 0.768 0.245 0.058 22 2.2 entorhinal 3839 3492 8197 2.570 0.648 0.151 0.036 81 5.9 fusiform 6951 5937 14122 2.575 0.523 0.136 0.028 91 8.1 inferiorparietal 3988 3977 9873 2.807 0.661 0.164 0.038 88 6.0 inferiortemporal 873 642 1219 2.120 0.746 0.136 0.045 15 1.1 isthmuscingulate 6370 4904 10333 2.283 0.576 0.129 0.031 128 8.0 lateraloccipital 3022 2705 6698 2.662 0.759 0.167 0.042 130 5.3 lateralorbitofrontal 4754 3854 7041 2.053 0.564 0.135 0.033 72 6.1 lingual 2562 2465 5084 2.342 0.747 0.160 0.038 49 3.9 medialorbitofrontal 4524 4295 10643 2.802 0.598 0.137 0.025 46 4.5 middletemporal 1033 891 2040 2.647 0.756 0.148 0.035 16 1.6 parahippocampal 2097 1476 3498 2.533 0.507 0.116 0.027 54 2.1 paracentral 1531 1522 3617 2.677 0.561 0.156 0.030 17 1.9 parsopercularis 860 1162 2545 2.727 0.669 0.204 0.040 11 1.5 parsorbitalis 1680 1612 3456 2.396 0.620 0.156 0.032 24 1.9 parstriangularis 2235 1278 2409 1.768 0.497 0.117 0.038 74 3.1 pericalcarine 6248 4714 9104 2.117 0.577 0.100 0.018 37 4.7 postcentral 930 805 1847 2.665 0.604 0.173 0.061 36 2.2 posteriorcingulate 6388 4743 12246 2.693 0.555 0.104 0.019 56 4.9 precentral 4716 3836 9229 2.508 0.515 0.134 0.031 80 5.6 precuneus 696 809 1957 2.860 0.923 0.205 0.043 10 1.1 rostralanteriorcingulate 5559 6175 13855 2.525 0.752 0.186 0.035 86 8.6 rostralmiddlefrontal 8029 8479 19860 2.616 0.705 0.167 0.036 147 11.5 superiorfrontal 6131 4978 11725 2.563 0.423 0.133 0.032 96 7.5 superiorparietal 5844 4631 10798 2.559 0.686 0.098 0.016 31 3.8 superiortemporal 4833 3831 9199 2.527 0.539 0.127 0.025 48 4.9 supramarginal 387 733 1556 3.082 0.761 0.288 0.053 6 0.9 frontalpole 577 870 2400 3.660 0.799 0.226 0.046 9 1.3 temporalpole 634 428 890 2.365 0.477 0.093 0.017 3 0.4 transversetemporal 3276 2321 6833 2.890 0.854 0.134 0.035 55 4.4 insula PIDs (3581149 3581153 3581156 3581160) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Oct 14 12:57:01 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 2 rh Mon Oct 14 12:57:01 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma rh white Waiting for PID 3587860 of (3587860 3587863) to complete... Waiting for PID 3587863 of (3587860 3587863) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208577 Total vertex volume 208333 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 822 605 2129 2.693 0.819 0.131 0.033 12 1.2 G_and_S_frontomargin 1118 772 2442 2.585 0.510 0.141 0.029 15 1.3 G_and_S_occipital_inf 1445 973 2920 2.403 0.662 0.116 0.029 13 1.9 G_and_S_paracentral 1184 832 2794 2.809 0.536 0.133 0.038 14 1.7 G_and_S_subcentral 499 408 1905 2.988 0.731 0.161 0.048 11 1.1 G_and_S_transv_frontopol 1976 1493 4179 2.607 0.729 0.136 0.035 29 2.8 G_and_S_cingul-Ant 1085 768 2095 2.684 0.783 0.133 0.040 20 1.9 G_and_S_cingul-Mid-Ant 1143 787 2009 2.581 0.598 0.118 0.031 14 1.3 G_and_S_cingul-Mid-Post 501 344 927 2.602 0.544 0.170 0.042 16 1.0 G_cingul-Post-dorsal 315 213 454 2.091 0.633 0.145 0.046 6 0.6 G_cingul-Post-ventral 1769 1138 2619 1.960 0.470 0.146 0.039 28 2.6 G_cuneus 1082 740 2552 2.601 0.492 0.128 0.035 14 1.6 G_front_inf-Opercular 316 239 877 2.767 0.419 0.149 0.034 5 0.5 G_front_inf-Orbital 875 678 2453 2.724 0.552 0.152 0.039 16 1.4 G_front_inf-Triangul 3123 2597 9447 2.652 0.604 0.153 0.042 68 5.3 G_front_middle 4896 3860 14613 2.822 0.694 0.145 0.044 88 8.7 G_front_sup 620 424 1715 3.346 0.672 0.152 0.050 11 1.3 G_Ins_lg_and_S_cent_ins 605 405 2081 3.841 0.736 0.136 0.047 7 1.1 G_insular_short 1674 1114 3926 2.641 0.540 0.134 0.038 26 2.3 G_occipital_middle 1049 690 1958 2.455 0.659 0.142 0.042 15 1.8 G_occipital_sup 1507 1054 3788 2.736 0.518 0.133 0.032 25 1.8 G_oc-temp_lat-fusifor 2906 1864 4711 2.110 0.513 0.134 0.039 45 4.1 G_oc-temp_med-Lingual 1441 919 3139 2.569 0.787 0.110 0.035 14 1.6 G_oc-temp_med-Parahip 1709 1312 5100 2.833 0.776 0.147 0.042 29 2.6 G_orbital 2213 1716 5665 2.597 0.554 0.156 0.041 45 3.3 G_pariet_inf-Angular 2201 1617 5071 2.524 0.538 0.136 0.032 30 2.7 G_pariet_inf-Supramar 2370 1796 5790 2.575 0.503 0.140 0.036 37 3.4 G_parietal_sup 2149 1320 3453 2.087 0.521 0.105 0.029 23 2.1 G_postcentral 2427 1631 5696 2.695 0.473 0.132 0.038 33 3.7 G_precentral 2081 1527 5074 2.668 0.588 0.157 0.042 39 3.4 G_precuneus 866 668 2473 2.647 0.802 0.162 0.044 17 1.4 G_rectus 835 555 874 1.821 0.965 0.143 0.060 15 2.1 G_subcallosal 595 288 877 2.345 0.523 0.085 0.030 5 0.6 G_temp_sup-G_T_transv 2006 1307 5485 2.979 0.583 0.123 0.033 32 2.6 G_temp_sup-Lateral 780 528 1538 2.611 0.557 0.063 0.011 1 0.3 G_temp_sup-Plan_polar 910 623 1625 2.387 0.544 0.103 0.026 8 1.0 G_temp_sup-Plan_tempo 1769 1459 5775 2.862 0.751 0.150 0.041 35 3.0 G_temporal_inf 2295 1593 6025 2.849 0.599 0.126 0.032 37 2.8 G_temporal_middle 205 147 234 1.702 0.326 0.094 0.015 1 0.1 Lat_Fis-ant-Horizont 338 237 467 2.265 0.331 0.080 0.014 1 0.2 Lat_Fis-ant-Vertical 1063 720 1355 2.225 0.536 0.108 0.029 6 1.2 Lat_Fis-post 1885 1215 2520 1.901 0.464 0.133 0.033 23 2.5 Pole_occipital 1285 1062 5605 3.174 0.866 0.165 0.058 28 2.7 Pole_temporal 2389 1631 2565 1.692 0.563 0.118 0.030 20 3.1 S_calcarine 3502 2464 4273 1.993 0.595 0.109 0.027 24 4.3 S_central 1002 677 1354 2.371 0.324 0.096 0.014 5 0.7 S_cingul-Marginalis 416 289 703 2.844 0.673 0.101 0.031 2 0.6 S_circular_insula_ant 1662 1083 2394 2.439 0.818 0.076 0.016 5 1.1 S_circular_insula_inf 1628 1082 2241 2.380 0.547 0.099 0.025 7 1.9 S_circular_insula_sup 774 548 1373 2.499 0.696 0.100 0.020 4 0.7 S_collat_transv_ant 356 277 510 2.153 0.371 0.143 0.030 2 0.6 S_collat_transv_post 2014 1369 3012 2.232 0.437 0.097 0.020 10 1.7 S_front_inf 963 692 1516 2.237 0.489 0.127 0.028 10 1.2 S_front_middle 1926 1370 3397 2.485 0.448 0.104 0.024 12 1.8 S_front_sup 250 182 390 2.328 0.444 0.110 0.024 1 0.3 S_interm_prim-Jensen 2484 1690 3589 2.385 0.454 0.110 0.025 16 3.1 S_intrapariet_and_P_trans 920 655 1245 2.235 0.363 0.129 0.028 6 1.1 S_oc_middle_and_Lunatus 1061 741 1611 2.557 0.416 0.119 0.025 8 1.1 S_oc_sup_and_transversal 551 396 806 2.409 0.440 0.115 0.023 3 0.6 S_occipital_ant 768 536 1197 2.442 0.426 0.104 0.018 3 0.7 S_oc-temp_lat 2033 1446 2936 2.216 0.521 0.107 0.020 12 1.7 S_oc-temp_med_and_Lingual 257 197 375 2.194 0.353 0.130 0.030 2 0.4 S_orbital_lateral 535 373 707 2.131 0.685 0.128 0.028 5 0.6 S_orbital_med-olfact 1062 786 2289 2.706 0.732 0.143 0.036 10 1.8 S_orbital-H_Shaped 1373 955 2139 2.516 0.519 0.119 0.024 10 1.4 S_parieto_occipital 779 500 847 2.081 0.998 0.123 0.038 13 1.4 S_pericallosal 2720 1878 3758 2.084 0.407 0.100 0.019 17 2.4 S_postcentral 1489 995 2163 2.406 0.431 0.093 0.018 6 1.2 S_precentral-inf-part 1183 793 1823 2.465 0.477 0.089 0.019 5 0.9 S_precentral-sup-part 651 479 1174 2.536 0.825 0.137 0.025 7 0.8 S_suborbital 779 562 1401 2.539 0.456 0.129 0.035 8 1.0 S_subparietal 1141 821 1674 2.273 0.517 0.123 0.020 9 1.3 S_temporal_inf 5276 3523 8117 2.410 0.483 0.093 0.019 28 4.5 S_temporal_sup 281 200 316 1.845 0.423 0.117 0.023 2 0.4 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 217158 Total vertex volume 216888 (mask=0) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 665 498 1608 2.492 0.735 0.142 0.041 13 1.0 G_and_S_frontomargin 1189 824 2404 2.572 0.486 0.140 0.032 15 1.5 G_and_S_occipital_inf 1500 943 2646 2.375 0.528 0.116 0.029 18 1.6 G_and_S_paracentral 1167 792 2570 2.763 0.497 0.120 0.025 12 1.3 G_and_S_subcentral 869 681 2866 2.821 0.807 0.135 0.034 16 1.3 G_and_S_transv_frontopol 2388 1672 5142 2.591 0.717 0.118 0.030 27 2.9 G_and_S_cingul-Ant 1185 804 1961 2.438 0.505 0.124 0.031 15 1.5 G_and_S_cingul-Mid-Ant 1134 775 1954 2.582 0.506 0.120 0.027 13 1.2 G_and_S_cingul-Mid-Post 288 190 468 2.325 0.821 0.146 0.038 5 0.6 G_cingul-Post-dorsal 316 192 447 2.269 0.624 0.132 0.038 4 0.5 G_cingul-Post-ventral 2105 1364 3141 2.004 0.468 0.141 0.035 31 2.8 G_cuneus 1099 854 3286 2.922 0.562 0.150 0.043 19 1.8 G_front_inf-Opercular 269 216 820 2.728 0.509 0.146 0.039 4 0.5 G_front_inf-Orbital 716 540 1969 2.696 0.551 0.127 0.034 9 1.0 G_front_inf-Triangul 2907 2325 9045 2.765 0.680 0.159 0.046 61 5.1 G_front_middle 5015 3902 15078 2.778 0.775 0.151 0.047 91 10.2 G_front_sup 781 569 1930 2.947 0.681 0.144 0.044 12 1.4 G_Ins_lg_and_S_cent_ins 620 444 2008 3.787 0.777 0.137 0.050 9 1.2 G_insular_short 1822 1257 4323 2.776 0.520 0.131 0.031 29 2.2 G_occipital_middle 1256 783 2337 2.374 0.483 0.111 0.026 14 1.2 G_occipital_sup 1661 1110 4086 2.802 0.566 0.125 0.029 26 1.8 G_oc-temp_lat-fusifor 2936 1953 4887 2.138 0.536 0.134 0.037 43 4.2 G_oc-temp_med-Lingual 1455 921 3682 2.948 0.767 0.119 0.035 20 1.8 G_oc-temp_med-Parahip 1955 1506 6222 2.959 0.760 0.147 0.045 32 3.2 G_orbital 2680 1903 6839 2.756 0.464 0.144 0.039 45 4.1 G_pariet_inf-Angular 2205 1547 5153 2.663 0.577 0.126 0.028 29 2.5 G_pariet_inf-Supramar 1746 1237 4254 2.674 0.458 0.140 0.034 29 2.4 G_parietal_sup 2173 1234 3296 2.132 0.520 0.096 0.027 21 2.1 G_postcentral 2345 1468 5646 2.922 0.463 0.117 0.033 25 2.9 G_precentral 2108 1632 5476 2.682 0.541 0.149 0.039 36 3.2 G_precuneus 805 624 2158 2.554 0.710 0.166 0.061 22 2.0 G_rectus 485 308 682 2.221 0.929 0.124 0.044 12 0.8 G_subcallosal 529 251 820 2.504 0.420 0.108 0.031 7 0.6 G_temp_sup-G_T_transv 1932 1117 4917 3.022 0.596 0.102 0.029 24 1.8 G_temp_sup-Lateral 819 530 1610 2.752 0.705 0.066 0.016 5 0.4 G_temp_sup-Plan_polar 776 497 1480 2.699 0.589 0.083 0.016 4 0.5 G_temp_sup-Plan_tempo 2084 1546 6493 3.005 0.726 0.150 0.044 46 3.2 G_temporal_inf 2621 1813 7427 2.982 0.558 0.126 0.033 40 3.4 G_temporal_middle 279 189 345 2.019 0.490 0.083 0.013 1 0.2 Lat_Fis-ant-Horizont 187 142 277 1.971 0.443 0.120 0.021 1 0.2 Lat_Fis-ant-Vertical 1438 952 1822 2.259 0.467 0.101 0.022 6 1.5 Lat_Fis-post 3269 2063 4089 1.875 0.487 0.131 0.035 41 4.5 Pole_occipital 1648 1205 5682 3.196 0.784 0.146 0.045 27 3.0 Pole_temporal 2474 1603 2526 1.741 0.580 0.118 0.029 24 3.3 S_calcarine 3173 2192 3865 2.063 0.645 0.097 0.020 15 3.0 S_central 1116 770 1685 2.484 0.347 0.095 0.014 5 0.7 S_cingul-Marginalis 507 327 814 2.918 0.695 0.107 0.070 26 0.7 S_circular_insula_ant 1565 1030 1904 2.141 0.628 0.080 0.016 6 1.1 S_circular_insula_inf 1109 713 1633 2.640 0.494 0.090 0.021 4 1.0 S_circular_insula_sup 1072 772 1665 2.178 0.522 0.107 0.022 9 1.0 S_collat_transv_ant 293 216 392 2.105 0.388 0.119 0.020 2 0.3 S_collat_transv_post 1543 1074 2327 2.195 0.545 0.106 0.026 11 2.0 S_front_inf 1511 1130 3242 2.399 0.704 0.127 0.028 19 1.9 S_front_middle 2105 1448 3460 2.449 0.457 0.102 0.020 12 1.9 S_front_sup 287 203 444 2.243 0.504 0.118 0.027 2 0.4 S_interm_prim-Jensen 2407 1687 4020 2.580 0.415 0.113 0.021 18 2.2 S_intrapariet_and_P_trans 817 591 1333 2.561 0.420 0.132 0.029 8 1.0 S_oc_middle_and_Lunatus 1069 727 1566 2.546 0.311 0.097 0.020 6 0.8 S_oc_sup_and_transversal 549 399 826 2.387 0.452 0.105 0.024 3 0.4 S_occipital_ant 832 575 1236 2.395 0.448 0.101 0.016 4 0.6 S_oc-temp_lat 1709 1269 2790 2.325 0.535 0.110 0.020 12 1.3 S_oc-temp_med_and_Lingual 327 243 587 2.147 0.685 0.137 0.028 3 0.4 S_orbital_lateral 605 418 914 2.167 0.752 0.116 0.023 4 0.7 S_orbital_med-olfact 1086 792 2024 2.416 0.657 0.141 0.038 13 1.9 S_orbital-H_Shaped 1982 1361 2986 2.400 0.423 0.107 0.022 14 1.9 S_parieto_occipital 580 360 665 2.269 1.000 0.107 0.025 6 0.8 S_pericallosal 2871 1860 3745 2.292 0.447 0.087 0.015 13 1.9 S_postcentral 1292 877 1861 2.437 0.432 0.106 0.023 7 1.5 S_precentral-inf-part 1249 840 1903 2.520 0.447 0.098 0.019 7 1.1 S_precentral-sup-part 315 223 427 2.034 0.627 0.112 0.015 2 0.2 S_suborbital 959 660 1731 2.478 0.490 0.107 0.022 5 0.8 S_subparietal 1148 792 1673 2.530 0.431 0.115 0.024 8 1.1 S_temporal_inf 6214 4173 9000 2.348 0.479 0.089 0.017 28 4.7 S_temporal_sup 243 168 294 1.863 0.340 0.114 0.019 2 0.2 S_temporal_transverse PIDs (3587860 3587863) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Mon Oct 14 12:57:17 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 3 rh Mon Oct 14 12:57:17 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma rh white Waiting for PID 3595151 of (3595151 3595155) to complete... Waiting for PID 3595155 of (3595151 3595155) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 208577 Total vertex volume 208333 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1171 848 2454 2.852 0.751 0.157 0.047 27 2.6 caudalanteriorcingulate 2916 2149 6234 2.535 0.492 0.120 0.031 30 3.8 caudalmiddlefrontal 2394 1579 3518 2.099 0.521 0.138 0.035 31 3.4 cuneus 556 367 1188 2.368 0.956 0.124 0.041 6 0.8 entorhinal 3405 2446 7064 2.566 0.593 0.125 0.028 39 3.8 fusiform 5345 3912 11181 2.530 0.563 0.134 0.035 72 7.4 inferiorparietal 3676 2856 9947 2.713 0.726 0.138 0.035 56 5.4 inferiortemporal 1195 784 1600 2.144 0.749 0.122 0.031 17 1.7 isthmuscingulate 5874 3941 9871 2.311 0.536 0.135 0.032 70 7.7 lateraloccipital 3243 2391 7801 2.725 0.829 0.142 0.041 47 5.4 lateralorbitofrontal 4277 2863 6380 2.040 0.543 0.128 0.033 54 5.5 lingual 1980 1465 4369 2.475 0.833 0.146 0.037 32 3.0 medialorbitofrontal 5315 3678 11303 2.623 0.611 0.112 0.025 59 5.5 middletemporal 1219 768 2222 2.426 0.653 0.083 0.021 6 0.8 parahippocampal 2185 1376 3974 2.595 0.566 0.097 0.024 14 2.1 paracentral 1787 1207 3352 2.490 0.470 0.104 0.025 14 1.8 parsopercularis 728 556 1621 2.496 0.546 0.138 0.034 9 1.0 parsorbitalis 1925 1399 3900 2.399 0.571 0.120 0.028 21 2.3 parstriangularis 1970 1304 2048 1.642 0.463 0.130 0.036 20 3.1 pericalcarine 6550 4387 10194 2.091 0.603 0.108 0.025 58 6.8 postcentral 1264 899 2420 2.608 0.602 0.133 0.035 24 1.7 posteriorcingulate 6804 4665 12563 2.500 0.559 0.119 0.032 65 9.2 precentral 4092 2975 8353 2.569 0.553 0.141 0.035 55 5.7 precuneus 1714 1266 3397 2.433 1.037 0.148 0.049 32 3.5 rostralanteriorcingulate 4242 3242 9853 2.477 0.614 0.128 0.031 57 5.2 rostralmiddlefrontal 7956 6164 20586 2.638 0.683 0.136 0.038 123 12.4 superiorfrontal 4972 3524 9685 2.502 0.480 0.122 0.029 54 6.1 superiorparietal 7400 4929 15850 2.634 0.662 0.099 0.025 64 7.3 superiortemporal 4531 3253 8309 2.353 0.525 0.124 0.029 48 5.3 supramarginal 746 400 941 2.160 0.534 0.094 0.028 5 0.8 transversetemporal 2726 1837 6155 3.025 0.941 0.114 0.035 24 4.