Wed Nov 20 20:58:10 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma -i /data/jsp/human2/SortedMRI/PIB/PIB15-273_VYr9_Bay3prisma/study7/1.3.12.2.1107.5.2.43.67064.30000024111115584701600000031-7-100-1sqivei.dcm -all subjid PIB15-273_VYr9_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 128Gi 53Gi 8.0Mi 69Gi 120Gi Swap: 111Gi 230Mi 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: 2024/11/21-02:58:10-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_and ProgramArguments: mri_and -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:10-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_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_info ProgramArguments: mri_info -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: 2024/11/21-02:58:11-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: 2024/11/21-02:58:11-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: 2024/11/21-02:58:11-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: 2024/11/21-02:58:11-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: 2024/11/21-02:58:11-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: 2024/11/21-02:58:11-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: 2024/11/21-02:58:11-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: 2024/11/21-02:58:11-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: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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 mri_motion_correct.fsl 7.3.2 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.3.2 TimeStamp: 2024/11/21-02:58:11-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 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/PIB15-273_VYr9_Bay3prisma mri_convert /data/jsp/human2/SortedMRI/PIB/PIB15-273_VYr9_Bay3prisma/study7/1.3.12.2.1107.5.2.43.67064.30000024111115584701600000031-7-100-1sqivei.dcm /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig/001.mgz mri_convert /data/jsp/human2/SortedMRI/PIB/PIB15-273_VYr9_Bay3prisma/study7/1.3.12.2.1107.5.2.43.67064.30000024111115584701600000031-7-100-1sqivei.dcm /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig/001.mgz reading from /data/jsp/human2/SortedMRI/PIB/PIB15-273_VYr9_Bay3prisma/study7/1.3.12.2.1107.5.2.43.67064.30000024111115584701600000031-7-100-1sqivei.dcm... mriio.cpp: starting sdcmLoadVolume() Starting sdcmLoadVolume() Getting Series No INFO: Found 210 files in /data/jsp/human2/SortedMRI/PIB/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/study7/1.3.12.2.1107.5.2.43.67064.30000024111115584701600000031-7-1-1ybw3sn.dcm Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName PIB15-273 Date and time StudyDate 20241114 StudyTime 092040.827000 SeriesTime 093102.698000 AcqTime 092254.222500 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 81.5804 144.4101 134.9155 VolRes 0.8984 0.8984 0.9000 VolDim 256 256 208 Vc 0.0683 -0.9975 0.0208 Vr 0.0324 -0.0186 -0.9993 Vs -0.9971 -0.0689 -0.0311 VolCenter -0.1724 21.1177 19.4754 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 = (0.0682767, -0.99745, 0.0207579) j_ras = (0.0324147, -0.0185776, -0.999302) k_ras = (-0.99714, -0.0689019, -0.0310636) writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig/001.mgz... @#@FSTIME 2024:11:20:20:58:11 mri_convert N 2 e 13.17 S 4.67 U 8.16 P 97% M 36464 F 0 R 53316 W 0 c 1148 w 14401 I 0 O 25264 L 13.79 14.60 18.48 @#@FSLOADPOST 2024:11:20:20:58:24 mri_convert N 2 14.38 14.70 18.45 #-------------------------------------------- #@# MotionCor Wed Nov 20 20:58:25 CST 2024 Found 1 runs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig/001.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz mri_info /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 0.0683, y_r = 0.0324, z_r = -0.9971, c_r = -0.1724 : x_a = -0.9975, y_a = -0.0186, z_a = -0.0689, c_a = 21.1177 : x_s = 0.0208, y_s = -0.9993, z_s = -0.0311, c_s = 19.4754 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.0613 0.0291 -0.8974 81.5804 -0.8961 -0.0167 -0.0620 144.4101 0.0186 -0.8978 -0.0280 134.9155 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.726471 ras to voxel transform: 0.0760 -1.1102 0.0231 151.0081 0.0361 -0.0207 -1.1123 150.1046 -1.1079 -0.0766 -0.0345 106.0979 -0.0000 -0.0000 -0.0000 1.0000 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma mri_convert /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz --conform mri_convert /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz --conform reading from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz... TR=2400.00, TE=3.18, TI=1000.00, flip angle=8.00 i_ras = (0.0682767, -0.99745, 0.0207579) j_ras = (0.0324147, -0.0185776, -0.999302) k_ras = (-0.99714, -0.0689019, -0.0310636) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 839 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz... @#@FSTIME 2024:11:20:20:58:28 mri_convert N 3 e 6.09 S 0.06 U 6.36 P 105% M 47904 F 0 R 35453 W 0 c 594 w 384 I 0 O 12128 L 14.51 14.72 18.43 @#@FSLOADPOST 2024:11:20:20:58:34 mri_convert N 3 14.47 14.71 18.41 mri_add_xform_to_header -c /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/transforms/talairach.xfm /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2024:11:20:20:58:35 mri_add_xform_to_header N 4 e 1.08 S 0.01 U 1.31 P 122% M 23400 F 0 R 4577 W 0 c 123 w 472 I 0 O 12128 L 14.47 14.71 18.41 @#@FSLOADPOST 2024:11:20:20:58:36 mri_add_xform_to_header N 4 14.47 14.71 18.41 mri_info /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz orig.mgz ======================================== Volume information for /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = -0.1724 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 21.1177 : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 19.4754 talairach xfm : /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 127.8276 0.0000 0.0000 1.0000 -106.8823 -0.0000 -1.0000 -0.0000 147.4754 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 127.8276 0.0000 -0.0000 -1.0000 147.4754 -0.0000 1.0000 0.0000 106.8823 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Wed Nov 20 20:58:36 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 Wed Nov 20 20:58:36 CST 2024 tmpdir is ./tmp.mri_nu_correct.mni.2554070 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2554070/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.2554070/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2554070/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2554070/nu0.mgz... TR=2400.00, TE=3.18, TI=1000.00, flip angle=8.00 i_ras = (-1, 0, -1.86265e-09) j_ras = (3.72529e-09, 6.98492e-10, -1) k_ras = (0, 1, -2.56114e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Wed Nov 20 21:02:00 CST 2024 mri_nu_correct.mni done @#@FSTIME 2024:11:20:20:58:36 mri_nu_correct.mni N 12 e 203.72 S 0.40 U 203.64 P 100% M 507208 F 0 R 171027 W 0 c 18687 w 702 I 0 O 22424 L 14.47 14.71 18.41 @#@FSLOADPOST 2024:11:20:21:02:00 mri_nu_correct.mni N 12 16.89 15.46 17.95 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/PIB15-273_VYr9_Bay3prisma/mri/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/transforms/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt Started at Wed Nov 20 21:02:00 CST 2024 Ended at Wed Nov 20 21:02:25 CST 2024 talairach_avi done @#@FSTIME 2024:11:20:21:02:00 talairach_avi N 6 e 25.58 S 1.70 U 16.87 P 72% M 255756 F 1 R 463091 W 0 c 1786 w 8199 I 0 O 296024 L 16.89 15.46 17.95 @#@FSLOADPOST 2024:11:20:21:02:25 talairach_avi N 6 15.77 15.31 17.84 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 1.14255 0.06348 0.04746 -1.89056; -0.08207 1.04552 0.23495 -45.31380; -0.05210 -0.20706 1.15286 -12.79144; 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 Wed Nov 20 21:02:27 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7834, pval=0.8469 >= threshold=0.0050) @#@FSTIME 2024:11:20:21:02:27 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 85% M 6012 F 0 R 228 W 0 c 0 w 9 I 0 O 0 L 15.77 15.31 17.84 @#@FSLOADPOST 2024:11:20:21:02:27 talairach_afd N 4 15.77 15.31 17.84 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/PIB15-273_VYr9_Bay3prisma/mri/transforms/talairach_avi.log tal_QC_AZS /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/transforms/talairach_avi.log TalAviQA: 0.97817 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Nov 20 21:02:28 CST 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/PIB15-273_VYr9_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 Wed Nov 20 21:02:28 CST 2024 tmpdir is ./tmp.mri_nu_correct.mni.2557062 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2557062/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.2557062/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2557062/ones.mgz 7.3.2 cwd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.2557062/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2557062/ones.mgz sysname Linux hostname chopin machine x86_64 user grossens input ./tmp.mri_nu_correct.mni.2557062/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2557062/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.2557062/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2557062/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2557062/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2557062/input.mean.dat 7.3.2 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2557062/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2557062/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2557062/input.mean.dat sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2557062/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.2557062/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2557062/ones.mgz --i ./tmp.mri_nu_correct.mni.2557062/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2557062/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2557062/output.mean.dat 7.3.2 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2557062/ones.mgz --i ./tmp.mri_nu_correct.mni.2557062/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2557062/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2557062/output.mean.dat sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2557062/ones.mgz Loading ./tmp.mri_nu_correct.mni.2557062/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.2557062/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2557062/nu0.mgz ./tmp.mri_nu_correct.mni.2557062/nu0.mgz mul 1.25386865625069650299 Saving result to './tmp.mri_nu_correct.mni.2557062/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2557062/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.2557062/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.2557062/nu0.mgz... TR=2400.00, TE=3.18, TI=1000.00, flip angle=8.00 i_ras = (-1, 0, -1.86265e-09) j_ras = (3.72529e-09, 6.98492e-10, -1) k_ras = (0, 1, -2.56114e-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 8 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 6, i2 = 68 #mri_make_uchar# mapping 15 175 to 3 110 : b -7.84839 m 0.672837 : thresh 11.6646 maxsat 390.657 : nzero 13278565 nsat 0 Wed Nov 20 21:06:36 CST 2024 mri_nu_correct.mni done @#@FSTIME 2024:11:20:21:02:28 mri_nu_correct.mni N 13 e 248.20 S 1.97 U 258.23 P 104% M 614100 F 2 R 783569 W 0 c 24325 w 1522 I 45656 O 63496 L 15.77 15.31 17.84 @#@FSLOADPOST 2024:11:20:21:06:36 mri_nu_correct.mni N 13 25.67 20.36 19.27 mri_add_xform_to_header -c /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2024:11:20:21:06:36 mri_add_xform_to_header N 4 e 0.68 S 0.01 U 1.61 P 237% M 23596 F 0 R 4580 W 0 c 155 w 209 I 6280 O 6280 L 25.67 20.36 19.27 @#@FSLOADPOST 2024:11:20:21:06:37 mri_add_xform_to_header N 4 25.67 20.36 19.27 #-------------------------------------------- #@# Intensity Normalization Wed Nov 20 21:06:37 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 1.14255 0.06348 0.04746 -1.89056; -0.08207 1.04552 0.23495 -45.31380; -0.05210 -0.20706 1.15286 -12.79144; 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 = 18 Starting OpenSpline(): npoints = 18 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 110 gm peak at 70 (70), valley at 35 (35) csf peak at 12, setting threshold to 50 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 70 (70), valley at 30 (30) csf peak at 12, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 42 seconds. @#@FSTIME 2024:11:20:21:06:37 mri_normalize N 7 e 102.50 S 0.80 U 112.62 P 110% M 583632 F 0 R 611115 W 0 c 10717 w 159 I 6280 O 6072 L 25.67 20.36 19.27 @#@FSLOADPOST 2024:11:20:21:08:19 mri_normalize N 7 23.95 21.44 19.78 #-------------------------------------------- #@# Skull Stripping Wed Nov 20 21:08:19 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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=13.0 skull bounding box = (48, 51, 34) --> (199, 244, 222) finding center of left hemi white matter using (98, 115, 128) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (79,91,105) --> (116, 138,151) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 106 +- 4.3 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.653 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.568874 @ (-10.526, -10.526, -10.526) max log p = -4.375300 @ (15.789, -5.263, -15.789) max log p = -4.368824 @ (-2.632, -2.632, 2.632) max log p = -4.352747 @ (-3.947, 1.316, 6.579) max log p = -4.352747 @ (0.000, 0.000, 0.000) max log p = -4.352747 @ (0.000, 0.000, 0.000) max log p = -4.352747 @ (0.000, 0.000, 0.000) max log p = -4.352747 @ (0.000, 0.000, 0.000) Found translation: (-1.3, -17.1, -17.1): log p = -4.353 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.998, old_max_log_p =-4.353 (thresh=-4.3) 1.14016 0.01959 -0.14882 -2.80901; 0.00000 1.22567 0.16136 -57.74742; 0.13885 -0.13766 1.04563 -27.88883; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 27 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.998, old_max_log_p =-3.998 (thresh=-4.0) 1.14016 0.01959 -0.14882 -2.80901; 0.00000 1.22567 0.16136 -57.74742; 0.13885 -0.13766 1.04563 -27.88883; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 25 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.895, old_max_log_p =-3.998 (thresh=-4.0) 1.09848 0.12573 -0.06152 -22.85055; -0.11022 1.19503 0.16516 -37.77449; 0.06398 -0.13865 1.05312 -15.47530; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 23 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.895, old_max_log_p =-3.895 (thresh=-3.9) 1.07788 0.12338 -0.06036 -20.07643; -0.11009 1.21216 0.20327 -45.27051; 0.06755 -0.17767 1.04715 -11.39683; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 23 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.868, old_max_log_p =-3.895 (thresh=-3.9) 1.07957 0.10638 -0.08093 -15.12082; -0.09321 1.21828 0.19416 -46.59534; 0.08445 -0.16599 1.04759 -13.85077; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.857, old_max_log_p =-3.868 (thresh=-3.9) 1.07877 0.11635 -0.07934 -16.65995; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.855, old_max_log_p =-3.857 (thresh=-3.9) 1.08130 0.11662 -0.07952 -16.99221; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 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 1.08130 0.11662 -0.07952 -16.99221; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.08130 0.11662 -0.07952 -16.99221; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 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: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08130 0.11662 -0.07952 -16.99221; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.855 (old=-4.653) transform before final EM align: 1.08130 0.11662 -0.07952 -16.99221; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 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 1.08130 0.11662 -0.07952 -16.99221; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.08130 0.11662 -0.07952 -16.99221; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 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: 011: -log(p) = 4.2 tol 0.000000 final transform: 1.08130 0.11662 -0.07952 -16.99221; -0.10216 1.21879 0.19504 -46.13038; 0.08454 -0.16619 1.04882 -13.52852; 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 0.0599 hours 4 threads registration took 3 minutes and 36 seconds. @#@FSTIME 2024:11:20:21:08:19 mri_em_register N 4 e 215.64 S 1.57 U 716.96 P 333% M 629304 F 0 R 1150156 W 0 c 67006 w 540 I 0 O 32 L 23.95 21.44 19.78 @#@FSLOADPOST 2024:11:20:21:11:55 mri_em_register N 4 20.45 21.44 20.17 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=128 y=124 z=128 r=78 first estimation of the main basin volume: 2056698 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=99, y=122, z=91, Imax=255 CSF=13, 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=1504192110350744 voxels, voxel volume =1.000 = 1504192110350744 mmm3 = 1504192170557.440 cm3 done. PostAnalyze...Basin Prior 18 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=127,y=127, z=123, r=9054 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 43920 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 3006 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = 3222 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 18594 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 18774 OTHER CSF_MIN=9, CSF_intensity=20, CSF_MAX=47 , nb = 324 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 24, 27, 33, 75 after analyzing : 24, 31, 33, 42 RIGHT_CER before analyzing : 4, 4, 25, 82 after analyzing : 4, 18, 25, 34 LEFT_CER before analyzing : 10, 16, 44, 80 after analyzing : 10, 34, 44, 45 RIGHT_BRAIN before analyzing : 24, 27, 35, 74 after analyzing : 24, 32, 35, 42 LEFT_BRAIN before analyzing : 24, 27, 34, 74 after analyzing : 24, 31, 34, 41 OTHER before analyzing : 47, 4, 0, 2 after analyzing : 4, 18, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.010 curvature mean = 66.645, std = 6.786 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.37, sigma = 4.08 after rotation: sse = 2.37, sigma = 4.08 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.55, its var is 3.80 before Erosion-Dilatation 0.43% 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...43 iterations mri_strip_skull: done peeling brain Brain Size = 1448264 voxels, voxel volume = 1.000 mm3 = 1448264 mmm3 = 1448.264 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed done @#@FSTIME 2024:11:20:21:11:55 mri_watershed N 6 e 18.09 S 0.66 U 23.89 P 135% M 806992 F 1 R 439284 W 0 c 2150 w 806 I 0 O 2352 L 20.45 21.44 20.17 @#@FSLOADPOST 2024:11:20:21:12:13 mri_watershed N 6 20.41 21.38 20.17 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Nov 20 21:12:14 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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=17.9 skull bounding box = (64, 72, 48) --> (190, 197, 210) finding center of left hemi white matter using (106, 114, 129) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (91,99,109) --> (121, 129,148) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 106 +- 4.5 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.343 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.151062 @ (-10.526, -10.526, -10.526) max log p = -3.961492 @ (5.263, 5.263, -5.263) max log p = -3.911309 @ (2.632, -7.895, -2.632) max log p = -3.892537 @ (-1.316, 1.316, -1.316) max log p = -3.875822 @ (1.974, 0.658, -0.658) max log p = -3.875822 @ (0.000, 0.000, 0.000) max log p = -3.875822 @ (0.000, 0.000, 0.000) max log p = -3.875822 @ (0.000, 0.000, 0.000) Found translation: (-2.0, -11.2, -20.4): log p = -3.876 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.609, old_max_log_p =-3.876 (thresh=-3.9) 1.14016 0.01457 -0.13007 -5.55898; 0.00000 1.22023 0.18169 -55.27797; 0.15011 -0.11066 0.98799 -23.77498; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 24 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.596, old_max_log_p =-3.609 (thresh=-3.6) 1.14016 0.01457 -0.13007 -5.55898; 0.00000 1.12871 0.16807 -42.18536; 0.16136 -0.11896 1.06209 -33.46468; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 23 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.596, old_max_log_p =-3.596 (thresh=-3.6) 1.14016 0.01457 -0.13007 -5.55898; 0.00000 1.12871 0.16807 -42.18536; 0.16136 -0.11896 1.06209 -33.46468; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 22 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.428, old_max_log_p =-3.596 (thresh=-3.6) 1.10210 0.01012 -0.09038 -4.94874; 0.00000 1.19299 0.17764 -53.25689; 0.12302 -0.11712 1.04563 -24.89471; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.428, old_max_log_p =-3.428 (thresh=-3.4) 1.10210 0.01012 -0.09038 -4.94874; 0.00000 1.19299 0.17764 -53.25689; 0.12302 -0.11712 1.04563 -24.89471; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.394, old_max_log_p =-3.428 (thresh=-3.4) 1.10637 0.02814 -0.07074 -10.19953; -0.02005 1.19305 0.16149 -48.69023; 0.10459 -0.09739 1.04605 -25.06692; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.390, old_max_log_p =-3.394 (thresh=-3.4) 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.390, old_max_log_p =-3.390 (thresh=-3.4) 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 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 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 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: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.390 (old=-4.343) transform before final EM align: 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 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 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 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: 012: -log(p) = 3.9 tol 0.000000 final transform: 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 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 0.0599 hours 4 threads registration took 3 minutes and 36 seconds. @#@FSTIME 2024:11:20:21:12:14 mri_em_register N 7 e 215.63 S 1.83 U 743.44 P 345% M 616628 F 0 R 1132591 W 0 c 69874 w 811 I 0 O 32 L 20.05 21.29 20.15 @#@FSLOADPOST 2024:11:20:21:15:50 mri_em_register N 7 30.97 25.20 21.85 #-------------------------------------- #@# CA Normalize Wed Nov 20 21:15:50 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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=17.9 skull bounding box = (64, 72, 48) --> (190, 197, 210) finding center of left hemi white matter using (106, 114, 129) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (91,99,109) --> (121, 129,148) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 106 +- 4.5 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246437 sample points... INFO: compute sample coordinates transform 1.10637 0.02814 -0.07074 -10.19953; -0.02003 1.19165 0.16130 -48.49337; 0.10446 -0.09728 1.04482 -24.91400; 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 (123, 70, 48) --> (187, 167, 207) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 1301 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 71, 51) --> (132, 167, 209) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 4 of 1240 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (126, 142, 71) --> (170, 182, 123) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 0 of 35 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (85, 142, 72) --> (126, 180, 127) Right_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 73 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 135, 106) --> (144, 194, 136) Brain_Stem: limiting intensities to 104.0 --> 132.0 13 of 25 (52.0%) samples deleted using 2674 total control points for intensity normalization... bias field = 0.963 +- 0.056 11 of 2657 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (123, 70, 48) --> (187, 167, 207) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 1749 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 71, 51) --> (132, 167, 209) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 4 of 1636 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (126, 142, 71) --> (170, 182, 123) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 105 (13.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (85, 142, 72) --> (126, 180, 127) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 61 (6.6%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 135, 106) --> (144, 194, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 24 of 121 (19.8%) samples deleted using 3672 total control points for intensity normalization... bias field = 1.017 +- 0.052 20 of 3596 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (123, 70, 48) --> (187, 167, 207) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 1728 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 71, 51) --> (132, 167, 209) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 6 of 1687 (0.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (126, 142, 71) --> (170, 182, 123) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 32 of 132 (24.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (85, 142, 72) --> (126, 180, 127) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 52 of 139 (37.4%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 135, 106) --> (144, 194, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 99 of 156 (63.5%) samples deleted using 3842 total control points for intensity normalization... bias field = 1.014 +- 0.045 12 of 3588 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 5 seconds. @#@FSTIME 2024:11:20:21:15:50 mri_ca_normalize N 8 e 64.67 S 1.06 U 67.21 P 105% M 696824 F 0 R 782901 W 0 c 6449 w 385 I 0 O 3456 L 30.97 25.20 21.85 @#@FSLOADPOST 2024:11:20:21:16:54 mri_ca_normalize N 8 30.04 26.29 22.47 #-------------------------------------- #@# CA Reg Wed Nov 20 21:16:54 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 0.830476 #FOTS# QuadFit found better minimum quadopt=(dt=182.232,rms=0.768681) vs oldopt=(dt=92.48,rms=0.782772) #GCMRL# 0 dt 182.231913 rms 0.769 7.441% neg 0 invalid 762 tFOTS 9.5150 tGradient 4.0680 tsec 14.3410 #FOTS# QuadFit found better minimum quadopt=(dt=192.514,rms=0.751276) vs oldopt=(dt=92.48,rms=0.755951) #GCMRL# 1 dt 192.514056 rms 0.751 2.264% neg 0 invalid 762 tFOTS 9.4690 tGradient 3.5570 tsec 13.7240 #FOTS# QuadFit found better minimum quadopt=(dt=138.191,rms=0.744655) vs oldopt=(dt=92.48,rms=0.74557) #GCMRL# 2 dt 138.191083 rms 0.745 0.881% neg 0 invalid 762 tFOTS 9.2330 tGradient 3.4370 tsec 13.3420 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.735333) vs oldopt=(dt=369.92,rms=0.73562) #GCMRL# 3 dt 443.904000 rms 0.735 1.252% neg 0 invalid 762 tFOTS 9.2250 tGradient 3.4690 tsec 13.3640 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.731523) vs oldopt=(dt=92.48,rms=0.731568) #GCMRL# 4 dt 110.976000 rms 0.732 0.518% neg 0 invalid 762 tFOTS 9.5920 tGradient 3.5220 tsec 13.7510 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.722679) vs oldopt=(dt=1479.68,rms=0.723787) #GCMRL# 5 dt 1183.744000 rms 0.723 1.209% neg 0 invalid 762 tFOTS 8.9610 tGradient 3.8850 tsec 13.5130 #FOTS# QuadFit found better minimum quadopt=(dt=95.0154,rms=0.717479) vs oldopt=(dt=92.48,rms=0.717491) #GCMRL# 6 dt 95.015385 rms 0.717 0.720% neg 0 invalid 762 tFOTS 9.0650 tGradient 3.2960 tsec 13.0050 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.712785) vs oldopt=(dt=1479.68,rms=0.713183) #GCMRL# 7 dt 1183.744000 rms 0.713 0.654% neg 0 invalid 762 tFOTS 10.0840 tGradient 3.6170 tsec 14.2930 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.71013) vs oldopt=(dt=92.48,rms=0.710457) #GCMRL# 8 dt 129.472000 rms 0.710 0.373% neg 0 invalid 762 tFOTS 9.7410 tGradient 3.7160 tsec 14.1080 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.709588) vs oldopt=(dt=92.48,rms=0.709685) #GCMRL# 9 dt 129.472000 rms 0.710 0.000% neg 0 invalid 762 tFOTS 9.3060 tGradient 4.5020 tsec 14.5440 #GCMRL# 10 dt 129.472000 rms 0.709 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7650 tsec 4.4380 #GCMRL# 11 dt 129.472000 rms 0.708 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7150 tsec 4.3900 #GCMRL# 12 dt 129.472000 rms 0.706 0.222% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4490 tsec 4.0480 #GCMRL# 13 dt 129.472000 rms 0.704 0.288% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0310 tsec 4.7240 #GCMRL# 14 dt 129.472000 rms 0.702 0.350% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5370 tsec 4.1870 #GCMRL# 15 dt 129.472000 rms 0.699 0.349% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5880 tsec 4.3570 #GCMRL# 16 dt 129.472000 rms 0.697 0.301% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5270 tsec 4.2140 #GCMRL# 17 dt 129.472000 