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 217158 Total vertex volume 216888 (mask=0) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 904 625 1611 2.646 0.686 0.124 0.028 15 1.2 caudalanteriorcingulate 2979 2127 6140 2.546 0.523 0.123 0.029 31 3.5 caudalmiddlefrontal 2632 1712 3867 2.094 0.453 0.134 0.031 33 3.4 cuneus 636 434 1736 2.976 0.793 0.128 0.036 8 0.9 entorhinal 3375 2412 6966 2.548 0.625 0.122 0.026 40 3.6 fusiform 6822 4821 13639 2.563 0.519 0.125 0.030 80 8.6 inferiorparietal 4496 3269 11391 2.804 0.672 0.135 0.035 71 5.9 inferiortemporal 913 564 1300 2.122 0.739 0.115 0.028 9 1.1 isthmuscingulate 6489 4303 10505 2.275 0.579 0.128 0.030 72 7.8 lateraloccipital 3333 2468 7990 2.690 0.775 0.149 0.043 50 6.0 lateralorbitofrontal 4679 3114 6860 2.044 0.568 0.128 0.033 59 6.2 lingual 1817 1331 3846 2.377 0.779 0.146 0.045 42 3.2 medialorbitofrontal 5438 3703 12195 2.781 0.594 0.105 0.024 52 5.4 middletemporal 1126 716 2237 2.651 0.743 0.098 0.023 10 0.9 parahippocampal 2209 1388 3772 2.554 0.522 0.109 0.026 19 2.2 paracentral 1747 1303 4017 2.619 0.579 0.131 0.034 21 2.4 parsopercularis 797 597 1986 2.556 0.628 0.129 0.055 31 0.9 parsorbitalis 1568 1135 3217 2.377 0.640 0.113 0.028 15 1.9 parstriangularis 2164 1418 2355 1.769 0.495 0.125 0.036 24 2.9 pericalcarine 6869 4331 10173 2.140 0.571 0.096 0.021 54 6.1 postcentral 1014 706 2022 2.656 0.587 0.125 0.029 15 1.2 posteriorcingulate 6188 4124 11858 2.692 0.558 0.110 0.027 47 7.0 precentral 4737 3441 9447 2.517 0.522 0.124 0.029 51 5.6 precuneus 1005 669 2433 2.642 0.954 0.121 0.036 15 1.6 rostralanteriorcingulate 3959 3084 9909 2.518 0.741 0.145 0.038 68 6.5 rostralmiddlefrontal 10059 7509 25089 2.622 0.714 0.131 0.036 135 15.5 superiorfrontal 4955 3408 9604 2.586 0.425 0.122 0.027 57 5.2 superiorparietal 7326 4612 14691 2.641 0.738 0.089 0.021 56 5.9 superiortemporal 4575 3184 8849 2.543 0.538 0.115 0.025 43 4.8 supramarginal 624 314 880 2.385 0.483 0.111 0.033 7 0.7 transversetemporal 3001 2042 6303 2.888 0.864 0.108 0.031 25 3.8 insula PIDs (3595151 3595155) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Mon Oct 14 12:57:31 CDT 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/ASegStatsLUT.txt --subject PIB23-310_VYr0_Bay3prisma setting seed for random number genererator to 1234 7.3.2 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/ASegStatsLUT.txt --subject PIB23-310_VYr0_Bay3prisma sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) Computing euler number orig.nofix lheno = -82, rheno = -64 orig.nofix lhholes = 42, rhholes = 33 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2024:10:14:12:57:31 mri_segstats N 32 e 86.92 S 1.27 U 305.11 P 352% M 291080 F 2 R 1000902 W 0 c 32848 w 1156 I 8016 O 24 L 52.42 54.04 63.52 @#@FSLOADPOST 2024:10:14:12:58:58 mri_segstats N 32 55.58 55.01 63.02 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label #-------------------------------------------- #@# BA_exvivo Labels lh Mon Oct 14 12:58:58 CDT 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 3638551 of (3638551 3638555 3638558 3638561 3638565) to complete... Waiting for PID 3638555 of (3638551 3638555 3638558 3638561 3638565) to complete... Waiting for PID 3638558 of (3638551 3638555 3638558 3638561 3638565) to complete... Waiting for PID 3638561 of (3638551 3638555 3638558 3638561 3638565) to complete... Waiting for PID 3638565 of (3638551 3638555 3638558 3638561 3638565) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4244 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8033 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4167 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6110 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 144 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5928 mri_label2label: Done PIDs (3638551 3638555 3638558 3638561 3638565) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 3641989 of (3641989 3641993 3641996 3642001) to complete... Waiting for PID 3641993 of (3641989 3641993 3641996 3642001) to complete... Waiting for PID 3641996 of (3641989 3641993 3641996 3642001) to complete... Waiting for PID 3642001 of (3641989 3641993 3641996 3642001) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 132 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4202 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 278 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13867 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4228 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3592 mri_label2label: Done PIDs (3641989 3641993 3641996 3642001) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 3645361 of (3645361 3645364 3645368 3645372 3645376) to complete... Waiting for PID 3645364 of (3645361 3645364 3645368 3645372 3645376) to complete... Waiting for PID 3645368 of (3645361 3645364 3645368 3645372 3645376) to complete... Waiting for PID 3645372 of (3645361 3645364 3645368 3645372 3645376) to complete... Waiting for PID 3645376 of (3645361 3645364 3645368 3645372 3645376) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 718 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5359 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 1168 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9282 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 108 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2126 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1399 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1259 mri_label2label: Done PIDs (3645361 3645364 3645368 3645372 3645376) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 3650095 of (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) to complete... Waiting for PID 3650098 of (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) to complete... Waiting for PID 3650102 of (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) to complete... Waiting for PID 3650105 of (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) to complete... Waiting for PID 3650108 of (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) to complete... Waiting for PID 3650111 of (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) to complete... Waiting for PID 3650115 of (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) to complete... Waiting for PID 3650120 of (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 414 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 474 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 703 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 762 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1873 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1946 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2101 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2160 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3877 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 623 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4500 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2919 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 417 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1286 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 264 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1550 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1006 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 187 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1193 mri_label2label: Done PIDs (3650095 3650098 3650102 3650105 3650108 3650111 3650115 3650120) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt Number of ctab entries 9 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 101193 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.mpm.vpnl.annot @#@FSTIME 2024:10:14:12:59:31 mris_label2annot N 26 e 0.71 S 0.08 U 0.75 P 117% M 134660 F 5 R 36599 W 0 c 82 w 198 I 8304 O 1792 L 62.31 56.94 63.42 @#@FSLOADPOST 2024:10:14:12:59:32 mris_label2annot N 26 60.05 56.56 63.26 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3653070 of (3653070 3653075 3653078 3653082 3653085) to complete... Waiting for PID 3653075 of (3653070 3653075 3653078 3653082 3653085) to complete... Waiting for PID 3653078 of (3653070 3653075 3653078 3653082 3653085) to complete... Waiting for PID 3653082 of (3653070 3653075 3653078 3653082 3653085) to complete... Waiting for PID 3653085 of (3653070 3653075 3653078 3653082 3653085) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1055 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2146 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1515 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2057 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2384 mri_label2label: Done PIDs (3653070 3653075 3653078 3653082 3653085) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3655444 of (3655444 3655461 3655465 3655489) to complete... Waiting for PID 3655461 of (3655444 3655461 3655465 3655489) to complete... Waiting for PID 3655465 of (3655444 3655461 3655465 3655489) to complete... Waiting for PID 3655489 of (3655444 3655461 3655465 3655489) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1620 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7134 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1930 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1208 mri_label2label: Done PIDs (3655444 3655461 3655465 3655489) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3658766 of (3658766 3658769 3658773 3658776 3658779) to complete... Waiting for PID 3658769 of (3658766 3658769 3658773 3658776 3658779) to complete... Waiting for PID 3658773 of (3658766 3658769 3658773 3658776 3658779) to complete... Waiting for PID 3658776 of (3658766 3658769 3658773 3658776 3658779) to complete... Waiting for PID 3658779 of (3658766 3658769 3658773 3658776 3658779) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 564 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3969 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 512 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 3846 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 548 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 501 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 114566 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 471 mri_label2label: Done PIDs (3658766 3658769 3658773 3658776 3658779) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 79073 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.BA_exvivo.annot @#@FSTIME 2024:10:14:12:59:53 mris_label2annot N 38 e 0.65 S 0.07 U 0.78 P 131% M 134888 F 0 R 36592 W 0 c 78 w 271 I 0 O 1792 L 69.43 58.88 63.88 @#@FSLOADPOST 2024:10:14:12:59:54 mris_label2annot N 38 69.43 58.88 63.88 mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi lh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi lh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 93070 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2024:10:14:12:59:54 mris_label2annot N 38 e 0.83 S 0.10 U 0.87 P 116% M 134588 F 2 R 36582 W 0 c 100 w 220 I 0 O 1792 L 69.43 58.88 63.88 @#@FSLOADPOST 2024:10:14:12:59:55 mris_label2annot N 38 69.43 58.88 63.88 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 208577 Total vertex volume 208333 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 1064 628 1959 2.290 0.544 0.127 0.037 17 1.3 BA1_exvivo 3527 2429 5783 2.197 0.517 0.103 0.022 26 3.3 BA2_exvivo 1089 805 1100 1.717 0.283 0.133 0.028 8 1.4 BA3a_exvivo 2230 1516 3206 1.893 0.614 0.104 0.024 18 2.3 BA3b_exvivo 1484 937 3111 2.795 0.528 0.105 0.032 11 1.8 BA4a_exvivo 1429 949 2264 2.515 0.512 0.113 0.038 13 2.2 BA4p_exvivo 7448 5449 17646 2.650 0.585 0.131 0.037 98 11.5 BA6_exvivo 1876 1261 3592 2.526 0.468 0.108 0.027 15 2.0 BA44_exvivo 2369 1749 4946 2.402 0.538 0.118 0.027 26 2.7 BA45_exvivo 3340 2197 3719 1.653 0.452 0.127 0.037 37 4.8 V1_exvivo 6698 4470 10292 2.106 0.522 0.140 0.034 91 9.3 V2_exvivo 1582 1072 3063 2.517 0.470 0.125 0.028 17 1.9 MT_exvivo 691 493 1466 2.567 0.820 0.131 0.039 7 1.1 perirhinal_exvivo 666 423 1349 2.232 1.105 0.121 0.044 8 1.2 entorhinal_exvivo @#@FSTIME 2024:10:14:12:59:55 mris_anatomical_stats N 12 e 4.82 S 0.35 U 6.12 P 134% M 405652 F 1 R 207592 W 0 c 687 w 323 I 0 O 136 L 69.43 58.88 63.88 @#@FSLOADPOST 2024:10:14:13:00:00 mris_anatomical_stats N 12 66.92 58.53 63.74 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB23-310_VYr0_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 208577 Total vertex volume 208333 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 747 404 1277 2.242 0.444 0.128 0.040 12 0.9 BA1_exvivo 1518 1013 2186 2.023 0.441 0.083 0.015 7 1.0 BA2_exvivo 892 659 877 1.713 0.279 0.136 0.029 7 1.1 BA3a_exvivo 1440 986 1588 1.594 0.318 0.088 0.017 7 1.1 BA3b_exvivo 1481 966 2956 2.721 0.574 0.111 0.036 13 2.3 BA4a_exvivo 1198 802 1920 2.501 0.490 0.113 0.037 10 1.7 BA4p_exvivo 4095 2909 9718 2.705 0.556 0.126 0.034 48 5.7 BA6_exvivo 1190 803 2400 2.571 0.492 0.115 0.030 12 1.5 BA44_exvivo 905 704 2310 2.605 0.561 0.128 0.030 12 1.1 BA45_exvivo 3554 2328 4030 1.669 0.452 0.125 0.036 39 4.8 V1_exvivo 3365 2222 4613 1.944 0.451 0.143 0.038 45 5.2 V2_exvivo 427 299 782 2.425 0.457 0.124 0.026 3 0.6 MT_exvivo 305 212 656 2.766 0.881 0.143 0.042 3 0.5 perirhinal_exvivo 379 258 788 2.401 0.970 0.105 0.027 2 0.5 entorhinal_exvivo @#@FSTIME 2024:10:14:13:00:00 mris_anatomical_stats N 12 e 4.44 S 0.35 U 5.91 P 141% M 405440 F 1 R 209692 W 0 c 618 w 347 I 0 O 136 L 66.92 58.53 63.74 @#@FSLOADPOST 2024:10:14:13:00:04 mris_anatomical_stats N 12 64.20 58.11 63.58 #-------------------------------------------- #@# BA_exvivo Labels rh Mon Oct 14 13:00:04 CDT 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 3665907 of (3665907 3665910 3665913 3665917 3665922) to complete... Waiting for PID 3665910 of (3665907 3665910 3665913 3665917 3665922) to complete... Waiting for PID 3665913 of (3665907 3665910 3665913 3665917 3665922) to complete... Waiting for PID 3665917 of (3665907 3665910 3665913 3665917 3665922) to complete... Waiting for PID 3665922 of (3665907 3665910 3665913 3665917 3665922) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4092 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 177 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6864 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4065 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 108 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4630 