rms 0.696 0.221% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9290 tsec 4.8080 #GCMRL# 18 dt 129.472000 rms 0.694 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3750 tsec 5.1540 #GCMRL# 19 dt 129.472000 rms 0.693 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0560 tsec 4.7710 #GCMRL# 20 dt 129.472000 rms 0.692 0.188% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8890 tsec 5.6200 #GCMRL# 21 dt 129.472000 rms 0.690 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7870 tsec 4.5160 #GCMRL# 22 dt 129.472000 rms 0.689 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0560 tsec 4.8580 #GCMRL# 23 dt 129.472000 rms 0.688 0.158% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1600 tsec 4.8410 #GCMRL# 24 dt 129.472000 rms 0.687 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7580 tsec 5.5880 #GCMRL# 25 dt 129.472000 rms 0.686 0.173% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3420 tsec 4.0180 #GCMRL# 26 dt 129.472000 rms 0.685 0.164% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9980 tsec 4.6960 #GCMRL# 27 dt 129.472000 rms 0.684 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5850 tsec 4.3320 #GCMRL# 28 dt 129.472000 rms 0.683 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6030 tsec 4.2470 #GCMRL# 29 dt 129.472000 rms 0.682 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2700 tsec 3.9220 #GCMRL# 30 dt 129.472000 rms 0.682 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4660 tsec 4.0780 #GCMRL# 31 dt 129.472000 rms 0.681 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0990 tsec 3.7830 #GCMRL# 32 dt 0.850000 rms 0.681 0.000% neg 0 invalid 762 tFOTS 8.7010 tGradient 3.1690 tsec 12.5650 #GCAMreg# pass 0 level1 5 level2 1 tsec 257.889 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 0.681471 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.680847) vs oldopt=(dt=92.48,rms=0.680865) #GCMRL# 34 dt 129.472000 rms 0.681 0.092% neg 0 invalid 762 tFOTS 7.6520 tGradient 4.1900 tsec 12.4280 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.680766) vs oldopt=(dt=92.48,rms=0.680783) #GCMRL# 35 dt 129.472000 rms 0.681 0.000% neg 0 invalid 762 tFOTS 7.9760 tGradient 3.0420 tsec 11.6410 #GCMRL# 36 dt 129.472000 rms 0.681 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2860 tsec 3.9300 #GCMRL# 37 dt 129.472000 rms 0.681 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2240 tsec 3.8040 #GCMRL# 38 dt 129.472000 rms 0.681 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1000 tsec 3.6920 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 0.691946 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.690564) vs oldopt=(dt=25.92,rms=0.690637) #GCMRL# 40 dt 36.288000 rms 0.691 0.200% neg 0 invalid 762 tFOTS 8.2320 tGradient 3.1160 tsec 11.9340 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.690145) vs oldopt=(dt=25.92,rms=0.690197) #GCMRL# 41 dt 36.288000 rms 0.690 0.000% neg 0 invalid 762 tFOTS 8.2480 tGradient 2.9830 tsec 11.8790 #GCMRL# 42 dt 36.288000 rms 0.690 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7440 tsec 3.3870 #GCMRL# 43 dt 36.288000 rms 0.689 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9130 tsec 3.5180 #GCMRL# 44 dt 36.288000 rms 0.689 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8070 tsec 3.4180 #GCMRL# 45 dt 36.288000 rms 0.688 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9270 tsec 3.5300 #GCMRL# 46 dt 36.288000 rms 0.686 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8390 tsec 3.4260 #GCMRL# 47 dt 36.288000 rms 0.684 0.391% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7960 tsec 3.3890 #GCMRL# 48 dt 36.288000 rms 0.680 0.485% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7540 tsec 3.3700 #GCMRL# 49 dt 36.288000 rms 0.677 0.518% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9340 tsec 3.6230 #GCMRL# 50 dt 36.288000 rms 0.674 0.480% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0260 tsec 3.6710 #GCMRL# 51 dt 36.288000 rms 0.671 0.409% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9530 tsec 3.5510 #GCMRL# 52 dt 36.288000 rms 0.669 0.307% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8720 tsec 3.4680 #GCMRL# 53 dt 36.288000 rms 0.667 0.212% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8380 tsec 3.4680 #GCMRL# 54 dt 36.288000 rms 0.667 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7930 tsec 3.3850 #GCMRL# 55 dt 36.288000 rms 0.666 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7430 tsec 3.3870 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.66605) vs oldopt=(dt=103.68,rms=0.66608) #GCMRL# 56 dt 62.208000 rms 0.666 0.000% neg 0 invalid 762 tFOTS 9.4100 tGradient 2.9440 tsec 12.9850 #GCAMreg# pass 0 level1 4 level2 1 tsec 91.979 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 0.66662 #GCMRL# 58 dt 0.000000 rms 0.666 0.087% neg 0 invalid 762 tFOTS 8.0860 tGradient 2.7980 tsec 11.4810 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 0.696004 #FOTS# QuadFit found better minimum quadopt=(dt=0.175,rms=0.695445) vs oldopt=(dt=0.125,rms=0.695446) #GCMRL# 60 dt 0.175000 rms 0.695 0.080% neg 0 invalid 762 tFOTS 7.8590 tGradient 2.8810 tsec 11.4000 #FOTS# QuadFit found better minimum quadopt=(dt=0.1,rms=0.695442) vs oldopt=(dt=0.125,rms=0.695442) #GCMRL# 61 dt 0.100000 rms 0.695 0.000% neg 0 invalid 762 tFOTS 8.9500 tGradient 2.9250 tsec 12.5130 #GCAMreg# pass 0 level1 3 level2 1 tsec 30.836 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 0.695998 #GCMRL# 63 dt 0.500000 rms 0.695 0.083% neg 0 invalid 762 tFOTS 7.4440 tGradient 2.6720 tsec 10.6930 #FOTS# QuadFit found better minimum quadopt=(dt=0.04375,rms=0.695422) vs oldopt=(dt=0.03125,rms=0.695422) #GCMRL# 64 dt 0.043750 rms 0.695 0.000% neg 0 invalid 762 tFOTS 7.3110 tGradient 2.6340 tsec 10.5490 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 0.780381 #FOTS# QuadFit found better minimum quadopt=(dt=2.56151,rms=0.753631) vs oldopt=(dt=2.88,rms=0.754044) #GCMRL# 66 dt 2.561505 rms 0.754 3.428% neg 0 invalid 762 tFOTS 7.4780 tGradient 2.6240 tsec 10.7240 #FOTS# QuadFit found better minimum quadopt=(dt=1.5,rms=0.751461) vs oldopt=(dt=0.72,rms=0.75205) #GCMRL# 67 dt 1.500000 rms 0.751 0.288% neg 0 invalid 762 tFOTS 7.6090 tGradient 2.5110 tsec 10.6940 #FOTS# QuadFit found better minimum quadopt=(dt=0.84375,rms=0.751152) vs oldopt=(dt=0.72,rms=0.751155) #GCMRL# 68 dt 0.843750 rms 0.751 0.000% neg 0 invalid 762 tFOTS 7.1690 tGradient 2.4380 tsec 10.2090 #GCAMreg# pass 0 level1 2 level2 1 tsec 37.89 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 0.75164 #FOTS# QuadFit found better minimum quadopt=(dt=0.054,rms=0.751143) vs oldopt=(dt=0.045,rms=0.751143) #GCMRL# 70 dt 0.054000 rms 0.751 0.066% neg 0 invalid 762 tFOTS 7.2710 tGradient 2.7070 tsec 10.5580 #FOTS# QuadFit found better minimum quadopt=(dt=0.01575,rms=0.751143) vs oldopt=(dt=0.01125,rms=0.751143) #GCMRL# 71 dt 0.015750 rms 0.751 0.000% neg 0 invalid 762 tFOTS 7.4190 tGradient 2.4380 tsec 10.4690 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 0.821532 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.819154) vs oldopt=(dt=0.32,rms=0.819321) #GCMRL# 73 dt 0.448000 rms 0.819 0.289% neg 0 invalid 762 tFOTS 7.5120 tGradient 2.4380 tsec 10.5180 #FOTS# QuadFit found better minimum quadopt=(dt=0.831441,rms=0.812689) vs oldopt=(dt=1.28,rms=0.814209) #GCMRL# 74 dt 0.831441 rms 0.813 0.789% neg 0 invalid 762 tFOTS 7.2900 tGradient 2.3600 tsec 10.2200 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.811427) vs oldopt=(dt=0.08,rms=0.811685) #GCMRL# 75 dt 0.112000 rms 0.811 0.000% neg 0 invalid 762 tFOTS 7.1270 tGradient 2.4740 tsec 10.2290 #GCMRL# 76 dt 0.112000 rms 0.811 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4060 tsec 2.9690 #GCMRL# 77 dt 0.112000 rms 0.811 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3460 tsec 2.9140 #GCMRL# 78 dt 0.112000 rms 0.811 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5670 tsec 3.1780 #FOTS# QuadFit found better minimum quadopt=(dt=0.454167,rms=0.806744) vs oldopt=(dt=0.32,rms=0.807324) #GCMRL# 79 dt 0.454167 rms 0.807 0.484% neg 0 invalid 762 tFOTS 7.5380 tGradient 2.6060 tsec 10.7160 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.806381) vs oldopt=(dt=0.08,rms=0.806428) #GCMRL# 80 dt 0.112000 rms 0.806 0.000% neg 0 invalid 762 tFOTS 7.3450 tGradient 2.4330 tsec 10.3990 #GCMRL# 81 dt 0.112000 rms 0.806 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4110 tsec 2.9880 #GCMRL# 82 dt 0.112000 rms 0.806 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6750 tsec 3.2590 #GCMRL# 83 dt 0.112000 rms 0.806 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8140 tsec 3.4050 #GCMRL# 84 dt 0.112000 rms 0.804 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5540 tsec 3.1400 #GCMRL# 85 dt 0.112000 rms 0.803 0.189% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3850 tsec 2.9590 #GCMRL# 86 dt 0.112000 rms 0.802 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6210 tsec 3.2100 #GCMRL# 87 dt 0.112000 rms 0.800 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5120 tsec 3.1520 #GCMRL# 88 dt 0.112000 rms 0.800 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7100 tsec 3.3050 #GCMRL# 89 dt 0.112000 rms 0.799 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4350 tsec 3.0650 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.797417) vs oldopt=(dt=1.28,rms=0.797674) #GCMRL# 90 dt 1.792000 rms 0.797 0.253% neg 0 invalid 762 tFOTS 7.3600 tGradient 2.7280 tsec 10.6560 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.796299) vs oldopt=(dt=0.32,rms=0.796373) #GCMRL# 91 dt 0.256000 rms 0.796 0.000% neg 0 invalid 762 tFOTS 7.6180 tGradient 2.3550 tsec 10.6400 #GCMRL# 92 dt 0.256000 rms 0.796 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6440 tsec 3.2580 #GCMRL# 93 dt 0.256000 rms 0.795 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6020 tsec 3.2120 #GCMRL# 94 dt 0.256000 rms 0.795 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5920 tsec 3.2070 #GCMRL# 95 dt 0.256000 rms 0.794 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4330 tsec 3.0720 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.79361) vs oldopt=(dt=0.32,rms=0.793656) #GCMRL# 96 dt 0.448000 rms 0.794 0.076% neg 0 invalid 762 tFOTS 7.9540 tGradient 2.5240 tsec 11.0750 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.793509) vs oldopt=(dt=0.08,rms=0.79352) #GCAMreg# pass 0 level1 1 level2 1 tsec 148.214 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 0.794003 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.793169) vs oldopt=(dt=0.32,rms=0.793172) #GCMRL# 98 dt 0.384000 rms 0.793 0.105% neg 0 invalid 762 tFOTS 7.6090 tGradient 2.4320 tsec 10.6170 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.792997) vs oldopt=(dt=0.32,rms=0.793013) #GCMRL# 99 dt 0.256000 rms 0.793 0.000% neg 0 invalid 762 tFOTS 7.6040 tGradient 2.6620 tsec 10.8940 #GCMRL# 100 dt 0.256000 rms 0.793 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4630 tsec 3.0600 #GCMRL# 101 dt 0.256000 rms 0.793 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4050 tsec 3.0100 #GCMRL# 102 dt 0.256000 rms 0.792 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4270 tsec 3.0030 #GCMRL# 103 dt 0.256000 rms 0.792 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4670 tsec 3.0710 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 0.763487 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.757341) vs oldopt=(dt=0.32,rms=0.757796) #GCMRL# 105 dt 0.256000 rms 0.757 0.805% neg 0 invalid 762 tFOTS 7.6210 tGradient 1.6870 tsec 9.9380 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.756937) vs oldopt=(dt=0.02,rms=0.75697) #GCMRL# 106 dt 0.028000 rms 0.757 0.000% neg 0 invalid 762 tFOTS 7.6630 tGradient 1.8650 tsec 10.1430 #GCAMreg# pass 0 level1 0 level2 1 tsec 25.797 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 0.757462 #FOTS# QuadFit found better minimum quadopt=(dt=0.012,rms=0.756887) vs oldopt=(dt=0.02,rms=0.756903) #GCMRL# 108 dt 0.012000 rms 0.757 0.076% neg 0 invalid 762 tFOTS 7.4860 tGradient 1.7570 tsec 9.8110 #FOTS# QuadFit found better minimum quadopt=(dt=0.0004375,rms=0.756884) vs oldopt=(dt=0.0003125,rms=0.756884) #GCMRL# 109 dt 0.000438 rms 0.757 0.000% neg 0 invalid 762 tFOTS 7.3970 tGradient 1.6020 tsec 9.6440 #GCMRL# 110 dt 0.000438 rms 0.757 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5700 tsec 2.1270 GCAMregister done in 13.01 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.15814 (23) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (1497 voxels, overlap=0.704) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (1497 voxels, peak = 16), gca=15.6 gca peak = 0.17690 (16) mri peak = 0.16698 (23) Right_Lateral_Ventricle (43): linear fit = 1.23 x + 0.0 (1410 voxels, overlap=0.619) Right_Lateral_Ventricle (43): linear fit = 1.23 x + 0.0 (1410 voxels, peak = 20), gca=19.6 gca peak = 0.28275 (96) mri peak = 0.11491 (95) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (654 voxels, overlap=0.719) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (654 voxels, peak = 94), gca=93.6 gca peak = 0.18948 (93) mri peak = 0.08885 (96) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (616 voxels, overlap=1.001) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (616 voxels, peak = 94), gca=94.4 gca peak = 0.20755 (55) mri peak = 0.07778 (67) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (533 voxels, overlap=0.055) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (533 voxels, peak = 65), gca=65.2 gca peak = 0.31831 (58) mri peak = 0.10068 (69) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (596 voxels, overlap=0.013) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (596 voxels, peak = 69), gca=68.7 gca peak = 0.11957 (102) mri peak = 0.11211 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (46812 voxels, overlap=0.711) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (46812 voxels, peak = 106), gca=105.6 gca peak = 0.11429 (102) mri peak = 0.11721 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (49562 voxels, overlap=0.597) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (49562 voxels, peak = 108), gca=107.6 gca peak = 0.14521 (59) mri peak = 0.03509 (65) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (14405 voxels, overlap=0.296) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (14405 voxels, peak = 68), gca=67.6 gca peak = 0.14336 (58) mri peak = 0.03505 (69) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (14827 voxels, overlap=0.152) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (14827 voxels, peak = 71), gca=71.1 gca peak = 0.13305 (70) mri peak = 0.15280 (73) Right_Caudate (50): linear fit = 1.11 x + 0.0 (406 voxels, overlap=0.258) Right_Caudate (50): linear fit = 1.11 x + 0.0 (406 voxels, peak = 77), gca=77.3 gca peak = 0.15761 (71) mri peak = 0.10190 (83) Left_Caudate (11): linear fit = 1.12 x + 0.0 (849 voxels, overlap=0.342) Left_Caudate (11): linear fit = 1.12 x + 0.0 (849 voxels, peak = 79), gca=79.2 gca peak = 0.13537 (57) mri peak = 0.04453 (62) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (16753 voxels, overlap=0.567) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (16753 voxels, peak = 64), gca=63.6 gca peak = 0.13487 (56) mri peak = 0.05325 (65) Right_Cerebellum_Cortex (47): linear fit = 1.16 x + 0.0 (19093 voxels, overlap=0.479) Right_Cerebellum_Cortex (47): linear fit = 1.16 x + 0.0 (19093 voxels, peak = 65), gca=65.2 gca peak = 0.19040 (84) mri peak = 0.08044 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (7843 voxels, overlap=0.668) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (7843 voxels, peak = 88), gca=87.8 gca peak = 0.18871 (83) mri peak = 0.10686 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (7130 voxels, overlap=0.769) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (7130 voxels, peak = 86), gca=85.9 gca peak = 0.24248 (57) mri peak = 0.10476 (67) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (286 voxels, overlap=0.249) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (286 voxels, peak = 68), gca=67.5 gca peak = 0.35833 (56) mri peak = 0.10849 (71) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (422 voxels, overlap=0.047) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (422 voxels, peak = 67), gca=67.5 gca peak = 0.12897 (85) mri peak = 0.06923 (88) Left_Thalamus (10): linear fit = 1.03 x + 0.0 (4298 voxels, overlap=0.890) Left_Thalamus (10): linear fit = 1.03 x + 0.0 (4298 voxels, peak = 88), gca=88.0 gca peak = 0.13127 (83) mri peak = 0.09031 (82) Right_Thalamus (49): linear fit = 1.02 x + 0.0 (3298 voxels, overlap=0.879) Right_Thalamus (49): linear fit = 1.02 x + 0.0 (3298 voxels, peak = 85), gca=85.1 gca peak = 0.12974 (78) mri peak = 0.07486 (88) Left_Putamen (12): linear fit = 1.14 x + 0.0 (1837 voxels, overlap=0.354) Left_Putamen (12): linear fit = 1.14 x + 0.0 (1837 voxels, peak = 89), gca=89.3 gca peak = 0.17796 (79) mri peak = 0.09961 (87) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2048 voxels, overlap=0.558) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2048 voxels, peak = 87), gca=86.5 gca peak = 0.10999 (80) mri peak = 0.10625 (85) Brain_Stem (16): linear fit = 1.09 x + 0.0 (10380 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.09 x + 0.0 (10380 voxels, peak = 87), gca=86.8 gca peak = 0.13215 (88) mri peak = 0.08874 (92) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1001 voxels, overlap=0.578) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1001 voxels, peak = 95), gca=95.5 gca peak = 0.11941 (89) mri peak = 0.10390 (92) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1151 voxels, overlap=0.547) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1151 voxels, peak = 96), gca=95.7 gca peak = 0.20775 (25) mri peak = 0.30000 (22) gca peak = 0.13297 (21) mri peak = 0.12450 (21) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (220 voxels, overlap=0.576) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (220 voxels, peak = 20), gca=20.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) 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 1.19 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.06 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 4.54562 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 0.790194 #FOTS# QuadFit found better minimum quadopt=(dt=163.716,rms=0.755984) vs oldopt=(dt=92.48,rms=0.762555) #GCMRL# 112 dt 163.716440 rms 0.756 4.329% neg 0 invalid 762 tFOTS 7.5640 tGradient 3.0180 tsec 11.1870 #FOTS# QuadFit found better minimum quadopt=(dt=337.446,rms=0.738681) vs oldopt=(dt=369.92,rms=0.738825) #GCMRL# 113 dt 337.445560 rms 0.739 2.289% neg 0 invalid 762 tFOTS 8.1450 tGradient 3.3180 tsec 12.1610 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.732592) vs oldopt=(dt=92.48,rms=0.733146) #GCMRL# 114 dt 129.472000 rms 0.733 0.824% neg 0 invalid 762 tFOTS 7.6730 tGradient 3.2250 tsec 11.5730 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.72378) vs oldopt=(dt=369.92,rms=0.724412) #GCMRL# 115 dt 517.888000 rms 0.724 1.203% neg 0 invalid 762 tFOTS 7.2740 tGradient 3.1640 tsec 10.9920 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.718641) vs oldopt=(dt=92.48,rms=0.718815) #GCMRL# 116 dt 110.976000 rms 0.719 0.710% neg 0 invalid 762 tFOTS 8.1900 tGradient 3.0510 tsec 12.2890 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.712801) vs oldopt=(dt=369.92,rms=0.713779) #GCMRL# 117 dt 517.888000 rms 0.713 0.813% neg 0 invalid 762 tFOTS 7.6800 tGradient 3.1010 tsec 11.3510 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.71104) vs oldopt=(dt=92.48,rms=0.711058) #GCMRL# 118 dt 110.976000 rms 0.711 0.247% neg 0 invalid 762 tFOTS 7.8530 tGradient 3.0340 tsec 11.4580 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.707006) vs oldopt=(dt=369.92,rms=0.707808) #GCMRL# 119 dt 517.888000 rms 0.707 0.567% neg 0 invalid 762 tFOTS 7.9180 tGradient 3.2810 tsec 11.7980 #GCMRL# 120 dt 92.480000 rms 0.706 0.123% neg 0 invalid 762 tFOTS 8.2050 tGradient 3.3060 tsec 12.0860 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.695395) vs oldopt=(dt=1479.68,rms=0.697529) #GCMRL# 121 dt 2071.552000 rms 0.695 1.521% neg 0 invalid 762 tFOTS 8.5680 tGradient 3.1420 tsec 12.2890 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.694244) vs oldopt=(dt=92.48,rms=0.694411) #GCMRL# 122 dt 129.472000 rms 0.694 0.165% neg 0 invalid 762 tFOTS 7.7750 tGradient 3.0080 tsec 11.3460 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.691782) vs oldopt=(dt=369.92,rms=0.692253) #GCMRL# 123 dt 517.888000 rms 0.692 0.355% neg 0 invalid 762 tFOTS 8.5120 tGradient 3.0570 tsec 12.1470 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.691114) vs oldopt=(dt=92.48,rms=0.691179) #GCMRL# 124 dt 129.472000 rms 0.691 0.097% neg 0 invalid 762 tFOTS 7.7650 tGradient 3.1510 tsec 11.4750 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.690212) vs oldopt=(dt=369.92,rms=0.690244) #GCMRL# 125 dt 443.904000 rms 0.690 0.131% neg 0 invalid 762 tFOTS 7.5830 tGradient 2.9800 tsec 11.1200 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.689129) vs oldopt=(dt=92.48,rms=0.689274) #GCMRL# 126 dt 129.472000 rms 0.689 0.157% neg 0 invalid 762 tFOTS 7.6050 tGradient 3.0960 tsec 11.2620 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.688628) vs oldopt=(dt=369.92,rms=0.688702) #GCMRL# 127 dt 295.936000 rms 0.689 0.073% neg 0 invalid 762 tFOTS 7.9490 tGradient 3.0330 tsec 11.5440 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.687669) vs oldopt=(dt=92.48,rms=0.687825) #GCMRL# 128 dt 129.472000 rms 0.688 0.139% neg 0 invalid 762 tFOTS 7.8830 tGradient 3.1000 tsec 11.5520 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.687323) vs oldopt=(dt=369.92,rms=0.687395) #GCMRL# 129 dt 221.952000 rms 0.687 0.050% neg 0 invalid 762 tFOTS 7.6850 tGradient 2.9920 tsec 11.2290 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.68635) vs oldopt=(dt=369.92,rms=0.686447) #GCMRL# 130 dt 295.936000 rms 0.686 0.142% neg 0 invalid 762 tFOTS 9.4630 tGradient 3.1320 tsec 13.1480 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.685937) vs oldopt=(dt=92.48,rms=0.685938) #GCMRL# 131 dt 73.984000 rms 0.686 0.060% neg 0 invalid 762 tFOTS 7.7330 tGradient 3.0950 tsec 11.3940 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.685267) vs oldopt=(dt=369.92,rms=0.685357) #GCMRL# 132 dt 517.888000 rms 0.685 0.098% neg 0 invalid 762 tFOTS 7.6360 tGradient 3.0640 tsec 11.2850 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.684174) vs oldopt=(dt=92.48,rms=0.684332) #GCMRL# 133 dt 129.472000 rms 0.684 0.160% neg 0 invalid 762 tFOTS 7.5830 tGradient 3.2320 tsec 11.3810 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.684002) vs oldopt=(dt=92.48,rms=0.684025) #GCMRL# 134 dt 129.472000 rms 0.684 0.000% neg 0 invalid 762 tFOTS 7.5400 tGradient 2.9890 tsec 11.1320 #GCMRL# 135 dt 129.472000 rms 0.684 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1410 tsec 3.6960 #GCMRL# 136 dt 129.472000 rms 0.683 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0890 tsec 3.6390 #GCMRL# 137 dt 129.472000 rms 0.682 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1090 tsec 3.6640 #GCMRL# 138 dt 129.472000 rms 0.681 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1660 tsec 3.7120 #GCMRL# 139 dt 129.472000 rms 0.680 0.185% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0950 tsec 3.6540 #GCMRL# 140 dt 129.472000 rms 0.678 0.207% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2330 tsec 3.7960 #GCMRL# 141 dt 129.472000 rms 0.677 0.207% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0010 tsec 3.5630 #GCMRL# 142 dt 129.472000 rms 0.676 0.210% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7170 tsec 4.3580 #GCMRL# 143 dt 129.472000 rms 0.674 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5940 tsec 4.2150 #GCMRL# 144 dt 129.472000 rms 0.673 0.218% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1320 tsec 3.7040 #GCMRL# 145 dt 129.472000 rms 0.671 0.215% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1740 tsec 3.7530 #GCMRL# 146 dt 129.472000 rms 0.670 0.200% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2490 tsec 3.8060 #GCMRL# 147 dt 129.472000 rms 0.669 0.183% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1150 tsec 3.6780 #GCMRL# 148 dt 129.472000 rms 0.668 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1480 tsec 3.7190 #GCMRL# 149 dt 129.472000 rms 0.667 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1390 tsec 3.7080 #GCMRL# 150 dt 129.472000 rms 0.666 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1420 tsec 3.7010 #GCMRL# 151 dt 129.472000 rms 0.665 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2030 tsec 3.7880 #GCMRL# 152 dt 129.472000 rms 0.664 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1940 tsec 3.7570 #GCMRL# 153 dt 129.472000 rms 0.663 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1820 tsec 3.7440 #GCMRL# 154 dt 129.472000 rms 0.662 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2490 tsec 3.8260 #GCMRL# 155 dt 129.472000 rms 0.662 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1170 tsec 3.6740 #GCMRL# 156 dt 129.472000 rms 0.661 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1280 tsec 3.7030 #GCMRL# 157 dt 129.472000 rms 0.660 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9670 tsec 3.5260 #GCMRL# 158 dt 129.472000 rms 0.660 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0760 tsec 3.6250 #GCMRL# 159 dt 129.472000 rms 0.659 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0990 tsec 3.6620 #GCMRL# 160 dt 129.472000 rms 0.659 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2590 tsec 3.8250 #GCMRL# 161 dt 129.472000 rms 0.658 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9800 tsec 4.7180 #GCMRL# 162 dt 129.472000 rms 0.657 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3240 tsec 3.9400 #GCMRL# 163 dt 129.472000 rms 0.657 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1190 tsec 3.6990 #GCMRL# 164 dt 129.472000 rms 0.656 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1380 tsec 3.7150 #GCMRL# 165 dt 129.472000 rms 0.656 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0570 tsec 3.6290 #GCMRL# 166 dt 129.472000 rms 0.655 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1140 tsec 3.7010 #GCMRL# 167 dt 129.472000 rms 0.655 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1910 tsec 3.7570 #GCMRL# 168 dt 129.472000 rms 0.654 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1480 tsec 3.7610 #GCMRL# 169 dt 129.472000 rms 0.654 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0960 tsec 3.6500 #GCMRL# 170 dt 129.472000 rms 0.653 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1870 tsec 3.7510 #GCMRL# 171 dt 129.472000 rms 0.652 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1990 tsec 3.7680 #GCMRL# 172 dt 129.472000 rms 0.652 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1030 tsec 3.6600 #GCMRL# 173 dt 129.472000 rms 0.651 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0530 tsec 3.6240 #GCMRL# 174 dt 129.472000 rms 0.651 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2160 tsec 3.7790 #GCMRL# 175 dt 129.472000 rms 0.650 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0770 tsec 3.6450 #GCMRL# 176 dt 129.472000 rms 0.650 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0850 tsec 3.6550 #GCMRL# 177 dt 129.472000 rms 0.650 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0700 tsec 3.6280 #GCMRL# 178 dt 129.472000 rms 0.649 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0360 tsec 3.6150 #GCMRL# 179 dt 129.472000 rms 0.649 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1040 tsec 3.6740 #GCMRL# 180 dt 129.472000 rms 0.648 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1240 tsec 3.7950 #GCMRL# 181 dt 129.472000 rms 0.648 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9160 tsec 4.6550 #GCMRL# 182 dt 129.472000 rms 0.647 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4530 tsec 4.0930 #GCMRL# 183 dt 129.472000 rms 0.647 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1750 tsec 3.7480 #GCMRL# 184 dt 129.472000 rms 0.647 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0820 tsec 3.6870 #GCMRL# 185 dt 129.472000 rms 0.646 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2060 tsec 3.8700 #GCMRL# 186 dt 129.472000 rms 0.646 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0750 tsec 3.6550 #GCMRL# 187 dt 129.472000 rms 0.646 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0510 tsec 3.6010 #GCMRL# 188 dt 129.472000 rms 0.645 