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5876 mri_label2label: Done PIDs (3665907 3665910 3665913 3665917 3665922) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 3669271 of (3669271 3669275 3669278 3669310) to complete... Waiting for PID 3669275 of (3669271 3669275 3669278 3669310) to complete... Waiting for PID 3669278 of (3669271 3669275 3669278 3669310) to complete... Waiting for PID 3669310 of (3669271 3669275 3669278 3669310) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4600 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 198 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12454 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 6980 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5488 mri_label2label: Done PIDs (3669271 3669275 3669278 3669310) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 3674048 of (3674048 3674052 3674058 3674065 3674068) to complete... Waiting for PID 3674052 of (3674048 3674052 3674058 3674065 3674068) to complete... Waiting for PID 3674058 of (3674048 3674052 3674058 3674065 3674068) to complete... Waiting for PID 3674065 of (3674048 3674052 3674058 3674065 3674068) to complete... Waiting for PID 3674068 of (3674048 3674052 3674058 3674065 3674068) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 1215 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5942 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 1904 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9920 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2135 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1141 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 89 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 841 mri_label2label: Done PIDs (3674048 3674052 3674058 3674065 3674068) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 3676780 of (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) to complete... Waiting for PID 3676784 of (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) to complete... Waiting for PID 3676788 of (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) to complete... Waiting for PID 3676791 of (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) to complete... Waiting for PID 3676795 of (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) to complete... Waiting for PID 3676798 of (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) to complete... Waiting for PID 3676802 of (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) to complete... Waiting for PID 3676806 of (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 541 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 637 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 721 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 850 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1523 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1584 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1586 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1719 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3667 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 937 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4604 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2719 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 737 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3456 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1228 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 476 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1704 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1025 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 323 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1348 mri_label2label: Done PIDs (3676780 3676784 3676788 3676791 3676795 3676798 3676802 3676806) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt Number of ctab entries 9 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 104652 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.mpm.vpnl.annot @#@FSTIME 2024:10:14:13:00:38 mris_label2annot N 26 e 1.01 S 0.08 U 0.96 P 103% M 139176 F 1 R 37954 W 0 c 192 w 223 I 8344 O 1864 L 69.27 60.08 64.04 @#@FSLOADPOST 2024:10:14:13:00:40 mris_label2annot N 26 69.27 60.08 64.04 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3680462 of (3680462 3680465 3680493 3680498 3680504) to complete... Waiting for PID 3680465 of (3680462 3680465 3680493 3680498 3680504) to complete... Waiting for PID 3680493 of (3680462 3680465 3680493 3680498 3680504) to complete... Waiting for PID 3680498 of (3680462 3680465 3680493 3680498 3680504) to complete... Waiting for PID 3680504 of (3680462 3680465 3680493 3680498 3680504) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 937 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2766 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1711 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2221 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1416 mri_label2label: Done PIDs (3680462 3680465 3680493 3680498 3680504) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3684986 of (3684986 3684989 3684993 3684997) to complete... Waiting for PID 3684989 of (3684986 3684989 3684993 3684997) to complete... Waiting for PID 3684993 of (3684986 3684989 3684993 3684997) to complete... Waiting for PID 3684997 of (3684986 3684989 3684993 3684997) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1575 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7019 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1041 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1196 mri_label2label: Done PIDs (3684986 3684989 3684993 3684997) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3687025 of (3687025 3687028 3687032 3687036 3687039) to complete... Waiting for PID 3687028 of (3687025 3687028 3687032 3687036 3687039) to complete... Waiting for PID 3687032 of (3687025 3687028 3687032 3687036 3687039) to complete... Waiting for PID 3687036 of (3687025 3687028 3687032 3687036 3687039) to complete... Waiting for PID 3687039 of (3687025 3687028 3687032 3687036 3687039) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 814 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4046 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 1044 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4481 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 315 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 756 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB23-310_VYr0_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PIB23-310_VYr0_Bay3prisma trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 118830 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 323 mri_label2label: Done PIDs (3687025 3687028 3687032 3687036 3687039) completed and logs appended. mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 82298 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.BA_exvivo.annot @#@FSTIME 2024:10:14:13:01:01 mris_label2annot N 38 e 2.15 S 0.14 U 1.14 P 59% M 139424 F 3 R 38031 W 0 c 151 w 236 I 0 O 1864 L 60.29 58.63 63.47 @#@FSLOADPOST 2024:10:14:13:01:03 mris_label2annot N 38 63.55 59.34 63.68 mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt Number of ctab entries 15 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label cmdline mris_label2annot --s PIB23-310_VYr0_Bay3prisma --hemi rh --ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname chopin machine x86_64 user grossens subject PIB23-310_VYr0_Bay3prisma hemi rh SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing ColorTable /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 97053 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2024:10:14:13:01:03 mris_label2annot N 38 e 0.76 S 0.09 U 0.89 P 128% M 139276 F 2 R 38021 W 0 c 102 w 281 I 0 O 1864 L 63.55 59.34 63.68 @#@FSLOADPOST 2024:10:14:13:01:04 mris_label2annot N 38 63.55 59.34 63.68 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 217158 Total vertex volume 216888 (mask=0) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 997 504 1664 2.344 0.481 0.117 0.039 15 1.4 BA1_exvivo 3301 2129 4743 2.243 0.448 0.083 0.015 17 2.1 BA2_exvivo 1112 792 1168 1.826 0.415 0.110 0.022 6 1.1 BA3a_exvivo 2011 1319 2535 1.780 0.435 0.094 0.018 13 1.6 BA3b_exvivo 1465 873 2722 2.730 0.534 0.103 0.027 12 1.6 BA4a_exvivo 1307 847 2207 2.763 0.567 0.107 0.031 10 1.6 BA4p_exvivo 6374 4578 14799 2.672 0.596 0.129 0.034 80 9.8 BA6_exvivo 2711 1937 5630 2.632 0.555 0.125 0.031 28 3.6 BA44_exvivo 2951 2237 6653 2.399 0.632 0.128 0.032 34 4.1 BA45_exvivo 3887 2454 4677 1.812 0.508 0.128 0.039 48 5.8 V1_exvivo 7515 4955 10887 2.040 0.531 0.134 0.031 96 9.7 V2_exvivo 1827 1268 3313 2.563 0.492 0.125 0.028 19 2.1 MT_exvivo 431 305 924 3.018 0.602 0.118 0.027 3 0.5 perirhinal_exvivo 643 430 1728 2.921 0.814 0.098 0.031 4 0.7 entorhinal_exvivo @#@FSTIME 2024:10:14:13:01:04 mris_anatomical_stats N 12 e 5.49 S 0.47 U 6.67 P 130% M 419784 F 3 R 189960 W 0 c 803 w 365 I 0 O 136 L 63.55 59.34 63.68 @#@FSLOADPOST 2024:10:14:13:01:09 mris_anatomical_stats N 12 61.02 58.88 63.51 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB23-310_VYr0_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 217158 Total vertex volume 216888 (mask=0) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1592716 mm^3 (det: 1.223135 ) 731 340 1021 2.122 0.474 0.105 0.038 11 0.9 BA1_exvivo 1975 1244 2853 2.185 0.487 0.075 0.012 8 1.2 BA2_exvivo 1000 718 1006 1.812 0.383 0.111 0.021 5 1.0 BA3a_exvivo 1601 1062 1782 1.669 0.333 0.088 0.016 8 1.2 BA3b_exvivo 896 515 1716 2.775 0.541 0.108 0.034 9 1.0 BA4a_exvivo 1137 736 1965 2.880 0.565 0.108 0.032 9 1.6 BA4p_exvivo 4151 2901 9308 2.708 0.568 0.121 0.031 47 5.9 BA6_exvivo 687 532 1938 2.782 0.591 0.157 0.047 12 1.3 BA44_exvivo 777 632 2102 2.508 0.586 0.139 0.036 10 1.2 BA45_exvivo 3710 2329 4369 1.796 0.519 0.126 0.039 44 5.6 V1_exvivo 4160 2697 5680 1.938 0.497 0.139 0.034 59 5.8 V2_exvivo 284 192 507 2.240 0.481 0.128 0.034 4 0.4 MT_exvivo 40 30 81 3.231 0.316 0.119 0.025 0 0.0 perirhinal_exvivo 628 429 1515 2.899 0.708 0.096 0.025 3 0.6 entorhinal_exvivo @#@FSTIME 2024:10:14:13:01:10 mris_anatomical_stats N 12 e 5.73 S 0.45 U 6.86 P 127% M 419536 F 2 R 197766 W 0 c 866 w 344 I 0 O 136 L 61.02 58.88 63.51 @#@FSLOADPOST 2024:10:14:13:01:15 mris_anatomical_stats N 12 59.26 58.55 63.37 Started at Mon Oct 14 11:35:05 CDT 2024 Ended at Mon Oct 14 13:01:15 CDT 2024 #@#%# recon-all-run-time-hours 1.436 recon-all -s PIB23-310_VYr0_Bay3prisma finished without error at Mon Oct 14 13:01:15 CDT 2024 #New# invocation of recon-all Mon Jan 6 14:05:57 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/recon-all -3T -parallel -s PIB23-310_VYr0_Bay3prisma_AT/ -autorecon2-wm -autorecon3 subjid PIB23-310_VYr0_Bay3prisma_AT setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 Actual FREESURFER_HOME /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04 build-stamp.txt: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 1029556 maxlocks unlimited maxsignal 1029556 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 251Gi 154Gi 15Gi 133Mi 80Gi 94Gi Swap: 111Gi 953Mi 110Gi ######################################## program versions used 7.3.2 (freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275) 7.3.2 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 7.3.2 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2025/01/06-20:05:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 User: tanenbauma Machine: chopin Platform: Linux PlatformVersion: 5.15.0-117-generic CompilerName: GCC CompilerVersion: 8.4.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Mask BFS Mon Jan 6 14:05:57 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1592378 voxels in mask (pct= 9.49) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2025:01:06:14:05:57 mri_mask N 5 e 1.28 S 0.05 U 1.64 P 131% M 74272 F 0 R 20717 W 0 c 177 w 112 I 5472 O 2728 L 37.42 35.85 39.16 @#@FSLOADPOST 2025:01:06:14:05:58 mri_mask N 5 37.42 35.85 39.16 #-------------------------------------------- #@# Fill Mon Jan 6 14:05:58 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/SubCorticalMassLUT.txt -auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01708 0.03299 0.01521 -9.14641; -0.03326 1.05500 0.21471 -43.02063; -0.00859 -0.18744 0.96628 16.29088; 0.00000 0.00000 0.00000 1.00000; Using auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt ndiff 20442 voxel to talairach voxel transform 1.01708 0.03299 0.01521 -9.14641; -0.03326 1.05500 0.21471 -43.02063; -0.00859 -0.18744 0.96628 16.29088; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 2125 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) need search nearby using seed (128, 119, 157), TAL = (0.0, 29.0, 9.0) talairach voxel to voxel transform 0.98208 -0.03219 -0.00831 7.73326; 0.02807 0.91094 -0.20286 42.75090; 0.01417 0.17642 0.99548 -8.49771; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (128, 119, 157) --> (0.0, 29.0, 9.0) done. filling took 1.4 minutes talairach cc position changed to (0.00, 29.