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1990 tsec 3.7730 #GCMRL# 189 dt 129.472000 rms 0.645 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0720 tsec 3.6210 #GCMRL# 190 dt 129.472000 rms 0.645 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2580 tsec 3.8080 #GCMRL# 191 dt 129.472000 rms 0.644 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9990 tsec 3.5630 #GCMRL# 192 dt 129.472000 rms 0.644 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0640 tsec 3.6290 #GCMRL# 193 dt 129.472000 rms 0.644 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0360 tsec 3.5900 #GCMRL# 194 dt 129.472000 rms 0.644 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1130 tsec 3.6970 #GCMRL# 195 dt 129.472000 rms 0.643 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1140 tsec 3.6890 #GCMRL# 196 dt 129.472000 rms 0.643 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1260 tsec 3.7020 #GCMRL# 197 dt 129.472000 rms 0.643 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0110 tsec 3.5600 #GCMRL# 198 dt 129.472000 rms 0.643 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1580 tsec 3.7170 #GCMRL# 199 dt 129.472000 rms 0.642 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1690 tsec 3.7230 #GCMRL# 200 dt 129.472000 rms 0.642 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2130 tsec 3.8090 #GCMRL# 201 dt 129.472000 rms 0.642 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4950 tsec 4.1390 #GCMRL# 202 dt 129.472000 rms 0.642 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5330 tsec 4.2070 #GCMRL# 203 dt 129.472000 rms 0.641 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5520 tsec 4.2340 #GCMRL# 204 dt 129.472000 rms 0.641 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5600 tsec 4.2130 #GCMRL# 205 dt 129.472000 rms 0.641 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5520 tsec 4.2140 #GCMRL# 206 dt 129.472000 rms 0.641 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5430 tsec 4.2080 #GCMRL# 207 dt 129.472000 rms 0.640 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4680 tsec 4.1660 #GCMRL# 208 dt 129.472000 rms 0.640 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7210 tsec 4.3790 #GCMRL# 209 dt 129.472000 rms 0.640 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5440 tsec 4.2030 #GCMRL# 210 dt 129.472000 rms 0.640 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5540 tsec 4.2300 #GCMRL# 211 dt 129.472000 rms 0.640 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5710 tsec 4.2320 #GCMRL# 212 dt 129.472000 rms 0.639 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4810 tsec 4.1590 #GCMRL# 213 dt 129.472000 rms 0.639 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5270 tsec 4.2040 #GCMRL# 214 dt 129.472000 rms 0.639 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3900 tsec 4.0120 #GCMRL# 215 dt 129.472000 rms 0.639 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3080 tsec 3.9040 #GCMRL# 216 dt 129.472000 rms 0.638 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2980 tsec 3.8610 #GCMRL# 217 dt 129.472000 rms 0.638 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0960 tsec 3.6680 #GCMRL# 218 dt 129.472000 rms 0.638 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2400 tsec 3.8520 #GCMRL# 219 dt 129.472000 rms 0.638 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4480 tsec 4.1210 #GCMRL# 220 dt 129.472000 rms 0.638 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4590 tsec 4.1290 #GCMRL# 221 dt 129.472000 rms 0.637 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6020 tsec 4.2740 #GCMRL# 222 dt 129.472000 rms 0.637 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6110 tsec 4.2750 #GCMRL# 223 dt 129.472000 rms 0.637 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6130 tsec 4.2760 #GCMRL# 224 dt 129.472000 rms 0.637 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5720 tsec 4.2270 #GCMRL# 225 dt 129.472000 rms 0.637 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5000 tsec 4.1650 #GCMRL# 226 dt 129.472000 rms 0.636 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5660 tsec 4.2230 #GCMRL# 227 dt 129.472000 rms 0.636 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5300 tsec 4.1870 #GCMRL# 228 dt 129.472000 rms 0.636 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4820 tsec 4.1600 #GCMRL# 229 dt 129.472000 rms 0.636 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5480 tsec 4.2040 #GCMRL# 230 dt 129.472000 rms 0.636 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5820 tsec 4.2430 #GCMRL# 231 dt 129.472000 rms 0.636 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4960 tsec 4.1800 #GCMRL# 232 dt 129.472000 rms 0.635 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4040 tsec 4.0790 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.635229) vs oldopt=(dt=1479.68,rms=0.635251) #GCMRL# 233 dt 2071.552000 rms 0.635 0.000% neg 0 invalid 762 tFOTS 8.6310 tGradient 3.3590 tsec 12.6150 #GCAMreg# pass 0 level1 5 level2 1 tsec 667.61 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 0.635591 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.634596) vs oldopt=(dt=369.92,rms=0.63463) #GCMRL# 235 dt 295.936000 rms 0.635 0.157% neg 0 invalid 762 tFOTS 8.1710 tGradient 3.2740 tsec 12.0560 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.63451) vs oldopt=(dt=92.48,rms=0.634524) #GCMRL# 236 dt 129.472000 rms 0.635 0.000% neg 0 invalid 762 tFOTS 8.8110 tGradient 3.3010 tsec 12.7770 #GCMRL# 237 dt 129.472000 rms 0.634 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2970 tsec 3.9310 #GCMRL# 238 dt 129.472000 rms 0.634 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3690 tsec 3.9760 #GCMRL# 239 dt 129.472000 rms 0.634 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4190 tsec 4.0700 #GCMRL# 240 dt 129.472000 rms 0.634 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4040 tsec 4.0180 #GCMRL# 241 dt 129.472000 rms 0.634 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5190 tsec 4.1590 #GCMRL# 242 dt 129.472000 rms 0.633 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4090 tsec 4.0100 #GCMRL# 243 dt 129.472000 rms 0.633 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2230 tsec 3.8390 #GCMRL# 244 dt 129.472000 rms 0.633 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3650 tsec 4.0150 #GCMRL# 245 dt 129.472000 rms 0.633 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1870 tsec 3.8010 #GCMRL# 246 dt 129.472000 rms 0.633 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2350 tsec 3.8000 #GCMRL# 247 dt 129.472000 rms 0.632 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1550 tsec 3.7410 #GCMRL# 248 dt 129.472000 rms 0.632 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2970 tsec 3.9010 #GCMRL# 249 dt 129.472000 rms 0.632 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3050 tsec 3.9900 #FOTS# QuadFit found better minimum quadopt=(dt=0.07225,rms=0.632119) vs oldopt=(dt=0.0903125,rms=0.632119) 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 0.635498 #FOTS# QuadFit found better minimum quadopt=(dt=207.36,rms=0.629225) vs oldopt=(dt=103.68,rms=0.630562) #GCMRL# 251 dt 207.360000 rms 0.629 0.987% neg 0 invalid 762 tFOTS 8.0680 tGradient 2.8030 tsec 11.5180 #FOTS# QuadFit found better minimum quadopt=(dt=176,rms=0.622731) vs oldopt=(dt=103.68,rms=0.623731) #GCMRL# 252 dt 176.000000 rms 0.623 1.032% neg 0 invalid 762 tFOTS 8.2130 tGradient 2.8780 tsec 11.7520 #FOTS# QuadFit found better minimum quadopt=(dt=65.1837,rms=0.618857) vs oldopt=(dt=103.68,rms=0.619965) #GCMRL# 253 dt 65.183724 rms 0.619 0.622% neg 0 invalid 762 tFOTS 7.7910 tGradient 3.2560 tsec 11.6280 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.61592) vs oldopt=(dt=103.68,rms=0.616445) #GCMRL# 254 dt 145.152000 rms 0.616 0.475% neg 0 invalid 762 tFOTS 7.4850 tGradient 2.9130 tsec 11.0160 #FOTS# QuadFit found better minimum quadopt=(dt=92.9811,rms=0.613284) vs oldopt=(dt=103.68,rms=0.613318) #GCMRL# 255 dt 92.981132 rms 0.613 0.428% neg 0 invalid 762 tFOTS 8.1510 tGradient 2.7160 tsec 11.4420 #FOTS# QuadFit found better minimum quadopt=(dt=95.7594,rms=0.611233) vs oldopt=(dt=103.68,rms=0.611249) #GCMRL# 256 dt 95.759398 rms 0.611 0.334% neg 0 invalid 762 tFOTS 8.3000 tGradient 2.6450 tsec 11.5260 #FOTS# QuadFit found better minimum quadopt=(dt=95.7168,rms=0.60909) vs oldopt=(dt=103.68,rms=0.609107) #GCMRL# 257 dt 95.716814 rms 0.609 0.351% neg 0 invalid 762 tFOTS 8.0910 tGradient 2.9220 tsec 11.5760 #FOTS# QuadFit found better minimum quadopt=(dt=98.1525,rms=0.607301) vs oldopt=(dt=103.68,rms=0.60731) #GCMRL# 258 dt 98.152466 rms 0.607 0.294% neg 0 invalid 762 tFOTS 8.1710 tGradient 2.6070 tsec 11.3730 #FOTS# QuadFit found better minimum quadopt=(dt=91.6923,rms=0.605467) vs oldopt=(dt=103.68,rms=0.605507) #GCMRL# 259 dt 91.692308 rms 0.605 0.302% neg 0 invalid 762 tFOTS 8.1690 tGradient 2.7950 tsec 11.5240 #FOTS# QuadFit found better minimum quadopt=(dt=99.5556,rms=0.603972) vs oldopt=(dt=103.68,rms=0.603976) #GCMRL# 260 dt 99.555556 rms 0.604 0.247% neg 0 invalid 762 tFOTS 8.3560 tGradient 2.7750 tsec 11.7400 #FOTS# QuadFit found better minimum quadopt=(dt=87.7303,rms=0.602425) vs oldopt=(dt=103.68,rms=0.602474) #GCMRL# 261 dt 87.730337 rms 0.602 0.256% neg 0 invalid 762 tFOTS 8.0190 tGradient 2.5870 tsec 11.1590 #GCMRL# 262 dt 103.680000 rms 0.601 0.225% neg 0 invalid 762 tFOTS 8.0150 tGradient 2.7330 tsec 11.3430 #FOTS# QuadFit found better minimum quadopt=(dt=82.5562,rms=0.599769) vs oldopt=(dt=103.68,rms=0.599851) #GCMRL# 263 dt 82.556213 rms 0.600 0.216% neg 0 invalid 762 tFOTS 8.5940 tGradient 2.8360 tsec 11.9990 #GCMRL# 264 dt 103.680000 rms 0.599 0.193% neg 0 invalid 762 tFOTS 8.0100 tGradient 2.6180 tsec 11.1890 #FOTS# QuadFit found better minimum quadopt=(dt=84.3636,rms=0.597491) vs oldopt=(dt=103.68,rms=0.597545) #GCMRL# 265 dt 84.363636 rms 0.597 0.188% neg 0 invalid 762 tFOTS 8.5210 tGradient 2.8320 tsec 11.9810 #GCMRL# 266 dt 103.680000 rms 0.596 0.169% neg 0 invalid 762 tFOTS 7.9530 tGradient 2.6600 tsec 11.1780 #FOTS# QuadFit found better minimum quadopt=(dt=78.3284,rms=0.595435) vs oldopt=(dt=103.68,rms=0.595517) #GCMRL# 267 dt 78.328358 rms 0.595 0.175% neg 0 invalid 762 tFOTS 8.5130 tGradient 2.5820 tsec 11.7000 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.594448) vs oldopt=(dt=103.68,rms=0.594465) #GCMRL# 268 dt 124.416000 rms 0.594 0.166% neg 0 invalid 762 tFOTS 7.7290 tGradient 2.7530 tsec 11.0840 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.593453) vs oldopt=(dt=103.68,rms=0.59374) #GCMRL# 269 dt 62.208000 rms 0.593 0.167% neg 0 invalid 762 tFOTS 8.4830 tGradient 2.7810 tsec 11.8390 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.592361) vs oldopt=(dt=103.68,rms=0.592551) #GCMRL# 270 dt 145.152000 rms 0.592 0.184% neg 0 invalid 762 tFOTS 7.8130 tGradient 2.7300 tsec 11.1160 #FOTS# QuadFit found better minimum quadopt=(dt=65.9104,rms=0.591518) vs oldopt=(dt=103.68,rms=0.591688) #GCMRL# 271 dt 65.910448 rms 0.592 0.142% neg 0 invalid 762 tFOTS 8.4100 tGradient 2.6290 tsec 11.6240 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.590577) vs oldopt=(dt=103.68,rms=0.590691) #GCMRL# 272 dt 145.152000 rms 0.591 0.159% neg 0 invalid 762 tFOTS 7.9100 tGradient 2.9330 tsec 11.4410 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.589873) vs oldopt=(dt=25.92,rms=0.589999) #GCMRL# 273 dt 36.288000 rms 0.590 0.119% neg 0 invalid 762 tFOTS 7.4710 tGradient 2.6520 tsec 10.6940 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.587501) vs oldopt=(dt=414.72,rms=0.587705) #GCMRL# 274 dt 580.608000 rms 0.588 0.402% neg 0 invalid 762 tFOTS 7.9530 tGradient 2.8610 tsec 11.4300 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.585629) vs oldopt=(dt=25.92,rms=0.586047) #GCMRL# 275 dt 36.288000 rms 0.586 0.319% neg 0 invalid 762 tFOTS 8.0280 tGradient 2.7280 tsec 11.3300 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.584786) vs oldopt=(dt=103.68,rms=0.584804) #GCMRL# 276 dt 82.944000 rms 0.585 0.144% neg 0 invalid 762 tFOTS 8.0080 tGradient 2.7930 tsec 11.3480 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.584238) vs oldopt=(dt=103.68,rms=0.584241) #GCMRL# 277 dt 82.944000 rms 0.584 0.094% neg 0 invalid 762 tFOTS 8.0010 tGradient 2.7550 tsec 11.3600 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.583648) vs oldopt=(dt=103.68,rms=0.583663) #GCMRL# 278 dt 124.416000 rms 0.584 0.101% neg 0 invalid 762 tFOTS 8.0220 tGradient 2.8330 tsec 11.4800 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.583151) vs oldopt=(dt=25.92,rms=0.583239) #GCMRL# 279 dt 36.288000 rms 0.583 0.085% neg 0 invalid 762 tFOTS 7.7620 tGradient 2.8690 tsec 11.1990 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.581832) vs oldopt=(dt=414.72,rms=0.581838) #GCMRL# 280 dt 497.664000 rms 0.582 0.226% neg 0 invalid 762 tFOTS 8.2180 tGradient 2.8500 tsec 11.6700 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.580517) vs oldopt=(dt=25.92,rms=0.580815) #GCMRL# 281 dt 36.288000 rms 0.581 0.226% neg 0 invalid 762 tFOTS 8.6000 tGradient 2.9220 tsec 12.1250 #GCMRL# 282 dt 103.680000 rms 0.580 0.123% neg 0 invalid 762 tFOTS 8.4390 tGradient 2.7820 tsec 11.8310 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.579413) vs oldopt=(dt=25.92,rms=0.579477) #GCMRL# 283 dt 36.288000 rms 0.579 0.067% neg 0 invalid 762 tFOTS 9.0450 tGradient 3.0800 tsec 12.7340 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.578212) vs oldopt=(dt=414.72,rms=0.578276) #GCMRL# 284 dt 580.608000 rms 0.578 0.207% neg 0 invalid 762 tFOTS 8.4200 tGradient 3.0390 tsec 12.1690 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.577042) vs oldopt=(dt=25.92,rms=0.577318) #GCMRL# 285 dt 36.288000 rms 0.577 0.202% neg 0 invalid 762 tFOTS 8.4140 tGradient 2.7680 tsec 11.7860 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.57634) vs oldopt=(dt=103.68,rms=0.576372) #GCMRL# 286 dt 82.944000 rms 0.576 0.122% neg 0 invalid 762 tFOTS 7.6180 tGradient 2.9050 tsec 11.1100 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.575969) vs oldopt=(dt=103.68,rms=0.575983) #GCMRL# 287 dt 82.944000 rms 0.576 0.064% neg 0 invalid 762 tFOTS 8.0230 tGradient 2.9790 tsec 11.5640 #GCMRL# 288 dt 103.680000 rms 0.576 0.057% neg 0 invalid 762 tFOTS 8.2700 tGradient 2.7890 tsec 11.6360 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.575248) vs oldopt=(dt=103.68,rms=0.575267) #GCMRL# 289 dt 82.944000 rms 0.575 0.069% neg 0 invalid 762 tFOTS 8.8570 tGradient 3.2330 tsec 12.7390 #GCMRL# 290 dt 103.680000 rms 0.575 0.052% neg 0 invalid 762 tFOTS 8.4740 tGradient 2.9600 tsec 12.0070 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.574556) vs oldopt=(dt=103.68,rms=0.574587) #GCMRL# 291 dt 82.944000 rms 0.575 0.068% neg 0 invalid 762 tFOTS 8.0230 tGradient 2.7340 tsec 11.3190 #GCMRL# 292 dt 103.680000 rms 0.574 0.057% neg 0 invalid 762 tFOTS 7.6960 tGradient 2.7980 tsec 11.0550 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.573864) vs oldopt=(dt=103.68,rms=0.573888) #GCMRL# 293 dt 82.944000 rms 0.574 0.064% neg 0 invalid 762 tFOTS 8.5220 tGradient 3.0550 tsec 12.2320 #GCMRL# 294 dt 103.680000 rms 0.574 0.000% neg 0 invalid 762 tFOTS 8.5040 tGradient 2.8560 tsec 12.1920 #GCMRL# 295 dt 103.680000 rms 0.573 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2030 tsec 3.9520 #GCMRL# 296 dt 103.680000 rms 0.572 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0630 tsec 3.6870 #GCMRL# 297 dt 103.680000 rms 0.572 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9700 tsec 3.5560 #GCMRL# 298 dt 103.680000 rms 0.570 0.247% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1400 tsec 3.7460 #GCMRL# 299 dt 103.680000 rms 0.569 0.198% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8610 tsec 3.5150 #GCMRL# 300 dt 103.680000 rms 0.568 0.254% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9680 tsec 3.5770 #GCMRL# 301 dt 103.680000 rms 0.566 0.273% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6790 tsec 3.2720 #GCMRL# 302 dt 103.680000 rms 0.565 0.251% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6430 tsec 3.2370 #GCMRL# 303 dt 103.680000 rms 0.563 0.258% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7250 tsec 3.2920 #GCMRL# 304 dt 103.680000 rms 0.562 0.223% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5790 tsec 3.1540 #GCMRL# 305 dt 103.680000 rms 0.561 0.243% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5280 tsec 3.1030 #GCMRL# 306 dt 103.680000 rms 0.559 0.222% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5040 tsec 3.0640 #GCMRL# 307 dt 103.680000 rms 0.558 0.200% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5850 tsec 3.1270 #GCMRL# 308 dt 103.680000 rms 0.557 0.201% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5910 tsec 3.1600 #GCMRL# 309 dt 103.680000 rms 0.556 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4970 tsec 3.0550 #GCMRL# 310 dt 103.680000 rms 0.555 0.184% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5320 tsec 3.0950 #GCMRL# 311 dt 103.680000 rms 0.554 0.179% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5190 tsec 3.0790 #GCMRL# 312 dt 103.680000 rms 0.553 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5100 tsec 3.0610 #GCMRL# 313 dt 103.680000 rms 0.552 0.162% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5130 tsec 3.0740 #GCMRL# 314 dt 103.680000 rms 0.552 0.160% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5060 tsec 3.0610 #GCMRL# 315 dt 103.680000 rms 0.551 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4650 tsec 3.0080 #GCMRL# 316 dt 103.680000 rms 0.550 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5080 tsec 3.0620 #GCMRL# 317 dt 103.680000 rms 0.549 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5270 tsec 3.0790 #GCMRL# 318 dt 103.680000 rms 0.549 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4580 tsec 3.0080 #GCMRL# 319 dt 103.680000 rms 0.548 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4830 tsec 3.0470 #GCMRL# 320 dt 103.680000 rms 0.547 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5200 tsec 3.0780 #GCMRL# 321 dt 103.680000 rms 0.547 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4900 tsec 3.0420 #GCMRL# 322 dt 103.680000 rms 0.546 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4750 tsec 3.0160 #GCMRL# 323 dt 103.680000 rms 0.546 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5270 tsec 3.0780 #GCMRL# 324 dt 103.680000 rms 0.545 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5430 tsec 3.0940 #GCMRL# 325 dt 103.680000 rms 0.545 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4940 tsec 3.0350 #GCMRL# 326 dt 103.680000 rms 0.544 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5500 tsec 3.0980 #GCMRL# 327 dt 103.680000 rms 0.544 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5090 tsec 3.0650 #GCMRL# 328 dt 103.680000 rms 0.544 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5640 tsec 3.1150 #GCMRL# 329 dt 103.680000 rms 0.543 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6100 tsec 3.1640 #GCMRL# 330 dt 103.680000 rms 0.543 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5900 tsec 3.1440 #GCMRL# 331 dt 103.680000 rms 0.543 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6370 tsec 3.1880 #GCMRL# 332 dt 103.680000 rms 0.542 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6430 tsec 3.1890 #GCMRL# 333 dt 103.680000 rms 0.542 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6350 tsec 3.1840 #GCMRL# 334 dt 103.680000 rms 0.542 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6800 tsec 3.2370 #GCMRL# 335 dt 103.680000 rms 0.541 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6740 tsec 3.2180 #GCMRL# 336 dt 103.680000 rms 0.541 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5780 tsec 3.1370 #GCMRL# 337 dt 103.680000 rms 0.541 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6390 tsec 3.2080 #GCMRL# 338 dt 103.680000 rms 0.541 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5730 tsec 3.1210 #GCMRL# 339 dt 103.680000 rms 0.540 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5650 tsec 3.1080 #GCMRL# 340 dt 103.680000 rms 0.540 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5670 tsec 3.1110 #GCMRL# 341 dt 103.680000 rms 0.540 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5590 tsec 3.1070 #GCMRL# 342 dt 103.680000 rms 0.540 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6870 tsec 3.2490 #GCMRL# 343 dt 103.680000 rms 0.540 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5940 tsec 3.1590 #GCMRL# 344 dt 103.680000 rms 0.540 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5590 tsec 3.3700 #GCMRL# 345 dt 103.680000 rms 0.540 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5390 tsec 3.0880 #GCMRL# 346 dt 103.680000 rms 0.539 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5570 tsec 3.0990 #GCMRL# 347 dt 103.680000 rms 0.539 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5480 tsec 3.1280 #GCMRL# 348 dt 103.680000 rms 0.539 0.000% neg 0 invalid 762 tFOTS 7.0390 tGradient 2.5580 tsec 10.1920 #GCAMreg# pass 0 level1 4 level2 1 tsec 695.308 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 0.539821 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.538779) vs oldopt=(dt=25.92,rms=0.538931) #GCMRL# 350 dt 36.288000 rms 0.539 0.193% neg 0 invalid 762 tFOTS 6.5380 tGradient 2.5480 tsec 9.6400 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.538378) vs oldopt=(dt=25.92,rms=0.538486) #GCMRL# 351 dt 36.288000 rms 0.538 0.074% neg 0 invalid 762 tFOTS 6.4950 tGradient 2.5430 tsec 9.6010 #GCMRL# 352 dt 6.480000 rms 0.538 0.000% neg 0 invalid 762 tFOTS 6.1150 tGradient 2.5640 tsec 9.2670 #GCMRL# 353 dt 0.810000 rms 0.538 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5620 tsec 4.0640 #GCMRL# 354 dt 0.101250 rms 0.538 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5750 tsec 4.1060 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 0.553783 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.550986) vs oldopt=(dt=32,rms=0.551171) #GCMRL# 356 dt 44.800000 rms 0.551 0.505% neg 0 invalid 762 tFOTS 7.5220 tGradient 2.4370 tsec 10.5070 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.547071) vs oldopt=(dt=32,rms=0.547999) #GCMRL# 357 dt 44.800000 rms 0.547 0.711% neg 0 invalid 762 tFOTS 7.0470 tGradient 2.3590 tsec 9.9540 #FOTS# QuadFit found better minimum quadopt=(dt=90.4327,rms=0.543255) vs oldopt=(dt=128,rms=0.543747) #GCMRL# 358 dt 90.432678 rms 0.543 0.697% neg 0 invalid 762 tFOTS 7.4530 tGradient 2.3980 tsec 10.3940 #GCMRL# 359 dt 32.000000 rms 0.540 0.620% neg 0 invalid 762 tFOTS 7.0690 tGradient 2.4450 tsec 10.0560 #FOTS# QuadFit found better minimum quadopt=(dt=71.68,rms=0.537218) vs oldopt=(dt=32,rms=0.537597) #GCMRL# 360 dt 71.680000 rms 0.537 0.495% neg 0 invalid 762 tFOTS 7.4930 tGradient 2.4900 tsec 10.5470 #FOTS# QuadFit found better minimum quadopt=(dt=30.9046,rms=0.534609) vs oldopt=(dt=32,rms=0.534623) #GCMRL# 361 dt 30.904645 rms 0.535 0.486% neg 0 invalid 762 tFOTS 7.5340 tGradient 2.4510 tsec 10.5290 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.53281) vs oldopt=(dt=32,rms=0.53305) #GCMRL# 362 dt 44.800000 rms 0.533 0.336% neg 0 invalid 762 tFOTS 7.5590 tGradient 2.4810 tsec 10.5800 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.53137) vs oldopt=(dt=32,rms=0.531448) #GCMRL# 363 dt 44.800000 rms 0.531 0.270% neg 0 invalid 762 tFOTS 7.5730 tGradient 2.5180 tsec 10.6430 #GCMRL# 364 dt 32.000000 rms 0.530 0.220% neg 0 invalid 762 tFOTS 7.6660 tGradient 2.3610 tsec 10.5700 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.528967) vs oldopt=(dt=32,rms=0.529034) #GCMRL# 365 dt 44.800000 rms 0.529 0.232% neg 0 invalid 762 tFOTS 7.4920 tGradient 2.4740 tsec 10.5180 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.528171) vs oldopt=(dt=32,rms=0.528172) #GCMRL# 366 dt 25.600000 rms 0.528 0.151% neg 0 invalid 762 tFOTS 7.0870 tGradient 2.4320 tsec 10.0600 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.526911) vs oldopt=(dt=32,rms=0.527112) #GCMRL# 367 dt 44.800000 rms 0.527 0.239% neg 0 invalid 762 tFOTS 7.6050 tGradient 2.4940 tsec 10.6720 #GCMRL# 368 dt 32.000000 rms 0.526 0.107% neg 0 invalid 762 tFOTS 7.1970 tGradient 2.7490 tsec 10.4900 #GCMRL# 369 dt 32.000000 rms 0.525 0.168% neg 0 invalid 762 tFOTS 7.5360 tGradient 2.4070 tsec 10.4940 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.52497) vs oldopt=(dt=32,rms=0.524971) #GCMRL# 370 dt 25.600000 rms 0.525 0.094% neg 0 invalid 762 tFOTS 7.1000 tGradient 2.4050 tsec 10.0750 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.524082) vs oldopt=(dt=32,rms=0.524172) #GCMRL# 371 dt 44.800000 rms 0.524 0.169% neg 0 invalid 762 tFOTS 7.5430 tGradient 2.3920 tsec 10.5230 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.523594) vs oldopt=(dt=32,rms=0.52362) #GCMRL# 372 dt 25.600000 rms 0.524 0.093% neg 0 invalid 762 tFOTS 7.1920 tGradient 2.3870 tsec 10.1480 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.522728) vs oldopt=(dt=32,rms=0.522819) #GCMRL# 373 dt 44.800000 rms 0.523 0.165% neg 0 invalid 762 tFOTS 7.7930 tGradient 2.4600 tsec 10.8270 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.522324) vs oldopt=(dt=32,rms=0.522355) #GCMRL# 374 dt 25.600000 rms 0.522 0.077% neg 0 invalid 762 tFOTS 7.1300 tGradient 2.4580 tsec 10.1510 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.521599) vs oldopt=(dt=32,rms=0.521642) #GCMRL# 375 dt 44.800000 rms 0.522 0.139% neg 0 invalid 762 tFOTS 7.5160 tGradient 2.3380 tsec 10.4000 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.521195) vs oldopt=(dt=32,rms=0.521246) #GCMRL# 376 dt 25.600000 rms 0.521 0.077% neg 0 invalid 762 tFOTS 7.0170 tGradient 2.4240 tsec 9.9980 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.520479) vs oldopt=(dt=32,rms=0.520529) #GCMRL# 377 dt 44.800000 rms 0.520 0.137% neg 0 invalid 762 tFOTS 7.4630 tGradient 2.3570 tsec 10.3770 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.520137) vs oldopt=(dt=32,rms=0.520187) #GCMRL# 378 dt 25.600000 rms 0.520 0.066% neg 0 invalid 762 tFOTS 6.9890 tGradient 2.4010 tsec 9.9480 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.519534) vs oldopt=(dt=32,rms=0.519547) #GCMRL# 379 dt 38.400000 rms 0.520 0.116% neg 0 invalid 762 tFOTS 7.4190 tGradient 2.3590 tsec 10.3220 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.519238) vs oldopt=(dt=32,rms=0.519272) #GCMRL# 380 dt 25.600000 rms 0.519 0.057% neg 0 invalid 762 tFOTS 7.0880 tGradient 2.3890 tsec 10.0360 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.518716) vs oldopt=(dt=32,rms=0.518727) #GCMRL# 381 dt 38.400000 rms 0.519 0.100% neg 0 invalid 762 tFOTS 7.5350 tGradient 2.3380 tsec 10.4310 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.518427) vs oldopt=(dt=32,rms=0.518456) #GCMRL# 382 dt 25.600000 rms 0.518 0.056% neg 0 invalid 762 tFOTS 7.0390 tGradient 2.3610 tsec 9.9590 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.517944) vs oldopt=(dt=32,rms=0.517951) #GCMRL# 383 dt 38.400000 rms 0.518 0.093% neg 0 invalid 762 tFOTS 7.5040 tGradient 2.3290 tsec 10.3800 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.517665) vs oldopt=(dt=32,rms=0.517692) #GCMRL# 384 dt 25.600000 rms 0.518 0.054% neg 0 invalid 762 tFOTS 7.0560 tGradient 2.3600 tsec 9.9710 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.517237) vs oldopt=(dt=32,rms=0.517237) #GCMRL# 385 dt 38.400000 rms 0.517 0.083% neg 0 invalid 762 tFOTS 7.4100 tGradient 2.3210 tsec 10.2850 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.51697) vs oldopt=(dt=32,rms=0.517003) #GCMRL# 386 dt 25.600000 rms 0.517 0.052% neg 0 invalid 762 tFOTS 6.9260 tGradient 2.3810 tsec 9.8500 #GCMRL# 387 dt 32.000000 rms 0.517 0.077% neg 0 invalid 762 tFOTS 7.4250 tGradient 2.3310 tsec 10.3070 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.51636) vs oldopt=(dt=32,rms=0.516371) #GCMRL# 388 dt 25.600000 rms 0.516 0.000% neg 0 invalid 762 tFOTS 7.1770 tGradient 2.4040 tsec 10.1700 #GCMRL# 389 dt 25.600000 rms 0.516 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3560 tsec 2.9140 #GCMRL# 390 dt 25.600000 rms 0.516 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3590 tsec 2.9330 #GCMRL# 391 dt 25.600000 rms 0.515 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3550 tsec 2.9140 #GCMRL# 392 dt 25.600000 rms 0.514 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3720 tsec 2.9330 #GCMRL# 393 dt 25.600000 rms 0.513 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3450 tsec 2.9100 #GCMRL# 394 dt 25.600000 rms 0.512 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3440 tsec 2.9050 #GCMRL# 395 dt 25.600000 rms 0.511 0.184% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3410 tsec 2.9010 #GCMRL# 396 dt 25.600000 rms 0.510 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3290 tsec 2.8840 #GCMRL# 397 dt 25.600000 rms 0.509 0.186% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3380 tsec 2.9080 #GCMRL# 398 dt 25.600000 rms 0.509 0.170% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3440 tsec 2.8950 #GCMRL# 399 dt 25.600000 rms 0.509 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3250 tsec 3.1450 #GCMRL# 400 dt 25.600000 rms 0.508 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3340 tsec 2.8860 #GCMRL# 401 dt 25.600000 rms 0.508 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3540 tsec 2.9070 #GCMRL# 402 dt 25.600000 rms 0.508 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3380 tsec 2.8970 #GCMRL# 403 dt 25.600000 rms 0.508 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3490 tsec 2.8990 #GCMRL# 404 dt 25.600000 rms 0.507 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3450 tsec 2.8910 #GCMRL# 405 dt 25.600000 rms 0.507 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3350 tsec 2.9000 #GCMRL# 406 dt 25.600000 rms 0.507 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3370 tsec 2.9040 #GCMRL# 407 dt 25.600000 rms 0.506 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3890 tsec 2.9490 #GCMRL# 408 dt 25.600000 rms 0.506 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3540 tsec 2.9240 #GCMRL# 409 dt 25.600000 rms 0.505 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3500 tsec 2.9110 #GCMRL# 410 dt 25.600000 rms 0.505 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3580 tsec 2.9040 #GCMRL# 411 dt 25.600000 rms 0.505 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3960 tsec 2.9540 #GCMRL# 412 dt 25.600000 rms 0.504 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3530 tsec 2.9150 #GCMRL# 413 dt 25.600000 rms 0.504 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3730 tsec 2.9310 #GCMRL# 414 dt 12.800000 rms 0.504 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3420 tsec 3.4240 #GCMRL# 415 dt 3.200000 rms 0.504 -0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3670 tsec 4.1320 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.503586) vs oldopt=(dt=2,rms=0.503587) #GCMRL# 416 dt 2.800000 rms 0.504 0.001% neg 0 invalid 762 tFOTS 6.2510 tGradient 2.3500 tsec 9.1590 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.503576) vs oldopt=(dt=2,rms=0.503577) #GCMRL# 417 dt 2.800000 rms 0.504 0.002% neg 0 invalid 762 tFOTS 6.2320 tGradient 2.3490 tsec 9.1500 #GCAMreg# pass 0 level1 3 level2 1 tsec 450.456 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 0.503939 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.501591) vs oldopt=(dt=32,rms=0.501848) #GCMRL# 419 dt 44.800000 rms 0.502 0.466% neg 0 invalid 762 tFOTS 7.2220 tGradient 2.3210 tsec 10.1160 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.500807) vs oldopt=(dt=32,rms=0.500927) #GCMRL# 420 dt 44.800000 rms 0.501 0.156% neg 0 invalid 762 tFOTS 7.1100 tGradient 2.3390 tsec 10.0140 #GCMRL# 421 dt 32.000000 rms 0.500 0.062% neg 0 invalid 762 tFOTS 7.2060 tGradient 2.3590 tsec 10.1210 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.500114) vs oldopt=(dt=32,rms=0.500116) #GCMRL# 422 dt 25.600000 rms 0.500 0.076% neg 0 invalid 762 tFOTS 7.5630 tGradient 2.4210 tsec 10.5290 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.499986) vs oldopt=(dt=32,rms=0.500023) #GCMRL# 423 dt 19.200000 rms 0.500 0.000% neg 0 invalid 762 tFOTS 7.0320 tGradient 2.3570 tsec 9.9800 #GCMRL# 424 dt 19.200000 rms 0.500 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3700 tsec 2.9280 #GCMRL# 425 dt 19.200000 rms 0.500 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3030 tsec 2.8670 #GCMRL# 426 dt 19.200000 rms 0.499 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3460 tsec 2.9000 #GCMRL# 427 dt 19.200000 rms 0.499 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3450 tsec 2.8920 #GCMRL# 428 dt 19.200000 rms 0.499 0.062% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3560 tsec 2.9240 #GCMRL# 429 dt 19.200000 rms 0.498 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8340 tsec 3.4050 #GCMRL# 430 dt 19.200000 rms 0.498 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3660 tsec 2.9240 #GCMRL# 431 dt 19.200000 rms 0.498 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8590 tsec 3.4210 #GCMRL# 432 dt 19.200000 rms 0.498 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3520 tsec 2.9050 #GCMRL# 433 dt 19.200000 rms 0.497 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7460 tsec 3.3100 #GCMRL# 434 dt 19.200000 rms 0.497 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3530 tsec 2.9020 #GCMRL# 435 dt 19.200000 rms 0.497 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3490 tsec 2.9130 #GCMRL# 436 dt 19.200000 rms 0.496 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3280 tsec 2.8800 #GCMRL# 437 dt 19.200000 rms 0.496 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7760 tsec 3.3500 #GCMRL# 438 dt 19.200000 rms 0.496 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3470 tsec 2.9070 #GCMRL# 439 dt 19.200000 rms 0.495 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2970 tsec 2.8550 #GCMRL# 440 dt 19.200000 rms 0.495 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3490 tsec 2.9140 #GCMRL# 441 dt 19.200000 rms 0.495 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6750 tsec 3.2660 #GCMRL# 442 dt 19.200000 rms 0.494 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3710 tsec 2.9170 #GCMRL# 443 dt 19.200000 rms 0.494 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3320 tsec 2.8880 #GCMRL# 444 dt 19.200000 rms 0.494 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3640 tsec 2.9360 #GCMRL# 445 dt 19.200000 rms 0.493 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3200 tsec 2.8850 #GCMRL# 446 dt 19.200000 rms 0.493 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7000 tsec 3.2650 #GCMRL# 447 dt 19.200000 rms 0.493 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3440 tsec 2.8960 #GCMRL# 448 dt 19.200000 rms 0.493 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3630 tsec 2.9320 #GCMRL# 449 dt 19.200000 rms 0.493 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3970 tsec 2.9660 #GCMRL# 450 dt 19.200000 rms 0.492 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3530 tsec 2.9000 #GCMRL# 451 dt 19.200000 rms 0.492 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3310 tsec 2.8820 #GCMRL# 452 dt 19.200000 rms 0.492 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3360 tsec 2.9030 #GCMRL# 453 dt 19.200000 rms 0.492 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8290 tsec 3.3930 #GCMRL# 454 dt 19.200000 rms 0.492 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3590 tsec 2.9200 #GCMRL# 455 dt 19.200000 rms 0.491 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3670 tsec 2.9200 #GCMRL# 456 dt 19.200000 rms 0.491 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3680 tsec 2.9250 #GCMRL# 457 dt 19.200000 rms 0.491 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3550 tsec 2.9140 #GCMRL# 458 dt 19.200000 rms 0.491 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6900 tsec 3.2500 #GCMRL# 459 dt 19.200000 rms 0.491 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3780 tsec 2.9430 #GCMRL# 460 dt 19.200000 rms 0.490 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3420 tsec 2.9090 #GCMRL# 461 dt 19.200000 rms 0.490 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3550 tsec 2.9000 #GCMRL# 462 dt 19.200000 rms 0.490 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8770 tsec 3.4320 #GCMRL# 463 dt 19.200000 rms 0.490 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3720 tsec 2.9270 #GCMRL# 464 dt 19.200000 rms 0.490 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3450 tsec 2.9030 #GCMRL# 465 dt 19.200000 rms 0.490 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3960 tsec 2.9570 #GCMRL# 466 dt 19.200000 rms 0.490 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4260 tsec 3.1040 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.489644) vs oldopt=(dt=32,rms=0.489647) #GCMRL# 467 dt 19.200000 rms 0.490 0.000% neg 0 invalid 762 tFOTS 7.1480 tGradient 2.8710 tsec 10.6280 #GCMRL# 468 dt 19.200000 rms 0.490 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3820 tsec 2.9400 #GCMRL# 469 dt 19.200000 rms 0.490 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8400 tsec 3.3980 #GCMRL# 470 dt 19.200000 rms 0.490 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3430 tsec 2.9060 #GCMRL# 471 dt 19.200000 rms 0.490 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3850 tsec 2.9420 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 0.516635 #GCMRL# 473 dt 0.000000 rms 0.516 0.070% neg 0 invalid 762 tFOTS 7.1850 tGradient 2.7050 tsec 10.4470 #GCMRL# 474 dt 0.150000 rms 0.516 0.000% neg 0 invalid 762 tFOTS 7.0120 tGradient 2.6940 tsec 10.7500 #GCAMreg# pass 0 level1 2 level2 1 tsec 27.613 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 0.516635 #GCMRL# 476 dt 0.000000 rms 0.516 0.070% neg 0 invalid 762 tFOTS 7.0390 tGradient 2.6890 tsec 10.2790 #GCMRL# 477 dt 0.150000 rms 0.516 0.000% neg 0 invalid 762 tFOTS 7.1600 tGradient 2.6300 tsec 10.8280 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 0.569181 #FOTS# QuadFit found better minimum quadopt=(dt=0.768,rms=0.567251) vs oldopt=(dt=1.28,rms=0.567698) #GCMRL# 479 dt 0.768000 rms 0.567 0.339% neg 0 invalid 762 tFOTS 7.0110 tGradient 2.6590 tsec 10.2170 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.567216) vs oldopt=(dt=0.08,rms=0.567219) #GCMRL# 480 dt 0.112000 rms 0.567 0.000% neg 0 invalid 762 tFOTS 7.1110 tGradient 2.2620 tsec 9.9670 #GCAMreg# pass 0 level1 1 level2 1 tsec 26.098 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 0.56755 #GCMRL# 482 dt 0.320000 rms 0.567 0.092% neg 0 invalid 762 tFOTS 6.9670 tGradient 2.2280 tsec 9.7410 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.567015) vs oldopt=(dt=0.08,rms=0.567016) #GCMRL# 483 dt 0.064000 rms 0.567 0.000% neg 0 invalid 762 tFOTS 6.9970 tGradient 2.2510 tsec 9.8320 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 0.492886 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.478732) vs oldopt=(dt=0.32,rms=0.482493) #GCMRL# 485 dt 0.448000 rms 0.479 2.872% neg 0 invalid 762 tFOTS 6.7210 tGradient 1.4630 tsec 8.7340 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.475878) vs oldopt=(dt=0.32,rms=0.47667) #GCMRL# 486 dt 0.448000 rms 0.476 0.596% neg 0 invalid 762 tFOTS 6.6970 tGradient 1.4680 tsec 8.7200 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.474227) vs oldopt=(dt=0.32,rms=0.474688) #GCMRL# 487 dt 0.448000 rms 0.474 0.347% neg 0 invalid 762 tFOTS 6.6560 tGradient 1.4770 tsec 8.7000 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.473247) vs oldopt=(dt=0.32,rms=0.473524) #GCMRL# 488 dt 0.448000 rms 0.473 0.207% neg 0 invalid 762 tFOTS 6.6900 tGradient 1.5670 tsec 8.8200 #GCMRL# 489 dt 0.320000 rms 0.473 0.115% neg 0 invalid 762 tFOTS 6.6370 tGradient 1.5800 tsec 8.7650 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.472181) vs oldopt=(dt=0.32,rms=0.472265) #GCMRL# 490 dt 0.384000 rms 0.472 0.110% neg 0 invalid 762 tFOTS 6.6330 tGradient 1.5220 tsec 8.7050 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.471759) vs oldopt=(dt=0.32,rms=0.471825) #GCMRL# 491 dt 0.384000 rms 0.472 0.089% neg 0 invalid 762 tFOTS 6.6670 tGradient 1.5690 tsec 8.7970 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.471447) vs oldopt=(dt=0.32,rms=0.471498) #GCMRL# 492 dt 0.384000 rms 0.471 0.066% neg 0 invalid 762 tFOTS 6.6920 tGradient 1.5350 tsec 8.7690 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.471147) vs oldopt=(dt=0.32,rms=0.471191) #GCMRL# 493 dt 0.384000 rms 0.471 0.064% neg 0 invalid 762 tFOTS 6.7300 tGradient 1.5580 tsec 8.8340 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.470921) vs oldopt=(dt=0.32,rms=0.470954) #GCMRL# 494 dt 0.384000 rms 0.471 0.000% neg 0 invalid 762 tFOTS 6.6220 tGradient 1.4520 tsec 8.6760 #GCMRL# 495 dt 0.384000 rms 0.471 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4410 tsec 1.9990 #GCMRL# 496 dt 0.384000 rms 0.470 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4700 tsec 2.0160 #GCMRL# 497 dt 0.384000 rms 0.470 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4640 tsec 2.2590 #GCMRL# 498 dt 0.384000 rms 0.470 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4700 tsec 2.2820 #GCMRL# 499 dt 0.384000 rms 0.470 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4570 tsec 2.0160 #GCMRL# 500 dt 0.384000 rms 0.470 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5000 tsec 2.3510 #GCMRL# 501 dt 0.384000 rms 0.470 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4730 tsec 2.3580 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.46963) vs oldopt=(dt=0.32,rms=0.469636) #GCMRL# 502 dt 0.384000 rms 0.470 0.015% neg 0 invalid 762 tFOTS 6.6790 tGradient 1.5130 tsec 8.7330 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.469562) vs oldopt=(dt=0.32,rms=0.469571) #GCMRL# 503 dt 0.448000 rms 0.470 0.000% neg 0 invalid 762 tFOTS 6.6670 tGradient 1.4870 tsec 8.7370 #GCMRL# 504 dt 0.448000 rms 0.469 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4760 tsec 2.0420 #GCMRL# 505 dt 0.448000 rms 0.469 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4850 tsec 2.0330 #GCMRL# 506 dt 0.224000 rms 0.469 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5060 tsec 2.5330 #GCMRL# 507 dt 0.224000 rms 0.469 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4600 tsec 2.3200 #GCMRL# 508 dt 0.320000 rms 0.469 0.000% neg 0 invalid 762 tFOTS 7.0190 tGradient 1.4930 tsec 9.1190 #GCMRL# 509 dt 0.320000 rms 0.469 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5070 tsec 2.0470 #GCMRL# 510 dt 0.320000 rms 0.469 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5380 tsec 2.0940 #GCMRL# 511 dt 0.320000 rms 0.469 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4830 tsec 2.3030 #GCMRL# 512 dt 0.320000 rms 0.469 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5160 tsec 2.0770 #GCMRL# 513 dt 0.320000 rms 0.469 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5390 tsec 2.1560 #GCMRL# 514 dt 