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(18.00, 29.00, 9.00) SRC: (110.63, 122.39, 170.35) search lh wm seed point around talairach space (-18.00, 29.00, 9.00), SRC: (145.98, 123.40, 170.86) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... DoAutoMan 1 Applying edits to the output Applied 20442 edits Writing edits to ../tmp/filled.edits.txt Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2025:01:06:14:05:58 mri_fill N 14 e 82.07 S 1.55 U 81.12 P 100% M 990312 F 0 R 1017365 W 0 c 7808 w 92 I 1872 O 960 L 37.42 35.85 39.16 @#@FSLOADPOST 2025:01:06:14:07:21 mri_fill N 14 49.90 39.94 40.30 #-------------------------------------------- #@# Tessellate lh Mon Jan 6 14:07:21 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 16 found - 16 modified | TOTAL: 29 pass 2 (xy-): 0 found - 16 modified | TOTAL: 29 pass 1 (yz+): 15 found - 15 modified | TOTAL: 44 pass 2 (yz+): 0 found - 15 modified | TOTAL: 44 pass 1 (yz-): 9 found - 9 modified | TOTAL: 53 pass 2 (yz-): 0 found - 9 modified | TOTAL: 53 pass 1 (xz+): 11 found - 11 modified | TOTAL: 64 pass 2 (xz+): 0 found - 11 modified | TOTAL: 64 pass 1 (xz-): 12 found - 12 modified | TOTAL: 76 pass 2 (xz-): 0 found - 12 modified | TOTAL: 76 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 4 found - 4 modified | TOTAL: 11 pass 2 (+-): 0 found - 4 modified | TOTAL: 11 pass 1 (--): 6 found - 6 modified | TOTAL: 17 pass 2 (--): 0 found - 6 modified | TOTAL: 17 pass 1 (-+): 4 found - 4 modified | TOTAL: 21 pass 2 (-+): 0 found - 4 modified | TOTAL: 21 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 105 (out of 258986: 0.040543) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2025:01:06:14:07:21 mri_pretess N 4 e 2.75 S 0.04 U 3.31 P 121% M 40560 F 0 R 13157 W 0 c 298 w 63 I 2792 O 232 L 49.90 39.94 40.30 @#@FSLOADPOST 2025:01:06:14:07:24 mri_pretess N 4 49.90 39.94 40.30 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.3.2 7.3.2 slice 50: 1188 vertices, 1296 faces slice 60: 6672 vertices, 6921 faces slice 70: 14738 vertices, 15009 faces slice 80: 23291 vertices, 23576 faces slice 90: 31838 vertices, 32121 faces slice 100: 40104 vertices, 40452 faces slice 110: 49530 vertices, 49912 faces slice 120: 59001 vertices, 59363 faces slice 130: 67889 vertices, 68238 faces slice 140: 76548 vertices, 76920 faces slice 150: 85429 vertices, 85800 faces slice 160: 92717 vertices, 93005 faces slice 170: 99349 vertices, 99621 faces slice 180: 105024 vertices, 105246 faces slice 190: 109393 vertices, 109592 faces slice 200: 111907 vertices, 112032 faces slice 210: 112304 vertices, 112362 faces slice 220: 112304 vertices, 112362 faces slice 230: 112304 vertices, 112362 faces slice 240: 112304 vertices, 112362 faces slice 250: 112304 vertices, 112362 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2025:01:06:14:07:24 mri_tessellate N 3 e 1.94 S 0.02 U 2.08 P 108% M 35796 F 0 R 7900 W 0 c 191 w 79 I 0 O 5272 L 49.90 39.94 40.30 @#@FSLOADPOST 2025:01:06:14:07:25 mri_tessellate N 3 51.91 40.52 40.48 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 112096 voxel in cpt #1: X=-82 [v=112096,e=336534,f=224356] located at (-25.489214, -10.768796, 1.343911) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (-11.000000, -67.000000, -9.000000) 8 voxel in cpt #3: X=2 [v=8,e=18,f=12] located at (-11.000000, -66.000000, -14.000000) 66 voxel in cpt #4: X=2 [v=66,e=192,f=128] located at (-11.590909, -60.454544, -7.606061) 8 voxel in cpt #5: X=2 [v=8,e=18,f=12] located at (-9.000000, -63.000000, -19.000000) 8 voxel in cpt #6: X=2 [v=8,e=18,f=12] located at (-9.000000, -60.000000, -8.000000) 8 voxel in cpt #7: X=2 [v=8,e=18,f=12] located at (-9.000000, -60.000000, -10.000000) 28 voxel in cpt #8: X=2 [v=28,e=78,f=52] located at (-11.857142, -57.285713, -18.214285) 8 voxel in cpt #9: X=2 [v=8,e=18,f=12] located at (-15.000000, -49.000000, -24.000000) 30 voxel in cpt #10: X=2 [v=30,e=84,f=56] located at (-30.100000, 26.200001, 16.700001) 12 voxel in cpt #11: X=2 [v=12,e=30,f=20] located at (-13.000000, 29.000000, -9.500000) 8 voxel in cpt #12: X=2 [v=8,e=18,f=12] located at (-15.000000, 30.000000, -10.000000) 16 voxel in cpt #13: X=2 [v=16,e=42,f=28] located at (-33.375000, 44.000000, -32.375000) For the whole surface: X=-58 [v=112304,e=337086,f=224724] 13 components have been found keeping component #1 with 112096 vertices done @#@FSTIME 2025:01:06:14:07:26 mris_extract_main_component N 2 e 0.83 S 0.11 U 0.86 P 117% M 224148 F 3 R 59171 W 0 c 94 w 113 I 0 O 7888 L 51.91 40.52 40.48 @#@FSLOADPOST 2025:01:06:14:07:26 mris_extract_main_component N 2 51.91 40.52 40.48 #-------------------------------------------- #@# Tessellate rh Mon Jan 6 14:07:26 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 14 found - 14 modified | TOTAL: 31 pass 2 (xy-): 0 found - 14 modified | TOTAL: 31 pass 1 (yz+): 15 found - 15 modified | TOTAL: 46 pass 2 (yz+): 0 found - 15 modified | TOTAL: 46 pass 1 (yz-): 11 found - 11 modified | TOTAL: 57 pass 2 (yz-): 0 found - 11 modified | TOTAL: 57 pass 1 (xz+): 11 found - 11 modified | TOTAL: 68 pass 2 (xz+): 0 found - 11 modified | TOTAL: 68 pass 1 (xz-): 7 found - 7 modified | TOTAL: 75 pass 2 (xz-): 0 found - 7 modified | TOTAL: 75 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 3 found - 3 modified | TOTAL: 9 pass 2 (+++): 0 found - 3 modified | TOTAL: 9 pass 1 (+++): 4 found - 4 modified | TOTAL: 13 pass 2 (+++): 0 found - 4 modified | TOTAL: 13 Iteration Number : 1 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 7 found - 7 modified | TOTAL: 11 pass 2 (+-): 0 found - 7 modified | TOTAL: 11 pass 1 (--): 9 found - 9 modified | TOTAL: 20 pass 2 (--): 0 found - 9 modified | TOTAL: 20 pass 1 (-+): 6 found - 6 modified | TOTAL: 26 pass 2 (-+): 0 found - 6 modified | TOTAL: 26 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 123 (out of 259934: 0.047320) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2025:01:06:14:07:26 mri_pretess N 4 e 4.96 S 0.05 U 5.20 P 105% M 40600 F 0 R 21705 W 0 c 616 w 35 I 0 O 232 L 51.91 40.52 40.48 @#@FSLOADPOST 2025:01:06:14:07:31 mri_pretess N 4 51.11 40.55 40.49 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 50: 783 vertices, 866 faces slice 60: 6162 vertices, 6380 faces slice 70: 13448 vertices, 13699 faces slice 80: 22748 vertices, 23096 faces slice 90: 31604 vertices, 31845 faces slice 100: 40108 vertices, 40399 faces slice 110: 49313 vertices, 49633 faces slice 120: 58670 vertices, 59007 faces slice 130: 67643 vertices, 67979 faces slice 140: 76409 vertices, 76744 faces slice 150: 85206 vertices, 85529 faces slice 160: 93403 vertices, 93691 faces slice 170: 100486 vertices, 100721 faces slice 180: 106913 vertices, 107111 faces slice 190: 111293 vertices, 111463 faces slice 200: 114996 vertices, 115119 faces slice 210: 116310 vertices, 116336 faces slice 220: 116310 vertices, 116336 faces slice 230: 116310 vertices, 116336 faces slice 240: 116310 vertices, 116336 faces slice 250: 116310 vertices, 116336 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2025:01:06:14:07:32 mri_tessellate N 3 e 3.09 S 0.02 U 2.51 P 82% M 36100 F 0 R 8388 W 0 c 270 w 184 I 0 O 5456 L 51.11 40.55 40.49 @#@FSLOADPOST 2025:01:06:14:07:35 mri_tessellate N 3 48.54 40.19 40.37 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 116124 voxel in cpt #1: X=-64 [v=116124,e=348564,f=232376] located at (29.092625, -8.121482, 2.894948) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (21.000000, -61.000000, -8.000000) 8 voxel in cpt #3: X=2 [v=8,e=18,f=12] located at (21.000000, -61.000000, -10.000000) 8 voxel in cpt #4: X=2 [v=8,e=18,f=12] located at (20.000000, -61.000000, -12.000000) 8 voxel in cpt #5: X=2 [v=8,e=18,f=12] located at (19.000000, -60.000000, -18.000000) 30 voxel in cpt #6: X=2 [v=30,e=84,f=56] located at (19.000000, -57.500000, -10.500000) 8 voxel in cpt #7: X=2 [v=8,e=18,f=12] located at (20.000000, -57.000000, -8.000000) 8 voxel in cpt #8: X=2 [v=8,e=18,f=12] located at (25.000000, -55.000000, -25.000000) 8 voxel in cpt #9: X=2 [v=8,e=18,f=12] located at (21.000000, -54.000000, -8.000000) 8 voxel in cpt #10: X=2 [v=8,e=18,f=12] located at (22.000000, -54.000000, -16.000000) 12 voxel in cpt #11: X=2 [v=12,e=30,f=20] located at (21.000000, -51.500000, -11.000000) 8 voxel in cpt #12: X=2 [v=8,e=18,f=12] located at (28.000000, -51.000000, -5.000000) 8 voxel in cpt #13: X=2 [v=8,e=18,f=12] located at (30.000000, -51.000000, -6.000000) 8 voxel in cpt #14: X=2 [v=8,e=18,f=12] located at (21.000000, -51.000000, -23.000000) 8 voxel in cpt #15: X=2 [v=8,e=18,f=12] located at (22.000000, -49.000000, -9.000000) 8 voxel in cpt #16: X=2 [v=8,e=18,f=12] located at (25.000000, -39.000000, -18.000000) 12 voxel in cpt #17: X=2 [v=12,e=30,f=20] located at (42.000000, 12.000000, 11.500000) 8 voxel in cpt #18: X=2 [v=8,e=18,f=12] located at (32.000000, 27.000000, -12.000000) 8 voxel in cpt #19: X=2 [v=8,e=18,f=12] located at (32.000000, 28.000000, -10.000000) 12 voxel in cpt #20: X=2 [v=12,e=30,f=20] located at (15.000000, 29.500000, 28.000000) For the whole surface: X=-26 [v=116310,e=349008,f=232672] 20 components have been found keeping component #1 with 116124 vertices done @#@FSTIME 2025:01:06:14:07:35 mris_extract_main_component N 2 e 0.76 S 0.11 U 0.80 P 120% M 231884 F 1 R 61275 W 0 c 91 w 189 I 0 O 8176 L 48.54 40.19 40.37 @#@FSLOADPOST 2025:01:06:14:07:36 mris_extract_main_component N 2 48.54 40.19 40.37 #-------------------------------------------- #@# Smooth1 lh Mon Jan 6 14:07:36 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Mon Jan 6 14:07:36 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 2934605 of (2934605 2934608) to complete... Waiting for PID 2934608 of (2934605 2934608) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (2934605 2934608) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Mon Jan 6 14:07:39 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Mon Jan 6 14:07:39 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 2934717 of (2934717 2934724) to complete... Waiting for PID 2934724 of (2934717 2934724) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.7 mm, total surface area = 60242 mm^2 step 000: RMS=0.155 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.070 (target=0.015) step 025: RMS=0.064 (target=0.015) step 030: RMS=0.058 (target=0.015) step 035: RMS=0.056 (target=0.015) step 040: RMS=0.053 (target=0.015) step 045: RMS=0.051 (target=0.015) step 050: RMS=0.051 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.051 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 33.501075 mris_inflate stimesec 1.327774 mris_inflate ru_maxrss 179444 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 591543 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7920 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2719 mris_inflate ru_nivcsw 3309 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.2 mm, total surface area = 62674 mm^2 step 000: RMS=0.153 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.062 (target=0.015) step 030: RMS=0.057 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.051 (target=0.015) step 045: RMS=0.050 (target=0.015) step 050: RMS=0.049 (target=0.015) step 055: RMS=0.050 (target=0.015) step 060: RMS=0.050 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 32.100128 mris_inflate stimesec 1.306095 mris_inflate ru_maxrss 185952 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 624708 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8200 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 9675 mris_inflate ru_nivcsw 3229 PIDs (2934717 2934724) completed and logs appended. #-------------------------------------------- #@# QSphere lh Mon Jan 6 14:07:59 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Mon Jan 6 14:07:59 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 2935056 of (2935056 2935060) to complete... Waiting for PID 2935060 of (2935056 2935060) to complete... mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 scaling brain by 0.344... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.09 +- 0.61 (0.00-->6.06) (max @ vno 86685 --> 87493) face area 0.03 +- 0.04 (-0.17-->0.68) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.166, avgs=0 005/300: dt: 0.9000, rms radial error=175.909, avgs=0 010/300: dt: 0.9000, rms radial error=175.356, avgs=0 015/300: dt: 0.9000, rms radial error=174.630, avgs=0 020/300: dt: 0.9000, rms radial error=173.804, avgs=0 025/300: dt: 0.9000, rms radial error=172.919, avgs=0 030/300: dt: 0.9000, rms radial error=172.002, avgs=0 035/300: dt: 0.9000, rms radial error=171.068, avgs=0 040/300: dt: 0.9000, rms radial error=170.127, avgs=0 045/300: dt: 0.9000, rms radial error=169.183, avgs=0 050/300: dt: 0.9000, rms radial error=168.239, avgs=0 055/300: dt: 0.9000, rms radial error=167.298, avgs=0 060/300: dt: 0.9000, rms radial error=166.359, avgs=0 065/300: dt: 0.9000, rms radial error=165.425, avgs=0 070/300: dt: 0.9000, rms radial error=164.494, avgs=0 075/300: dt: 0.9000, rms radial error=163.568, avgs=0 080/300: dt: 0.9000, rms radial error=162.649, avgs=0 085/300: dt: 0.9000, rms radial error=161.737, avgs=0 090/300: dt: 0.9000, rms radial error=160.830, avgs=0 095/300: dt: 0.9000, rms radial error=159.928, avgs=0 100/300: dt: 0.9000, rms radial error=159.031, avgs=0 105/300: dt: 0.9000, rms radial error=158.138, avgs=0 110/300: dt: 0.9000, rms radial error=157.251, avgs=0 115/300: dt: 0.9000, rms radial error=156.368, avgs=0 120/300: dt: 0.9000, rms radial error=155.490, avgs=0 125/300: dt: 0.9000, rms radial error=154.618, avgs=0 130/300: dt: 0.9000, rms radial error=153.750, avgs=0 135/300: dt: 0.9000, rms radial error=152.886, avgs=0 140/300: dt: 0.9000, rms radial error=152.028, avgs=0 145/300: dt: 0.9000, rms radial error=151.174, avgs=0 150/300: dt: 0.9000, rms radial error=150.324, avgs=0 155/300: dt: 0.9000, rms radial error=149.480, avgs=0 160/300: dt: 0.9000, rms radial error=148.640, avgs=0 165/300: dt: 0.9000, rms radial error=147.804, avgs=0 170/300: dt: 0.9000, rms radial error=146.973, avgs=0 175/300: dt: 0.9000, rms radial error=146.147, avgs=0 180/300: dt: 0.9000, rms radial error=145.325, avgs=0 185/300: dt: 0.9000, rms radial error=144.508, avgs=0 190/300: dt: 0.9000, rms radial error=143.695, avgs=0 195/300: dt: 0.9000, rms radial error=142.886, avgs=0 200/300: dt: 0.9000, rms radial error=142.083, avgs=0 205/300: dt: 0.9000, rms radial error=141.283, avgs=0 210/300: dt: 0.9000, rms radial error=140.488, avgs=0 215/300: dt: 0.9000, rms radial error=139.698, avgs=0 220/300: dt: 0.9000, rms radial error=138.912, avgs=0 225/300: dt: 0.9000, rms radial error=138.130, avgs=0 230/300: dt: 0.9000, rms radial error=137.352, avgs=0 235/300: dt: 0.9000, rms radial error=136.579, avgs=0 240/300: dt: 0.9000, rms radial error=135.810, avgs=0 245/300: dt: 0.9000, rms radial error=135.046, avgs=0 250/300: dt: 0.9000, rms radial error=134.285, avgs=0 255/300: dt: 0.9000, rms radial error=133.529, avgs=0 260/300: dt: 0.9000, rms radial error=132.777, avgs=0 265/300: dt: 0.9000, rms radial error=132.029, avgs=0 270/300: dt: 0.9000, rms radial error=131.286, avgs=0 275/300: dt: 0.9000, rms radial error=130.546, avgs=0 280/300: dt: 0.9000, rms radial error=129.811, avgs=0 285/300: dt: 0.9000, rms radial error=129.080, avgs=0 290/300: dt: 0.9000, rms radial error=128.353, avgs=0 295/300: dt: 0.9000, rms radial error=127.630, avgs=0 300/300: dt: 0.9000, rms radial error=126.911, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12597.93 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00039 epoch 2 (K=40.0), pass 1, starting sse = 1888.62 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00079 epoch 3 (K=160.0), pass 1, starting sse = 155.07 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/15 = 0.00935 epoch 4 (K=640.0), pass 1, starting sse = 9.23 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/18 = 0.00449 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0294 hours FSRUNTIME@ mris_sphere 0.0294 hours 4 threads #VMPC# mris_sphere VmPeak 655464 mris_sphere done mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.3.2 available threads: 4 scaling brain by 0.331... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.07 +- 0.61 (0.00-->8.22) (max @ vno 52575 --> 53512) face area 0.03 +- 0.04 (-0.12-->0.80) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.557, avgs=0 005/300: dt: 0.9000, rms radial error=176.299, avgs=0 010/300: dt: 0.9000, rms radial error=175.746, avgs=0 015/300: dt: 0.9000, rms radial error=175.018, avgs=0 020/300: dt: 0.9000, rms radial error=174.193, avgs=0 025/300: dt: 0.9000, rms radial error=173.311, avgs=0 030/300: dt: 0.9000, rms radial error=172.397, avgs=0 035/300: dt: 0.9000, rms radial error=171.466, avgs=0 040/300: dt: 0.9000, rms radial error=170.526, avgs=0 045/300: dt: 0.9000, rms radial error=169.584, avgs=0 050/300: dt: 0.9000, rms radial error=168.641, avgs=0 055/300: dt: 0.9000, rms radial error=167.701, avgs=0 060/300: dt: 0.9000, rms radial error=166.764, avgs=0 065/300: dt: 0.9000, rms radial error=165.832, avgs=0 070/300: dt: 0.9000, rms radial error=164.903, avgs=0 075/300: dt: 0.9000, rms radial error=163.980, avgs=0 080/300: dt: 0.9000, rms radial error=163.061, avgs=0 085/300: dt: 0.9000, rms radial error=162.147, avgs=0 090/300: dt: 0.9000, rms radial error=161.238, avgs=0 095/300: dt: 0.9000, rms radial error=160.334, avgs=0 100/300: dt: 0.9000, rms radial error=159.435, avgs=0 105/300: dt: 0.9000, rms radial error=158.541, avgs=0 110/300: dt: 0.9000, rms radial error=157.651, avgs=0 115/300: dt: 0.9000, rms radial error=156.766, avgs=0 120/300: dt: 0.9000, rms radial error=155.885, avgs=0 125/300: dt: 0.9000, rms radial error=155.010, avgs=0 130/300: dt: 0.9000, rms radial error=154.139, avgs=0 135/300: dt: 0.9000, rms radial error=153.273, avgs=0 140/300: dt: 0.9000, rms radial error=152.411, avgs=0 145/300: dt: 0.9000, rms radial error=151.555, avgs=0 150/300: dt: 0.9000, rms radial error=150.703, avgs=0 155/300: dt: 0.9000, rms radial error=149.856, avgs=0 160/300: dt: 0.9000, rms radial error=149.013, avgs=0 165/300: dt: 0.9000, rms radial error=148.175, avgs=0 170/300: dt: 0.9000, rms radial error=147.341, avgs=0 175/300: dt: 0.9000, rms radial error=146.512, avgs=0 180/300: dt: 0.9000, rms radial error=145.688, avgs=0 185/300: dt: 0.9000, rms radial error=144.868, avgs=0 190/300: dt: 0.9000, rms radial error=144.052, avgs=0 195/300: dt: 0.9000, rms radial error=143.242, avgs=0 200/300: dt: 0.9000, rms radial error=142.435, avgs=0 205/300: dt: 0.9000, rms radial error=141.633, avgs=0 210/300: dt: 0.9000, rms radial error=140.836, avgs=0 215/300: dt: 0.9000, rms radial error=140.043, avgs=0 220/300: dt: 0.9000, rms radial error=139.255, avgs=0 225/300: dt: 0.9000, rms radial error=138.471, avgs=0 230/300: dt: 0.9000, rms radial error=137.691, avgs=0 235/300: dt: 0.9000, rms radial error=136.915, avgs=0 240/300: dt: 0.9000, rms radial error=136.144, avgs=0 245/300: dt: 0.9000, rms radial error=135.377, avgs=0 250/300: dt: 0.9000, rms radial error=134.615, avgs=0 255/300: dt: 0.9000, rms radial error=133.856, avgs=0 260/300: dt: 0.9000, rms radial error=133.102, avgs=0 265/300: dt: 0.9000, rms radial error=132.353, avgs=0 270/300: dt: 0.9000, rms radial error=131.607, avgs=0 275/300: dt: 0.9000, rms radial error=130.866, avgs=0 280/300: dt: 0.9000, rms radial error=130.128, avgs=0 285/300: dt: 0.9000, rms radial error=129.395, avgs=0 290/300: dt: 0.9000, rms radial error=128.666, avgs=0 295/300: dt: 0.9000, rms radial error=127.941, avgs=0 300/300: dt: 0.9000, rms radial error=127.220, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13239.80 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00031 epoch 2 (K=40.0), pass 1, starting sse = 2048.65 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00088 epoch 3 (K=160.0), pass 1, starting sse = 179.32 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/14 = 0.00860 epoch 4 (K=640.0), pass 1, starting sse = 10.87 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/17 = 0.00315 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0293 hours FSRUNTIME@ mris_sphere 0.0293 hours 4 threads #VMPC# mris_sphere VmPeak 775236 mris_sphere done PIDs (2935056 2935060) completed and logs appended. #@# Fix Topology lh Mon Jan 6 14:09:45 CST 2025 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma_AT lh #@# Fix Topology rh Mon Jan 6 14:09:45 CST 2025 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma_AT rh Waiting for PID 2936612 of (2936612 2936616) to complete... Waiting for PID 2936616 of (2936612 2936616) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma_AT lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-82 (nv=112096, nf=224356, ne=336534, g=42) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 14 iterations marking ambiguous vertices... 4512 ambiguous faces found in tessellation segmenting defects... 67 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 67 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7741 (-4.3870) -vertex loglikelihood: -6.2920 (-3.1460) -normal dot loglikelihood: -3.6149 (-3.6149) -quad curv loglikelihood: -5.8110 (-2.9055) Total Loglikelihood : -24.4919 CORRECTING DEFECT 0 (vertices=14, convex hull=25, v0=4196) After retessellation of defect 0 (v0=4196), euler #=-63 (109207,326263,216993) : difference with theory (-64) = -1 CORRECTING DEFECT 1 (vertices=9, convex hull=20, v0=6264) After retessellation of defect 1 (v0=6264), euler #=-62 (109208,326272,217002) : difference with theory (-63) = -1 CORRECTING DEFECT 2 (vertices=72, convex hull=101, v0=9072) After retessellation of defect 2 (v0=9072), euler #=-61 (109251,326441,217129) : difference with theory (-62) = -1 CORRECTING DEFECT 3 (vertices=5, convex hull=17, v0=9442) After retessellation of defect 3 (v0=9442), euler #=-60 (109251,326445,217134) : difference with theory (-61) = -1 CORRECTING DEFECT 4 (vertices=55, convex hull=87, v0=10124) After retessellation of defect 4 (v0=10124), euler #=-59 (109275,326554,217220) : difference with theory (-60) = -1 CORRECTING DEFECT 5 (vertices=32, convex hull=58, v0=11354) After retessellation of defect 5 (v0=11354), euler #=-58 (109291,326623,217274) : difference with theory (-59) = -1 CORRECTING DEFECT 6 (vertices=30, convex hull=77, v0=12282) After retessellation of defect 6 (v0=12282), euler #=-57 (109311,326715,217347) : difference with theory (-58) = -1 CORRECTING DEFECT 7 (vertices=53, convex hull=63, v0=14475) After retessellation of defect 7 (v0=14475), euler #=-56 (109336,326815,217423) : difference with theory (-57) = -1 CORRECTING DEFECT 8 (vertices=45, convex hull=73, v0=14714) After retessellation of defect 8 (v0=14714), euler #=-55 (109363,326927,217509) : difference with theory (-56) = -1 CORRECTING DEFECT 9 (vertices=69, convex hull=34, v0=18174) After retessellation of defect 9 (v0=18174), euler #=-54 (109369,326956,217533) : difference with theory (-55) = -1 CORRECTING DEFECT 10 (vertices=7, convex hull=17, v0=19410) After retessellation of defect 10 (v0=19410), euler #=-53 (109370,326963,217540) : difference with theory (-54) = -1 CORRECTING DEFECT 11 (vertices=49, convex hull=97, v0=22278) After retessellation of defect 11 (v0=22278), euler #=-52 (109400,327095,217643) : difference with theory (-53) = -1 CORRECTING DEFECT 12 (vertices=61, convex hull=91, v0=22400) After retessellation of defect 12 (v0=22400), euler #=-51 (109438,327251,217762) : difference with theory (-52) = -1 CORRECTING DEFECT 13 (vertices=197, convex hull=141, v0=22570) After retessellation of defect 13 (v0=22570), euler #=-50 (109465,327402,217887) : difference with theory (-51) = -1 CORRECTING DEFECT 14 (vertices=10, convex hull=19, v0=23049) After retessellation of defect 14 (v0=23049), euler #=-49 (109466,327411,217896) : difference with theory (-50) = -1 CORRECTING DEFECT 15 (vertices=22, convex hull=53, v0=25062) After retessellation of defect 15 (v0=25062), euler #=-48 (109477,327465,217940) : difference with theory (-49) = -1 CORRECTING DEFECT 16 (vertices=9, convex hull=14, v0=25287) After retessellation of defect 16 (v0=25287), euler #=-47 (109478,327471,217946) : difference with theory (-48) = -1 CORRECTING DEFECT 17 (vertices=8, convex hull=23, v0=28516) After retessellation of defect 17 (v0=28516), euler #=-46 (109479,327481,217956) : difference with theory (-47) = -1 CORRECTING DEFECT 18 (vertices=34, convex hull=80, v0=30297) After retessellation of defect 18 (v0=30297), euler #=-45 (109501,327579,218033) : difference with theory (-46) = -1 CORRECTING DEFECT 19 (vertices=25, convex hull=53, v0=30331) After retessellation of defect 19 (v0=30331), euler #=-44 (109517,327648,218087) : difference with theory (-45) = -1 CORRECTING DEFECT 20 (vertices=27, convex hull=27, v0=31342) After retessellation of defect 20 (v0=31342), euler #=-43 (109525,327680,218112) : difference with theory (-44) = -1 CORRECTING DEFECT 21 (vertices=27, convex hull=69, v0=32412) After retessellation of defect 21 (v0=32412), euler #=-42 (109537,327743,218164) : difference with theory (-43) = -1 CORRECTING DEFECT 22 (vertices=21, convex hull=54, v0=33280) After retessellation of defect 22 (v0=33280), euler #=-41 (109546,327788,218201) : difference with theory (-42) = -1 CORRECTING DEFECT 23 (vertices=45, convex hull=72, v0=35425) After retessellation of defect 23 (v0=35425), euler #=-40 (109570,327893,218283) : difference with theory (-41) = -1 CORRECTING DEFECT 24 (vertices=21, convex hull=51, v0=35596) After retessellation of defect 24 (v0=35596), euler #=-39 (109579,327939,218321) : difference with theory (-40) = -1 CORRECTING DEFECT 25 (vertices=17, convex hull=55, v0=39474) After retessellation of defect 25 (v0=39474), euler #=-38 (109590,327993,218365) : difference with theory (-39) = -1 CORRECTING DEFECT 26 (vertices=24, convex hull=34, v0=39784) After retessellation of defect 26 (v0=39784), euler #=-37 (109596,328022,218389) : difference with theory (-38) = -1 CORRECTING DEFECT 27 (vertices=19, convex hull=21, v0=42622) After retessellation of defect 27 (v0=42622), euler #=-36 (109601,328044,218407) : difference with theory (-37) = -1 CORRECTING DEFECT 28 (vertices=49, convex hull=77, v0=44475) After retessellation of defect 28 (v0=44475), euler #=-35 (109610,328102,218457) : difference with theory (-36) = -1 CORRECTING DEFECT 29 (vertices=179, convex hull=77, v0=45698) After retessellation of defect 29 (v0=45698), euler #=-34 (109619,328158,218505) : difference with theory (-35) = -1 CORRECTING DEFECT 30 (vertices=63, convex hull=134, v0=48731) After retessellation of defect 30 (v0=48731), euler #=-33 (109645,328291,218613) : difference with theory (-34) = -1 CORRECTING DEFECT 31 (vertices=6, convex hull=21, v0=51071) After retessellation of defect 31 (v0=51071), euler #=-32 (109647,328304,218625) : difference with theory (-33) = -1 CORRECTING DEFECT 32 (vertices=51, convex hull=68, v0=53332) After retessellation of defect 32 (v0=53332), euler #=-31 (109659,328361,218671) : difference with theory (-32) = -1 CORRECTING DEFECT 33 (vertices=62, convex hull=54, v0=56154) After retessellation of defect 33 (v0=56154), euler #=-30 (109680,328447,218737) : difference with theory (-31) = -1 CORRECTING DEFECT 34 (vertices=37, convex hull=21, v0=56291) After retessellation of defect 34 (v0=56291), euler #=-29 (109683,328463,218751) : difference with theory (-30) = -1 CORRECTING DEFECT 35 (vertices=10, convex hull=17, v0=62752) After retessellation of defect 35 (v0=62752), euler #=-28 (109684,328471,218759) : difference with theory (-29) = -1 CORRECTING DEFECT 36 (vertices=42, convex hull=83, v0=63612) After retessellation of defect 36 (v0=63612), euler #=-27 (109709,328579,218843) : difference with theory (-28) = -1 CORRECTING DEFECT 37 (vertices=29, convex hull=31, v0=64546) After retessellation of defect 37 (v0=64546), euler #=-26 (109712,328596,218858) : difference with theory (-27) = -1 CORRECTING DEFECT 38 (vertices=19, convex hull=16, v0=66016) After retessellation of defect 38 (v0=66016), euler #=-25 (109713,328602,218864) : difference with theory (-26) = -1 CORRECTING DEFECT 39 (vertices=18, convex hull=21, v0=66965) After retessellation of defect 39 (v0=66965), euler #=-24 (109714,328613,218875) : difference with theory (-25) = -1 CORRECTING DEFECT 40 (vertices=17, convex hull=19, v0=68741) After retessellation of defect 40 (v0=68741), euler #=-23 (109717,328625,218885) : difference with theory (-24) = -1 CORRECTING DEFECT 41 (vertices=33, convex hull=44, v0=72203) After retessellation of defect 41 (v0=72203), euler #=-22 (109730,328682,218930) : difference with theory (-23) = -1 CORRECTING DEFECT 42 (vertices=7, convex hull=15, v0=73472) After retessellation of defect 42 (v0=73472), euler #=-21 (109730,328686,218935) : difference with theory (-22) = -1 CORRECTING DEFECT 43 (vertices=111, convex hull=114, v0=75146) After retessellation of defect 43 (v0=75146), euler #=-21 (109739,328768,219008) : difference with theory (-21) = 0 CORRECTING DEFECT 44 (vertices=25, convex hull=24, v0=76609) After retessellation of defect 44 (v0=76609), euler #=-20 (109744,328790,219026) : difference with theory (-20) = 0 CORRECTING DEFECT 45 (vertices=21, convex hull=35, v0=79955) After retessellation of defect 45 (v0=79955), euler #=-19 (109747,328814,219048) : difference with theory (-19) = 0 CORRECTING DEFECT 46 (vertices=150, convex hull=91, v0=80087) After retessellation of defect 46 (v0=80087), euler #=-18 (109786,328975,219171) : difference with theory (-18) = 0 CORRECTING DEFECT 47 (vertices=57, convex hull=76, v0=80152) After retessellation of defect 47 (v0=80152), euler #=-17 (109813,329093,219263) : difference with theory (-17) = 0 CORRECTING DEFECT 48 (vertices=19, convex hull=27, v0=81397) After retessellation of defect 48 (v0=81397), euler #=-16 (109817,329117,219284) : difference with theory (-16) = 0 CORRECTING DEFECT 49 (vertices=27, convex hull=27, v0=83042) After retessellation of defect 49 (v0=83042), euler #=-15 (109824,329146,219307) : difference with theory (-15) = 0 CORRECTING DEFECT 50 (vertices=49, convex hull=23, v0=83687) After retessellation of defect 50 (v0=83687), euler #=-14 (109831,329176,219331) : difference with theory (-14) = 0 CORRECTING DEFECT 51 (vertices=50, convex hull=65, v0=84217) After retessellation of defect 51 (v0=84217), euler #=-13 (109846,329245,219386) : difference with theory (-13) = 0 CORRECTING DEFECT 52 (vertices=54, convex hull=84, v0=86411) After retessellation of defect 52 (v0=86411), euler #=-12 (109879,329378,219487) : difference with theory (-12) = 0 CORRECTING DEFECT 53 (vertices=14, convex hull=16, v0=86985) After retessellation of defect 53 (v0=86985), euler #=-11 (109882,329390,219497) : difference with theory (-11) = 0 CORRECTING DEFECT 54 (vertices=7, convex hull=21, v0=89195) After retessellation of defect 54 (v0=89195), euler #=-10 (109883,329398,219505) : difference with theory (-10) = 0 CORRECTING DEFECT 55 (vertices=22, convex hull=31, v0=89661) After retessellation of defect 55 (v0=89661), euler #=-9 (109887,329417,219521) : difference with theory (-9) = 0 CORRECTING DEFECT 56 (vertices=52, convex hull=43, v0=90368) After retessellation of defect 56 (v0=90368), euler #=-8 (109895,329458,219555) : difference with theory (-8) = 0 CORRECTING DEFECT 57 (vertices=19, convex hull=24, v0=90615) After retessellation of defect 57 (v0=90615), euler #=-7 (109896,329468,219565) : difference with theory (-7) = 0 CORRECTING DEFECT 58 (vertices=28, convex hull=26, v0=91907) After retessellation of defect 58 (v0=91907), euler #=-6 (109901,329490,219583) : difference with theory (-6) = 0 CORRECTING DEFECT 59 (vertices=5, convex hull=18, v0=92262) After retessellation of defect 59 (v0=92262), euler #=-5 (109902,329496,219589) : difference with theory (-5) = 0 CORRECTING DEFECT 60 (vertices=100, convex hull=126, v0=93614) After retessellation of defect 60 (v0=93614), euler #=-4 (109927,329626,219695) : difference with theory (-4) = 0 CORRECTING DEFECT 61 (vertices=104, convex hull=101, v0=93753) After retessellation of defect 61 (v0=93753), euler #=-3 (109967,329790,219820) : difference with theory (-3) = 0 CORRECTING DEFECT 62 (vertices=28, convex hull=65, v0=95399) After retessellation of defect 62 (v0=95399), euler #=-2 (109985,329867,219880) : difference with theory (-2) = 0 CORRECTING DEFECT 63 (vertices=155, convex hull=47, v0=100189) After retessellation of defect 63 (v0=100189), euler #=-1 (109994,329909,219914) : difference with theory (-1) = 0 CORRECTING DEFECT 64 (vertices=6, convex hull=27, v0=103916) After retessellation of defect 64 (v0=103916), euler #=0 (109996,329925,219929) : difference with theory (0) = 0 CORRECTING DEFECT 65 (vertices=135, convex hull=91, v0=108407) After retessellation of defect 65 (v0=108407), euler #=1 (110008,330004,219997) : difference with theory (1) = 0 CORRECTING DEFECT 66 (vertices=21, convex hull=44, v0=111145) After retessellation of defect 66 (v0=111145), euler #=2 (110018,330048,220032) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.03-->7.12) (max @ vno 105213 --> 107521) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.03-->7.12) (max @ vno 105213 --> 107521) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 253 mutations (36.3%), 444 crossovers (63.7%), 215 vertices were eliminated building final representation... 2078 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=110018, nf=220032, ne=330048, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 355 intersecting 001: 16 intersecting terminating search with 0 intersecting topology fixing took 3.7 minutes FSRUNTIME@ mris_fix_topology lh 0.0612 hours 4 threads #VMPC# mris_fix_topology VmPeak 949220 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB23-310_VYr0_Bay3prisma_AT rh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format writing corrected surface to 'orig.premesh' 7.3.2 7.3.2 before topology correction, eno=-64 (nv=116124, nf=232376, ne=348564, g=33) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... 4656 ambiguous faces found in tessellation segmenting defects... 53 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 17 into 13 -merging segment 23 into 19 51 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.7387 (-4.3693) -vertex loglikelihood: -6.2258 (-3.1129) -normal dot loglikelihood: -3.5771 (-3.5771) -quad curv loglikelihood: -6.1681 (-3.0840) Total Loglikelihood : -24.7097 CORRECTING DEFECT 0 (vertices=929, convex hull=316, v0=1075) After retessellation of defect 0 (v0=1075), euler #=-49 (113321,338918,225548) : difference with theory (-48) = 1 CORRECTING DEFECT 1 (vertices=64, convex hull=79, v0=7519) After retessellation of defect 1 (v0=7519), euler #=-48 (113345,339021,225628) : difference with theory (-47) = 1 CORRECTING DEFECT 2 (vertices=63, convex hull=103, v0=12765) After retessellation of defect 2 (v0=12765), euler #=-47 (113380,339166,225739) : difference with theory (-46) = 1 CORRECTING DEFECT 3 (vertices=12, convex hull=29, v0=15663) After retessellation of defect 3 (v0=15663), euler #=-46 (113384,339189,225759) : difference with theory (-45) = 1 CORRECTING DEFECT 4 (vertices=26, convex hull=27, v0=16294) After retessellation of defect 4 (v0=16294), euler #=-45 (113388,339209,225776) : difference with theory (-44) = 1 CORRECTING DEFECT 5 (vertices=24, convex hull=23, v0=18758) After retessellation of defect 5 (v0=18758), euler #=-44 (113390,339222,225788) : difference with theory (-43) = 1 CORRECTING DEFECT 6 (vertices=25, convex hull=45, v0=26282) After retessellation of defect 6 (v0=26282), euler #=-43 (113401,339274,225830) : difference with theory (-42) = 1 CORRECTING DEFECT 7 (vertices=25, convex hull=69, v0=32656) After retessellation of defect 7 (v0=32656), euler #=-42 (113417,339349,225890) : difference with theory (-41) = 1 CORRECTING DEFECT 8 (vertices=5, convex hull=18, v0=33503) After retessellation of defect 8 (v0=33503), euler #=-41 (113417,339352,225894) : difference with theory (-40) = 1 CORRECTING DEFECT 9 (vertices=38, convex hull=25, v0=33528) After retessellation of defect 9 (v0=33528), euler #=-40 (113424,339383,225919) : difference with theory (-39) = 1 CORRECTING DEFECT 10 (vertices=95, convex hull=30, v0=38540) After retessellation of defect 10 (v0=38540), euler #=-39 (113433,339420,225948) : difference with theory (-38) = 1 CORRECTING DEFECT 11 (vertices=187, convex hull=57, v0=43823) After retessellation of defect 11 (v0=43823), euler #=-38 (113444,339472,225990) : difference with theory (-37) = 1 CORRECTING DEFECT 12 (vertices=71, convex hull=96, v0=46060) After retessellation of defect 12 (v0=46060), euler #=-37 (113471,339593,226085) : difference with theory (-36) = 1 CORRECTING DEFECT 13 (vertices=18, convex hull=52, v0=48977) After retessellation of defect 13 (v0=48977), euler #=-35 (113475,339621,226111) : difference with theory (-35) = 0 CORRECTING DEFECT 14 (vertices=27, convex hull=20, v0=50155) After retessellation of defect 14 (v0=50155), euler #=-34 (113479,339638,226125) : difference with theory (-34) = 0 CORRECTING DEFECT 15 (vertices=8, convex hull=30, v0=51287) After retessellation of defect 15 (v0=51287), euler #=-33 (113480,339652,226139) : difference with theory (-33) = 0 CORRECTING DEFECT 16 (vertices=7, convex hull=13, v0=52484) After retessellation of defect 16 (v0=52484), euler #=-32 (113484,339666,226150) : difference with theory (-32) = 0 CORRECTING DEFECT 17 (vertices=5, convex hull=23, v0=53381) After retessellation of defect 17 (v0=53381), euler #=-31 (113486,339678,226161) : difference with theory (-31) = 0 CORRECTING DEFECT 18 (vertices=50, convex hull=89, v0=53679) After retessellation of defect 18 (v0=53679), euler #=-29 (113507,339786,226250) : difference with theory (-30) = -1 CORRECTING DEFECT 19 (vertices=61, convex hull=47, v0=53723) After retessellation of defect 19 (v0=53723), euler #=-28 (113519,339838,226291) : difference with theory (-29) = -1 CORRECTING DEFECT 20 (vertices=29, convex hull=71, v0=54081) After retessellation of defect 20 (v0=54081), euler #=-27 (113539,339927,226361) : difference with theory (-28) = -1 CORRECTING DEFECT 21 (vertices=26, convex hull=65, v0=56288) After retessellation of defect 21 (v0=56288), euler #=-26 (113554,339997,226417) : difference with theory (-27) = -1 CORRECTING DEFECT 22 (vertices=46, convex hull=36, v0=57588) After retessellation of defect 22 (v0=57588), euler #=-25 (113562,340032,226445) : difference with theory (-26) = -1 CORRECTING DEFECT 23 (vertices=37, convex hull=57, v0=61410) After retessellation of defect 23 (v0=61410), euler #=-24 (113571,340083,226488) : difference with theory (-25) = -1 CORRECTING DEFECT 24 (vertices=14, convex hull=24, v0=69785) After retessellation of defect 24 (v0=69785), euler #=-23 (113574,340102,226505) : difference with theory (-24) = -1 CORRECTING DEFECT 25 (vertices=69, convex hull=135, v0=76274) After retessellation of defect 25 (v0=76274), euler #=-22 (113599,340232,226611) : difference with theory (-23) = -1 CORRECTING DEFECT 26 (vertices=43, convex hull=37, v0=76360) After retessellation of defect 26 (v0=76360), euler #=-21 (113611,340281,226649) : difference with theory (-22) = -1 CORRECTING DEFECT 27 (vertices=21, convex hull=62, v0=77216) After retessellation of defect 27 (v0=77216), euler #=-20 (113621,340335,226694) : difference with theory (-21) = -1 CORRECTING DEFECT 28 (vertices=17, convex hull=23, v0=79927) After retessellation of defect 28 (v0=79927), euler #=-19 (113626,340355,226710) : difference with theory (-20) = -1 CORRECTING DEFECT 29 (vertices=11, convex hull=12, v0=80441) After retessellation of defect 29 (v0=80441), euler #=-18 (113626,340357,226713) : difference with theory (-19) = -1 CORRECTING DEFECT 30 (vertices=28, convex hull=38, v0=84821) After retessellation of defect 30 (v0=84821), euler #=-17 (113635,340400,226748) : difference with theory (-18) = -1 CORRECTING DEFECT 31 (vertices=49, convex hull=85, v0=91215) After retessellation of defect 31 (v0=91215), euler #=-16 (113661,340514,226837) : difference with theory (-17) = -1 CORRECTING DEFECT 32 (vertices=63, convex hull=46, v0=91708) After retessellation of defect 32 (v0=91708), euler #=-15 (113672,340564,226877) : difference with theory (-16) = -1 CORRECTING DEFECT 33 (vertices=19, convex hull=33, v0=92875) After retessellation of defect 33 (v0=92875), euler #=-14 (113675,340583,226894) : difference with theory (-15) = -1 CORRECTING DEFECT 34 (vertices=34, convex hull=58, v0=93637) After retessellation of defect 34 (v0=93637), euler #=-13 (113684,340632,226935) : difference with theory (-14) = -1 CORRECTING DEFECT 35 (vertices=68, convex hull=117, v0=94040) After retessellation of defect 35 (v0=94040), euler #=-12 (113719,340785,227054) : difference with theory (-13) = -1 CORRECTING DEFECT 36 (vertices=10, convex hull=25, v0=94110) After retessellation of defect 36 (v0=94110), euler #=-11 (113721,340802,227070) : difference with theory (-12) = -1 CORRECTING DEFECT 37 (vertices=61, convex hull=127, v0=98755) After retessellation of defect 37 (v0=98755), euler #=-10 (113733,340893,227150) : difference with theory (-11) = -1 CORRECTING DEFECT 38 (vertices=56, convex hull=85, v0=98796) After retessellation of defect 38 (v0=98796), euler #=-9 (113752,340985,227224) : difference with theory (-10) = -1 CORRECTING DEFECT 39 (vertices=64, convex hull=71, v0=99460) After retessellation of defect 39 (v0=99460), euler #=-8 (113764,341049,227277) : difference with theory (-9) = -1 CORRECTING DEFECT 40 (vertices=31, convex hull=49, v0=100153) After retessellation of defect 40 (v0=100153), euler #=-7 (113775,341101,227319) : difference with theory (-8) = -1 CORRECTING DEFECT 41 (vertices=59, convex hull=109, v0=100237) After retessellation of defect 41 (v0=100237), euler #=-6 (113798,341216,227412) : difference with theory (-7) = -1 CORRECTING DEFECT 42 (vertices=50, convex hull=31, v0=101487) After retessellation of defect 42 (v0=101487), euler #=-5 (113804,341248,227439) : difference with theory (-6) = -1 CORRECTING DEFECT 43 (vertices=30, convex hull=75, v0=102040) After retessellation of defect 43 (v0=102040), euler #=-4 (113821,341330,227505) : difference with theory (-5) = -1 CORRECTING DEFECT 44 (vertices=21, convex hull=33, v0=104215) After retessellation of defect 44 (v0=104215), euler #=-3 (113826,341359,227530) : difference with theory (-4) = -1 CORRECTING DEFECT 45 (vertices=59, convex hull=59, v0=108102) After retessellation of defect 45 (v0=108102), euler #=-3 (113845,341443,227595) : difference with theory (-3) = 0 CORRECTING DEFECT 46 (vertices=29, convex hull=65, v0=110223) After retessellation of defect 46 (v0=110223), euler #=-2 (113864,341526,227660) : difference with theory (-2) = 0 CORRECTING DEFECT 47 (vertices=27, convex hull=30, v0=113538) After retessellation of defect 47 (v0=113538), euler #=-1 (113867,341543,227675) : difference with theory (-1) = 0 CORRECTING DEFECT 48 (vertices=20, convex hull=47, v0=114047) After retessellation of defect 48 (v0=114047), euler #=0 (113876,341587,227711) : difference with theory (0) = 0 CORRECTING DEFECT 49 (vertices=23, convex hull=49, v0=114709) After retessellation of defect 49 (v0=114709), euler #=1 (113888,341643,227756) : difference with theory (1) = 0 CORRECTING DEFECT 50 (vertices=28, convex hull=38, v0=115049) After retessellation of defect 50 (v0=115049), euler #=2 (113893,341673,227782) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.11-->9.18) (max @ vno 11425 --> 18595) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.11-->9.18) (max @ vno 11425 --> 18595) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 184 mutations (35.2%), 339 crossovers (64.8%), 239 vertices were eliminated building final representation... 