0.320000 rms 0.469 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4870 tsec 2.0360 #GCMRL# 515 dt 0.320000 rms 0.469 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.9950 tsec 2.5450 #GCMRL# 516 dt 0.320000 rms 0.469 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1100 tsec 2.6530 #GCAMreg# pass 0 level1 0 level2 1 tsec 162.033 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 0.469135 #GCMRL# 518 dt 0.320000 rms 0.466 0.753% neg 0 invalid 762 tFOTS 6.7030 tGradient 1.9170 tsec 9.2040 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.465215) vs oldopt=(dt=0.08,rms=0.465328) #GCMRL# 519 dt 0.112000 rms 0.465 0.084% neg 0 invalid 762 tFOTS 6.6930 tGradient 1.9400 tsec 9.2000 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.464881) vs oldopt=(dt=0.08,rms=0.464972) #GCMRL# 520 dt 0.112000 rms 0.465 0.072% neg 0 invalid 762 tFOTS 6.4740 tGradient 1.4880 tsec 8.5200 #GCMRL# 521 dt 0.320000 rms 0.464 0.155% neg 0 invalid 762 tFOTS 6.7050 tGradient 1.5450 tsec 8.7950 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.464073) vs oldopt=(dt=0.08,rms=0.464102) #GCMRL# 522 dt 0.112000 rms 0.464 0.000% neg 0 invalid 762 tFOTS 6.3750 tGradient 1.4780 tsec 8.4490 #GCMRL# 523 dt 0.112000 rms 0.464 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4830 tsec 2.0440 #GCMRL# 524 dt 0.112000 rms 0.464 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4810 tsec 2.0410 #GCMRL# 525 dt 0.112000 rms 0.464 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5200 tsec 2.1140 #GCMRL# 526 dt 0.112000 rms 0.464 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5020 tsec 2.0370 #GCMRL# 527 dt 0.112000 rms 0.463 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4900 tsec 2.0450 #GCMRL# 528 dt 0.112000 rms 0.463 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4870 tsec 2.0880 #GCMRL# 529 dt 0.050000 rms 0.463 0.000% neg 0 invalid 762 tFOTS 5.8860 tGradient 1.4960 tsec 7.9800 GCAMregister done in 41.5529 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 0.461775 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.461314) vs oldopt=(dt=23.12,rms=0.461316) #GCMRL# 531 dt 32.368000 rms 0.461 0.100% neg 0 invalid 762 tFOTS 8.6390 tGradient 2.8560 tsec 12.0570 #GCAMreg# pass 0 level1 5 level2 1 tsec 27.185 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 0.461744 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.461016) vs oldopt=(dt=92.48,rms=0.461055) #GCMRL# 533 dt 129.472000 rms 0.461 0.158% neg 0 invalid 762 tFOTS 8.0980 tGradient 2.8670 tsec 11.5200 #FOTS# QuadFit found better minimum quadopt=(dt=55.488,rms=0.460902) vs oldopt=(dt=92.48,rms=0.460929) #GCMRL# 534 dt 55.488000 rms 0.461 0.000% neg 0 invalid 762 tFOTS 8.4730 tGradient 3.2650 tsec 12.4080 #GCMRL# 535 dt 55.488000 rms 0.461 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9920 tsec 3.6170 #GCMRL# 536 dt 55.488000 rms 0.461 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9670 tsec 3.5790 #GCMRL# 537 dt 55.488000 rms 0.461 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9420 tsec 3.5460 #GCMRL# 538 dt 55.488000 rms 0.461 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8340 tsec 3.3840 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 0.460877 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.460166) vs oldopt=(dt=25.92,rms=0.460188) #GCMRL# 540 dt 36.288000 rms 0.460 0.154% neg 0 invalid 762 tFOTS 9.6850 tGradient 2.6720 tsec 13.0070 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.460078) vs oldopt=(dt=25.92,rms=0.460079) #GCMRL# 541 dt 31.104000 rms 0.460 0.000% neg 0 invalid 762 tFOTS 8.9020 tGradient 2.6630 tsec 12.3180 #GCMRL# 542 dt 31.104000 rms 0.460 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2050 tsec 3.9170 #GCAMreg# pass 0 level1 4 level2 1 tsec 36.153 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 0.460451 #FOTS# QuadFit found better minimum quadopt=(dt=87.8756,rms=0.45856) vs oldopt=(dt=103.68,rms=0.458614) #GCMRL# 544 dt 87.875648 rms 0.459 0.411% neg 0 invalid 762 tFOTS 8.7240 tGradient 2.4360 tsec 11.7520 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.458071) vs oldopt=(dt=25.92,rms=0.458145) #GCMRL# 545 dt 36.288000 rms 0.458 0.000% neg 0 invalid 762 tFOTS 8.5170 tGradient 3.0180 tsec 12.1610 #GCMRL# 546 dt 36.288000 rms 0.458 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4290 tsec 2.9880 #GCMRL# 547 dt 36.288000 rms 0.457 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5520 tsec 3.1830 #GCMRL# 548 dt 36.288000 rms 0.457 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5820 tsec 3.1490 #GCMRL# 549 dt 36.288000 rms 0.456 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4920 tsec 3.0460 #GCMRL# 550 dt 36.288000 rms 0.456 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.5410 tsec 3.1140 #GCMRL# 551 dt 36.288000 rms 0.455 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7430 tsec 3.3170 #GCMRL# 552 dt 36.288000 rms 0.455 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6100 tsec 3.2050 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.454788) vs oldopt=(dt=103.68,rms=0.454821) 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 0.455445 #GCMRL# 554 dt 32.000000 rms 0.454 0.413% neg 0 invalid 762 tFOTS 9.3200 tGradient 2.3120 tsec 12.2120 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.452607) vs oldopt=(dt=32,rms=0.452665) #GCMRL# 555 dt 44.800000 rms 0.453 0.000% neg 0 invalid 762 tFOTS 8.5350 tGradient 2.2860 tsec 11.4140 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 556 dt 44.800000 rms 0.453 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2850 tsec 6.0130 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 557 dt 44.800000 rms 0.451 0.387% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2890 tsec 6.5420 iter 0, gcam->neg = 3 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 558 dt 44.800000 rms 0.451 -0.273% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2000 tsec 11.3570 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.4503) vs oldopt=(dt=8,rms=0.450349) #GCMRL# 559 dt 11.200000 rms 0.450 0.053% neg 0 invalid 762 tFOTS 8.5930 tGradient 2.2280 tsec 11.3850 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.449845) vs oldopt=(dt=32,rms=0.449922) #GCMRL# 560 dt 44.800000 rms 0.450 0.101% neg 0 invalid 762 tFOTS 8.1290 tGradient 2.2530 tsec 10.9370 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.449539) vs oldopt=(dt=32,rms=0.449558) #GCAMreg# pass 0 level1 3 level2 1 tsec 83.741 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 0.450115 #FOTS# QuadFit found better minimum quadopt=(dt=48.0627,rms=0.44546) vs oldopt=(dt=32,rms=0.445822) #GCMRL# 562 dt 48.062745 rms 0.445 1.034% neg 0 invalid 762 tFOTS 8.4190 tGradient 2.2120 tsec 11.1810 #FOTS# QuadFit found better minimum quadopt=(dt=22.6866,rms=0.44383) vs oldopt=(dt=32,rms=0.444169) #GCMRL# 563 dt 22.686567 rms 0.444 0.366% neg 0 invalid 762 tFOTS 8.4660 tGradient 2.2210 tsec 11.2300 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.442842) vs oldopt=(dt=32,rms=0.442855) #GCMRL# 564 dt 25.600000 rms 0.443 0.000% neg 0 invalid 762 tFOTS 8.4450 tGradient 2.1730 tsec 11.2020 #GCMRL# 565 dt 25.600000 rms 0.442 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1950 tsec 2.7500 #GCMRL# 566 dt 25.600000 rms 0.441 0.265% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1910 tsec 2.7480 #GCMRL# 567 dt 25.600000 rms 0.441 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1740 tsec 2.7310 #GCMRL# 568 dt 25.600000 rms 0.440 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2640 tsec 2.8140 #GCMRL# 569 dt 25.600000 rms 0.440 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2010 tsec 2.7510 #GCMRL# 570 dt 25.600000 rms 0.438 0.242% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2410 tsec 2.7930 #GCMRL# 571 dt 25.600000 rms 0.438 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2080 tsec 2.7500 #GCMRL# 572 dt 25.600000 rms 0.437 0.226% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3010 tsec 2.8520 #GCMRL# 573 dt 25.600000 rms 0.437 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2420 tsec 2.7900 #GCMRL# 574 dt 25.600000 rms 0.436 0.223% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2350 tsec 2.7860 #GCMRL# 575 dt 25.600000 rms 0.435 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1810 tsec 2.7440 #GCMRL# 576 dt 25.600000 rms 0.435 0.149% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2860 tsec 2.8400 #GCMRL# 577 dt 25.600000 rms 0.434 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2020 tsec 2.7490 #GCMRL# 578 dt 25.600000 rms 0.434 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3030 tsec 2.8440 #GCMRL# 579 dt 25.600000 rms 0.433 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3190 tsec 2.9150 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.433036) vs oldopt=(dt=8,rms=0.433084) #GCMRL# 580 dt 11.200000 rms 0.433 0.000% neg 0 invalid 762 tFOTS 8.3220 tGradient 2.2260 tsec 11.1470 #GCMRL# 581 dt 11.200000 rms 0.433 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2220 tsec 2.7750 #GCMRL# 582 dt 11.200000 rms 0.433 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1820 tsec 2.7370 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 0.437287 #GCMRL# 584 dt 0.000000 rms 0.437 0.100% neg 0 invalid 762 tFOTS 8.0810 tGradient 2.1980 tsec 10.8420 #GCAMreg# pass 0 level1 2 level2 1 tsec 24.851 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 0.437287 #FOTS# QuadFit found better minimum quadopt=(dt=0.432,rms=0.436849) vs oldopt=(dt=0.72,rms=0.43685) #GCMRL# 586 dt 0.432000 rms 0.437 0.100% neg 0 invalid 762 tFOTS 8.5110 tGradient 2.1810 tsec 11.2580 #FOTS# QuadFit found better minimum quadopt=(dt=0.25,rms=0.436839) vs oldopt=(dt=0.18,rms=0.436839) #GCMRL# 587 dt 0.250000 rms 0.437 0.000% neg 0 invalid 762 tFOTS 8.5130 tGradient 2.2330 tsec 11.3440 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 0.445457 #FOTS# QuadFit found better minimum quadopt=(dt=1.024,rms=0.44434) vs oldopt=(dt=1.28,rms=0.444371) #GCMRL# 589 dt 1.024000 rms 0.444 0.251% neg 0 invalid 762 tFOTS 8.5010 tGradient 2.1890 tsec 11.2400 #GCMRL# 590 dt 0.320000 rms 0.444 0.000% neg 0 invalid 762 tFOTS 8.4940 tGradient 2.1240 tsec 11.2180 #GCAMreg# pass 0 level1 1 level2 1 tsec 28.356 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 0.444725 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.443482) vs oldopt=(dt=1.28,rms=0.443519) #GCMRL# 592 dt 1.536000 rms 0.443 0.280% neg 0 invalid 762 tFOTS 8.5640 tGradient 2.1660 tsec 11.2710 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.443428) vs oldopt=(dt=0.32,rms=0.44344) #GCMRL# 593 dt 0.448000 rms 0.443 0.000% neg 0 invalid 762 tFOTS 8.5240 tGradient 2.0550 tsec 11.1790 #GCMRL# 594 dt 0.448000 rms 0.443 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0610 tsec 2.6240 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 0.437009 #FOTS# QuadFit found better minimum quadopt=(dt=2.29445,rms=0.405296) vs oldopt=(dt=1.28,rms=0.411477) iter 0, gcam->neg = 610 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 596 dt 2.294448 rms 0.409 6.328% neg 0 invalid 762 tFOTS 8.4790 tGradient 1.3690 tsec 21.3530 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.408946) vs oldopt=(dt=0.08,rms=0.408972) #GCMRL# 597 dt 0.112000 rms 0.409 0.000% neg 0 invalid 762 tFOTS 8.5740 tGradient 1.4900 tsec 10.6540 #GCAMreg# pass 0 level1 0 level2 1 tsec 37.178 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 0.409454 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.4088) vs oldopt=(dt=0.08,rms=0.408801) #GCMRL# 599 dt 0.064000 rms 0.409 0.160% neg 0 invalid 762 tFOTS 8.5140 tGradient 1.4600 tsec 10.5430 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.408781) vs oldopt=(dt=0.005,rms=0.408781) #GCMRL# 600 dt 0.007000 rms 0.409 0.000% neg 0 invalid 762 tFOTS 8.4450 tGradient 1.4690 tsec 10.5010 label assignment complete, 0 changed (0.00%) GCAMregister done in 8.69048 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 0.395118 #GCAMreg# pass 0 level1 5 level2 1 tsec 13.171 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 0.395118 #FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.395117) vs oldopt=(dt=5.78,rms=0.395117) #GCMRL# 603 dt 8.092000 rms 0.395 0.000% neg 0 invalid 762 tFOTS 7.8080 tGradient 2.0230 tsec 10.3680 #FOTS# QuadFit found better minimum quadopt=(dt=4.624,rms=0.395117) vs oldopt=(dt=5.78,rms=0.395117) #GCMRL# 604 dt 4.624000 rms 0.395 0.000% neg 0 invalid 762 tFOTS 8.0060 tGradient 2.0350 tsec 10.6160 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 0.395283 #GCAMreg# pass 0 level1 4 level2 1 tsec 13.006 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 0.395283 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.395199) vs oldopt=(dt=25.92,rms=0.39521) #GCMRL# 607 dt 36.288000 rms 0.395 0.021% neg 0 invalid 762 tFOTS 8.0660 tGradient 1.6870 tsec 10.2810 #GCMRL# 608 dt 103.680000 rms 0.395 0.025% neg 0 invalid 762 tFOTS 7.4850 tGradient 1.7020 tsec 9.7070 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.394829) vs oldopt=(dt=414.72,rms=0.394909) #GCMRL# 609 dt 248.832000 rms 0.395 0.069% neg 0 invalid 762 tFOTS 7.5860 tGradient 1.6940 tsec 9.8070 #FOTS# QuadFit found better minimum quadopt=(dt=20.736,rms=0.394816) vs oldopt=(dt=25.92,rms=0.394818) #GCMRL# 610 dt 20.736000 rms 0.395 0.000% neg 0 invalid 762 tFOTS 7.9800 tGradient 1.6820 tsec 10.2250 #GCMRL# 611 dt 20.736000 rms 0.395 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6900 tsec 2.2140 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 0.395454 #GCMRL# 613 dt 8.000000 rms 0.395 0.026% neg 0 invalid 762 tFOTS 7.8630 tGradient 1.5400 tsec 9.9230 #FOTS# QuadFit found better minimum quadopt=(dt=1.6,rms=0.395347) vs oldopt=(dt=2,rms=0.395347) #GCMRL# 614 dt 1.600000 rms 0.395 0.000% neg 0 invalid 762 tFOTS 7.7970 tGradient 1.5330 tsec 9.8910 #GCAMreg# pass 0 level1 3 level2 1 tsec 24.885 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 0.395347 #FOTS# QuadFit found better minimum quadopt=(dt=102.4,rms=0.392825) vs oldopt=(dt=128,rms=0.392965) #GCMRL# 616 dt 102.400000 rms 0.393 0.638% neg 0 invalid 762 tFOTS 7.7910 tGradient 1.5520 tsec 9.8620 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.392052) vs oldopt=(dt=32,rms=0.39208) #GCMRL# 617 dt 25.600000 rms 0.392 0.000