2231 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=113893, nf=227782, ne=341673, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 284 intersecting 001: 26 intersecting terminating search with 0 intersecting topology fixing took 12.5 minutes FSRUNTIME@ mris_fix_topology rh 0.2078 hours 4 threads #VMPC# mris_fix_topology VmPeak 953500 PIDs (2936612 2936616) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 110018 - 330048 + 220032 = 2 --> 0 holes F =2V-4: 220032 = 220036-4 (0) 2E=3F: 660096 = 660096 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 113893 - 341673 + 227782 = 2 --> 0 holes F =2V-4: 227782 = 227786-4 (0) 2E=3F: 683346 = 683346 (0) total defect index = 0 Mon Jan 6 14:22:15 CST 2025 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/defect2seg --s PIB23-310_VYr0_Bay3prisma_AT --cortex freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 defect2seg 7.3.2 Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 2947107 mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 26 non-cortical segments detected only using segment with 9174 vertices erasing segment 0 (vno[0] = 14409) erasing segment 1 (vno[0] = 16811) erasing segment 2 (vno[0] = 17711) erasing segment 3 (vno[0] = 18494) erasing segment 4 (vno[0] = 19391) erasing segment 5 (vno[0] = 21110) erasing segment 6 (vno[0] = 21198) erasing segment 7 (vno[0] = 21232) erasing segment 9 (vno[0] = 41303) erasing segment 10 (vno[0] = 51992) erasing segment 11 (vno[0] = 62734) erasing segment 12 (vno[0] = 66718) erasing segment 13 (vno[0] = 76631) erasing segment 14 (vno[0] = 78885) erasing segment 15 (vno[0] = 81540) erasing segment 16 (vno[0] = 82380) erasing segment 17 (vno[0] = 83403) erasing segment 18 (vno[0] = 84079) erasing segment 19 (vno[0] = 85676) erasing segment 20 (vno[0] = 85688) erasing segment 21 (vno[0] = 85990) erasing segment 22 (vno[0] = 86510) erasing segment 23 (vno[0] = 86520) erasing segment 24 (vno[0] = 88163) erasing segment 25 (vno[0] = 90319) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri/orig.mgz 1000 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/lh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 527388 mris_defects_pointset done mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 24 non-cortical segments detected only using segment with 8970 vertices erasing segment 0 (vno[0] = 6537) erasing segment 1 (vno[0] = 7879) erasing segment 2 (vno[0] = 8530) erasing segment 3 (vno[0] = 13830) erasing segment 4 (vno[0] = 13901) erasing segment 5 (vno[0] = 15663) erasing segment 6 (vno[0] = 22328) erasing segment 7 (vno[0] = 24370) erasing segment 8 (vno[0] = 27043) erasing segment 9 (vno[0] = 29534) erasing segment 10 (vno[0] = 29544) erasing segment 12 (vno[0] = 50815) erasing segment 13 (vno[0] = 70005) erasing segment 14 (vno[0] = 83918) erasing segment 15 (vno[0] = 83937) erasing segment 16 (vno[0] = 84721) erasing segment 17 (vno[0] = 85643) erasing segment 18 (vno[0] = 88872) erasing segment 19 (vno[0] = 90721) erasing segment 20 (vno[0] = 92058) erasing segment 21 (vno[0] = 99375) erasing segment 22 (vno[0] = 100061) erasing segment 23 (vno[0] = 102596) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri/surface.defects.mgz 2000 1 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/rh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 530620 mris_defects_pointset done Started at Mon Jan 6 14:22:15 CST 2025 Ended at Mon Jan 6 14:23:06 CST 2025 Defect2seg-Run-Time-Sec 51 Defect2seg-Run-Time-Min 1.02 Defect2seg-Run-Time-Hours 0.01 tkmeditfv PIB23-310_VYr0_Bay3prisma_AT brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2025:01:06:14:22:15 defect2seg N 3 e 51.04 S 1.25 U 50.16 P 100% M 374468 F 11 R 640813 W 0 c 4897 w 1165 I 11904 O 18664 L 55.83 52.08 48.23 @#@FSLOADPOST 2025:01:06:14:23:06 defect2seg N 3 45.46 50.02 47.76 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.710301 remeshing to edge length 0.710301 with 3 iterations avg qual before : 0.889824 after: 0.970646 Removing intersections removing intersecting faces 000: 2 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 110018 nv = 114566 1.04134 Area 229128 0.30193 0.03403 0.035230 0.4801 Corner 687384 60.00000 8.88789 13.881353 151.6772 Edge 343692 0.84314 0.08316 0.141007 1.2686 Hinge 343692 9.83137 10.74836 0.000000 155.0411 mris_remesh done @#@FSTIME 2025:01:06:14:23:06 mris_remesh N 7 e 32.71 S 1.12 U 30.24 P 95% M 690480 F 2 R 1005703 W 0 c 2843 w 887 I 0 O 8064 L 45.46 50.02 47.76 @#@FSLOADPOST 2025:01:06:14:23:39 mris_remesh N 7 44.93 49.52 47.67 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.710689 remeshing to edge length 0.710689 with 3 iterations avg qual before : 0.89093 after: 0.970896 Removing intersections Remeshed surface quality stats nv0 = 113893 nv = 118830 1.04335 Area 237656 0.30211 0.03378 0.082054 0.4549 Corner 712968 60.00000 8.84231 17.382693 143.2815 Edge 356484 0.84333 0.08276 0.477122 1.2434 Hinge 356484 9.67659 10.63101 0.000000 131.1914 mris_remesh done @#@FSTIME 2025:01:06:14:23:39 mris_remesh N 7 e 30.15 S 0.92 U 30.22 P 103% M 669140 F 2 R 794360 W 0 c 2856 w 594 I 0 O 8360 L 44.93 49.52 47.67 @#@FSLOADPOST 2025:01:06:14:24:09 mris_remesh N 7 48.83 50.03 47.90 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2025:01:06:14:24:09 mris_remove_intersection N 2 e 3.11 S 0.44 U 2.84 P 105% M 300116 F 3 R 164812 W 0 c 305 w 241 I 0 O 8064 L 48.83 50.03 47.90 @#@FSLOADPOST 2025:01:06:14:24:12 mris_remove_intersection N 2 49.57 50.16 47.96 rm -f ../surf/lh.inflated /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2025:01:06:14:24:12 mris_remove_intersection N 2 e 3.29 S 0.27 U 3.17 P 104% M 307536 F 2 R 197361 W 0 c 375 w 261 I 8232 O 8360 L 49.57 50.16 47.96 @#@FSLOADPOST 2025:01:06:14:24:16 mris_remove_intersection N 2 46.96 49.61 47.79 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Mon Jan 6 14:24:16 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 226679 voxels (1.35%) border gray 232711 voxels (1.39%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 100.2 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 80.8 +- 11.9 [30.0 --> 110.0] white_mean = 100.248 +/- 6.77433, gray_mean = 80.8221 +/- 11.8559 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=213 nbins=214 intensity peaks found at WM=102+-6.1, GM=80+-7.0 white_mode = 102, gray_mode = 80 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 68.1 (was 70.000000) setting MAX_BORDER_WHITE to 108.8 (was 105.000000) setting MIN_BORDER_WHITE to 80.0 (was 85.000000) setting MAX_CSF to 56.3 (was 40.000000) setting MAX_GRAY to 95.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40.000000) When placing the white surface white_border_hi = 108.774; white_border_low = 80; white_outside_low = 68.1441; white_inside_hi = 120; white_outside_hi = 108.774; When placing the pial surface pial_border_hi = 68.1441; pial_border_low = 44.4324; pial_outside_low = 10; pial_inside_hi = 95.2257; pial_outside_hi = 62.2162; #VMPC# mris_autodet_gwstats VmPeak 433648 mris_autodet_gwstats done @#@FSTIME 2025:01:06:14:24:16 mris_autodet_gwstats N 8 e 5.61 S 0.17 U 6.10 P 111% M 207084 F 0 R 109004 W 0 c 693 w 132 I 0 O 8 L 46.96 49.61 47.79 @#@FSLOADPOST 2025:01:06:14:24:22 mris_autodet_gwstats N 8 43.52 48.85 47.55 #-------------------------------------------- #@# AutoDetGWStats rh Mon Jan 6 14:24:22 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 226679 voxels (1.35%) border gray 232711 voxels (1.39%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (100.0): 100.2 +- 6.8 [70.0 --> 110.0] CCS GM (83.0) : 80.8 +- 11.9 [30.0 --> 110.0] white_mean = 100.248 +/- 6.77433, gray_mean = 80.8221 +/- 11.8559 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=213 nbins=214 intensity peaks found at WM=103+-5.2, GM=81+-7.0 white_mode = 103, gray_mode = 81 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 69.1 (was 70.000000) setting MAX_BORDER_WHITE to 109.8 (was 105.000000) setting MIN_BORDER_WHITE to 81.0 (was 85.000000) setting MAX_CSF to 57.3 (was 40.000000) setting MAX_GRAY to 96.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 69.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 45.4 (was 40.000000) When placing the white surface white_border_hi = 109.774; white_border_low = 81; white_outside_low = 69.1441; white_inside_hi = 120; white_outside_hi = 109.774; When placing the pial surface pial_border_hi = 69.1441; pial_border_low = 45.4324; pial_outside_low = 10; pial_inside_hi = 96.2257; pial_outside_hi = 63.2162; #VMPC# mris_autodet_gwstats VmPeak 567980 mris_autodet_gwstats done @#@FSTIME 2025:01:06:14:24:22 mris_autodet_gwstats N 8 e 5.88 S 0.11 U 6.64 P 114% M 211892 F 2 R 105052 W 0 c 863 w 111 I 0 O 8 L 43.52 48.85 47.55 @#@FSLOADPOST 2025:01:06:14:24:28 mris_autodet_gwstats N 8 46.28 49.34 47.72 #-------------------------------------------- #@# WhitePreAparc lh Mon Jan 6 14:24:28 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface before ripping with 5 iterations Area 229128 0.26718 0.06565 0.000423 0.5640 Corner 687384 60.00000 9.66063 3.257094 166.6307 Edge 343692 0.78878 0.11895 0.024812 1.3030 Hinge 343692 6.28576 6.79311 0.000000 150.3783 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 MRIfindBrightNonWM(): 371 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8259, nmarked2=4, nripped=8259 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57283: xyz = (-51.8696,2.31681,24.5631) oxyz = (-51.8696,2.31681,24.5631) wxzy = (-51.8696,2.31681,24.5631) pxyz = (0,0,0) CBVO Creating mask 114566 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8259 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8259, nmarked2=4, nripped=8259 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=2 had to be increased for 255 vertices, nripped=8259 mean border=86.7, 547 (547) missing vertices, mean dist 0.3 [1.1 (%31.2)->1.0 (%68.8))] %28 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0557 min Finding expansion regions mean absolute distance = 1.01 +- 1.19 4045 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1795488.0, rms=8.890 001: dt: 0.5000, sse=1000553.7, rms=6.450 (27.443%) 002: dt: 0.5000, sse=611141.4, rms=4.810 (25.435%) 003: dt: 0.5000, sse=427986.6, rms=3.769 (21.634%) 004: dt: 0.5000, sse=343760.4, rms=3.145 (16.563%) 005: dt: 0.5000, sse=300448.6, rms=2.755 (12.393%) 006: dt: 0.5000, sse=277312.7, rms=2.512 (8.831%) 007: dt: 0.5000, sse=263305.3, rms=2.350 (6.421%) 008: dt: 0.5000, sse=258458.0, rms=2.262 (3.754%) 009: dt: 0.5000, sse=248930.4, rms=2.208 (2.404%) rms = 2.1731/2.2078, sse=264409.5/248930.4, time step reduction 1 of 3 to 0.250 0 1 1 010: dt: 0.5000, sse=264409.5, rms=2.173 (1.574%) 011: dt: 0.2500, sse=206656.2, rms=1.627 (25.137%) 012: dt: 0.2500, sse=200173.5, rms=1.544 (5.087%) rms = 1.5280/1.5441, sse=192243.4/200173.5, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=192243.5, rms=1.528 (1.042%) rms = 1.5058/1.5280, sse=190632.0/192243.4, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=190632.0, rms=1.506 (1.452%) maximum number of reductions reached, breaking from loop positioning took 1.2 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8259 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8549, nmarked2=35, nripped=8549 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=1 had to be increased for 285 vertices, nripped=8549 mean border=88.9, 405 (171) missing vertices, mean dist -0.3 [0.7 (%63.3)->0.3 (%36.7))] %47 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0358 min Finding expansion regions mean absolute distance = 0.54 +- 0.88 4557 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=474915.3, rms=3.703 015: dt: 0.5000, sse=327404.5, rms=2.428 (34.437%) 016: dt: 0.5000, sse=286134.6, rms=2.007 (17.342%) 017: dt: 0.5000, sse=269183.8, rms=1.850 (7.814%) rms = 1.8214/1.8499, sse=260119.0/269183.8, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=260119.0, rms=1.821 (1.543%) 019: dt: 0.2500, sse=221458.5, rms=1.338 (26.518%) rms = 1.2509/1.3384, sse=231900.4/221458.5, time step reduction 2 of 3 to 0.125 0 1 0 020: dt: 0.2500, sse=231900.4, rms=1.251 (6.536%) rms = 1.2269/1.2509, sse=210645.9/231900.4, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=210645.9, rms=1.227 (1.918%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8549 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8619, nmarked2=35, nripped=8619 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 375 vertices, nripped=8619 mean border=91.3, 359 (113) missing vertices, mean dist -0.2 [0.4 (%72.2)->0.3 (%27.8))] %71 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0194 min Finding expansion regions mean absolute distance = 0.40 +- 0.52 3558 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=419218.3, rms=3.387 022: dt: 0.5000, sse=282548.4, rms=1.911 (43.586%) 023: dt: 0.5000, sse=250073.6, rms=1.678 (12.167%) rms = 1.6974/1.6781, sse=255028.1/250073.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=226924.4, rms=1.342 (20.020%) 025: dt: 0.2500, sse=224130.5, rms=1.162 (13.403%) rms = 1.1259/1.1622, sse=215072.5/224130.5, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=215072.5, rms=1.126 (3.130%) rms = 1.0987/1.1259, sse=214231.0/215072.5, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=214231.0, rms=1.099 (2.409%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8619 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8668, nmarked2=35, nripped=8668 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.7743300; border_low = 80.0000000; outside_low = 68.1441420; outside_hi = 108.7743300; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114566 Gdiag_no=-1 vno start=0, stop=114566 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 424 vertices, nripped=8668 mean border=92.3, 383 (100) missing vertices, mean dist -0.1 [0.3 (%59.7)->0.2 (%40.3))] %79 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0127 min Finding expansion regions mean absolute distance = 0.29 +- 0.39 2881 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=240736.3, rms=1.612 028: dt: 0.5000, sse=222784.2, rms=1.168 (27.567%) rms = 1.3658/1.1680, sse=230535.8/222784.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=208116.1, rms=0.943 (19.240%) rms = 0.9088/0.9432, sse=214325.8/208116.1, time step reduction 2 of 3 to 0.125 0 1 1 030: dt: 0.2500, sse=214325.8, rms=0.909 (3.648%) rms = 0.8693/0.9088, sse=208487.3/214325.8, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=208487.3, rms=0.869 (4.351%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 2.82 minutes #VMPC# mris_place_surfaces VmPeak 2067832 mris_place_surface done @#@FSTIME 2025:01:06:14:24:28 mris_place_surface N 18 e 177.64 S 3.91 U 293.11 P 167% M 1631188 F 2 R 4189512 W 0 c 27502 w 2459 I 0 O 8064 L 46.28 49.34 47.72 @#@FSLOADPOST 2025:01:06:14:27:26 mris_place_surface N 18 39.94 47.73 47.56 #-------------------------------------------- #@# WhitePreAparc rh Mon Jan 6 14:27:26 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.3.2 7.3.2 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface before ripping with 5 iterations Area 237656 0.26765 0.06509 0.001410 0.6267 Corner 712968 60.00000 9.58742 4.374291 142.9564 Edge 356484 0.78956 0.11786 0.022869 1.3505 Hinge 356484 6.23645 6.68355 0.000000 151.7714 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=24935, wmmin=5, clip=110 MRIfindBrightNonWM(): 371 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 #FML# MRISripMidline(): nmarked=8397, nmarked2=0, nripped=8397 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 59415: xyz = (35.4352,5.89772,-20.2586) oxyz = (35.4352,5.89772,-20.2586) wxzy = (35.4352,5.89772,-20.2586) pxyz = (0,0,0) CBVO Creating mask 118830 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8397 #FML# MRISripMidline(): nmarked=8397, nmarked2=0, nripped=8397 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=2 had to be increased for 156 vertices, nripped=8397 mean border=87.4, 484 (484) missing vertices, mean dist 0.3 [1.2 (%30.9)->0.9 (%69.1))] %31 local maxima, %61 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0433 min Finding expansion regions mean absolute distance = 1.01 +- 1.22 4628 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=chopi, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1731132.8, rms=8.538 001: dt: 0.5000, sse=951002.6, rms=6.131 (28.195%) 002: dt: 0.5000, sse=580196.2, rms=4.552 (25.750%) 003: dt: 0.5000, sse=406284.4, rms=3.568 (21.618%) 004: dt: 0.5000, sse=322642.8, rms=2.945 (17.470%) 005: dt: 0.5000, sse=284932.4, rms=2.548 (13.453%) 006: dt: 0.5000, sse=268194.2, rms=2.304 (9.575%) 007: dt: 0.5000, sse=255826.1, rms=2.154 (6.520%) 008: dt: 0.5000, sse=240275.0, rms=2.066 (4.112%) rms = 2.0192/2.0656, sse=241250.8/240275.0, time step reduction 1 of 3 to 0.250 0 1 1 009: dt: 0.5000, sse=241250.8, rms=2.019 (2.248%) 010: dt: 0.2500, sse=202050.2, rms=1.474 (26.987%) 011: dt: 0.2500, sse=193191.7, rms=1.391 (5.664%) rms = 1.3723/1.3908, sse=188861.8/193191.7, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=188861.8, rms=1.372 (1.329%) rms = 1.3527/1.3723, sse=203563.5/188861.8, time step reduction 3 of 3 to 0.062 0 1 1 013: dt: 0.1250, sse=203563.5, rms=1.353 (1.431%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8397 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8670, nmarked2=0, nripped=8670 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=1 had to be increased for 271 vertices, nripped=8670 mean border=89.5, 316 (139) missing vertices, mean dist -0.3 [0.6 (%63.8)->0.3 (%36.2))] %50 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0497 min Finding expansion regions mean absolute distance = 0.51 +- 0.83 4135 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=chopi, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=492160.2, rms=3.609 014: dt: 0.5000, sse=324368.1, rms=2.354 (34.781%) 015: dt: 0.5000, sse=278934.4, rms=1.918 (18.538%) 016: dt: 0.5000, sse=257184.4, rms=1.752 (8.617%) rms = 1.7180/1.7524, sse=262366.4/257184.4, time step reduction 1 of 3 to 0.250 0 1 1 017: dt: 0.5000, sse=262366.3, rms=1.718 (1.960%) 018: dt: 0.2500, sse=233703.5, rms=1.270 (26.093%) 019: dt: 0.2500, sse=231343.7, rms=1.191 (6.171%) rms = 1.1750/1.1914, sse=228074.3/231343.7, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=228074.3, rms=1.175 (1.374%) rms = 1.1573/1.1750, sse=249329.8/228074.3, time step reduction 3 of 3 to 0.062 0 1 1 021: dt: 0.1250, sse=249329.8, rms=1.157 (1.510%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8670 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8690, nmarked2=0, nripped=8690 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 336 vertices, nripped=8690 mean border=92.0, 296 (90) missing vertices, mean dist -0.3 [0.4 (%73.1)->0.3 (%26.9))] %73 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0175 min Finding expansion regions mean absolute distance = 0.39 +- 0.50 3198 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=chopi, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=469964.8, rms=3.395 022: dt: 0.5000, sse=296049.8, rms=1.920 (43.446%) 023: dt: 0.5000, sse=267758.6, rms=1.584 (17.491%) rms = 1.5878/1.5840, sse=285930.0/267758.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=245575.6, rms=1.277 (19.380%) 025: dt: 0.2500, sse=245035.2, rms=1.109 (13.151%) rms = 1.0742/1.1091, sse=254664.4/245035.2, time step reduction 2 of 3 to 0.125 0 1 1 026: dt: 0.2500, sse=254664.4, rms=1.074 (3.143%) rms = 1.0542/1.0742, sse=233948.0/254664.4, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=233948.0, rms=1.054 (1.860%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=8690 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8733, nmarked2=0, nripped=8733 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.7743300; border_low = 81.0000000; outside_low = 69.1441420; outside_hi = 109.7743300; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=118830 Gdiag_no=-1 vno start=0, stop=118830 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 390 vertices, nripped=8733 mean border=93.0, 336 (72) missing vertices, mean dist -0.1 [0.3 (%60.2)->0.2 (%39.8))] %80 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0275 min Finding expansion regions mean absolute distance = 0.28 +- 0.39 2684 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=chopi, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=262130.6, rms=1.597 028: dt: 0.5000, sse=245113.5, rms=1.087 (31.945%) rms = 1.2719/1.0869, sse=249596.4/245113.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=242589.9, rms=0.903 (16.940%) rms = 0.8654/0.9028, sse=229043.1/242589.9, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=229043.1, rms=0.865 (4.149%) rms = 0.8385/0.8654, sse=251422.0/229043.1, time step reduction 3 of 3 to 0.062 0 1 1 031: dt: 0.1250, sse=251422.0, rms=0.839 (3.102%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.87 minutes #VMPC# mris_place_surfaces VmPeak 2120712 mris_place_surface done @#@FSTIME 2025:01:06:14:27:26 mris_place_surface N 18 e 181.64 S 4.56 U 302.02 P 168% M 1685184 F 2 R 4758220 W 0 c 28320 w 2232 I 8232 O 8360 L 39.94 47.73 47.56 @#@FSLOADPOST 2025:01:06:14:30:27 mris_place_surface N 18 52.94 48.19 47.63 #-------------------------------------------- #@# CortexLabel lh Mon Jan 6 14:30:27 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 12 non-cortical segments detected only using segment with 10176 vertices erasing segment 0 (vno[0] = 17536) erasing segment 1 (vno[0] = 29399) erasing segment 3 (vno[0] = 42690) erasing segment 4 (vno[0] = 53433) erasing segment 5 (vno[0] = 64827) erasing segment 6 (vno[0] = 68816) erasing segment 7 (vno[0] = 70189) erasing segment 8 (vno[0] = 79404) erasing segment 9 (vno[0] = 97173) erasing segment 10 (vno[0] = 104586) erasing segment 11 (vno[0] = 105768) @#@FSTIME 2025:01:06:14:30:27 mri_label2label N 5 e 20.02 S 0.24 U 19.82 P 100% M 319772 F 1 R 172463 W 0 c 1818 w 307 I 0 O 9056 L 52.94 48.19 47.63 @#@FSLOADPOST 2025:01:06:14:30:48 mri_label2label N 5 53.54 48.64 47.80 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Mon Jan 6 14:30:48 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 15 non-cortical segments detected only using segment with 8747 vertices erasing segment 0 (vno[0] = 17536) erasing segment 1 (vno[0] = 29399) erasing segment 3 (vno[0] = 36204) erasing segment 4 (vno[0] = 38502) erasing segment 5 (vno[0] = 39231) erasing segment 6 (vno[0] = 39290) erasing segment 7 (vno[0] = 63748) erasing segment 8 (vno[0] = 64827) erasing segment 9 (vno[0] = 68816) erasing segment 10 (vno[0] = 70189) erasing segment 11 (vno[0] = 79404) erasing segment 12 (vno[0] = 97173) erasing segment 13 (vno[0] = 104586) erasing segment 14 (vno[0] = 105768) @#@FSTIME 2025:01:06:14:30:48 mri_label2label N 5 e 19.09 S 0.37 U 19.54 P 104% M 332008 F 1 R 161675 W 0 c 1771 w 142 I 0 O 9184 L 53.54 48.64 47.80 @#@FSLOADPOST 2025:01:06:14:31:07 mri_label2label N 5 52.46 48.83 47.88 #-------------------------------------------- #@# CortexLabel rh Mon Jan 6 14:31:07 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 11 non-cortical segments detected only using segment with 10075 vertices erasing segment 0 (vno[0] = 12843) erasing segment 2 (vno[0] = 30479) erasing segment 3 (vno[0] = 37298) erasing segment 4 (vno[0] = 54969) erasing segment 5 (vno[0] = 74071) erasing segment 6 (vno[0] = 74123) erasing segment 7 (vno[0] = 74153) erasing segment 8 (vno[0] = 76880) erasing segment 9 (vno[0] = 78133) erasing segment 10 (vno[0] = 106322) @#@FSTIME 2025:01:06:14:31:07 mri_label2label N 5 e 23.01 S 0.24 U 23.00 P 101% M 322280 F 2 R 155217 W 0 c 2153 w 182 I 8232 O 9240 L 52.46 48.83 47.88 @#@FSLOADPOST 2025:01:06:14:31:30 mri_label2label N 5 50.15 48.67 47.85 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Mon Jan 6 14:31:30 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 10 non-cortical segments detected only using segment with 8509 vertices erasing segment 0 (vno[0] = 12843) erasing segment 2 (vno[0] = 30479) erasing segment 3 (vno[0] = 37298) erasing segment 4 (vno[0] = 74071) erasing segment 5 (vno[0] = 74123) erasing segment 6 (vno[0] = 74153) erasing segment 7 (vno[0] = 76880) erasing segment 8 (vno[0] = 78133) erasing segment 9 (vno[0] = 106322) @#@FSTIME 2025:01:06:14:31:30 mri_label2label N 5 e 21.88 S 0.25 U 22.52 P 104% M 318112 F 2 R 153494 W 0 c 2064 w 247 I 0 O 9352 L 50.15 48.67 47.85 @#@FSLOADPOST 2025:01:06:14:31:52 mri_label2label N 5 47.45 48.26 47.75 #-------------------------------------------- #@# Smooth2 lh Mon Jan 6 14:31:52 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Mon Jan 6 14:31:52 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 2953777 of (2953777 2953782) to complete... Waiting for PID 2953782 of (2953777 2953782) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (2953777 2953782) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Mon Jan 6 14:31:56 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Mon Jan 6 14:31:56 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 2953894 of (2953894 2953897) to complete... Waiting for PID 2953897 of (2953894 2953897) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.7 mm, total surface area = 71086 mm^2 step 000: RMS=0.169 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.3 minutes mris_inflate utimesec 38.454585 mris_inflate stimesec 0.493213 mris_inflate ru_maxrss 178476 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 238353 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 96 mris_inflate ru_oublock 8984 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5888 mris_inflate ru_nivcsw 4114 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 47.1 mm, total surface area = 72856 mm^2 step 000: RMS=0.167 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 38.405506 mris_inflate stimesec 1.362126 mris_inflate ru_maxrss 183916 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 634059 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8456 mris_inflate ru_oublock 9320 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5334 mris_inflate ru_nivcsw 4413 PIDs (2953894 2953897) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Mon Jan 6 14:32:17 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf mris_curvature -w -seed 1234 lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Mon Jan 6 14:32:18 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/surf reconbatchjobs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB23-310_VYr0_Bay3prisma_AT/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 2954657 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954661 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954664 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954668 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954671 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954677 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954684 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954687 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954691 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954694 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954699 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... Waiting for PID 2954702 of (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 23.097*4pi (290.240) --> -22 handles ICI = 156.7, FI = 1325.6, variation=21640.338 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 123 vertices thresholded to be in k1 ~ [-1.94 0.65], k2 ~ [-0.22 0.21] total integrated curvature = 0.474*4pi (5.956) --> 1 handles ICI = 1.4, FI = 8.5, variation=148.627 96 vertices thresholded to be in [-0.14 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 93 vertices thresholded to be in [-0.65 0.23] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.019, std = 0.026 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 19.488*4pi (244.894) --> -18 handles ICI = 150.4, FI = 1312.9, variation=21321.204 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K ln: failed to create symbolic link 'rh.white.K': File exists mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 141 vertices thresholded to be in k1 ~ [-3.40 0.55], k2 ~ [-0.26 0.15] total integrated curvature = 0.480*4pi (6.028) --> 1 handles ICI = 1.5, FI = 10.4, variation=172.654 135 vertices thresholded to be in [-0.05 0.05] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 97 vertices thresholded to be in [-1.09 0.25] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.020, std = 0.034 done. PIDs (2954657 2954661 2954664 2954668 2954671 2954677 2954684 2954687 2954691 2954694 2954699 2954702) completed and logs appended. Linux chopin 5.15.0-117-generic #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PIB23-310_VYr0_Bay3prisma_AT exited with ERRORS at Mon Jan 6 14:33:12 CST 2025 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting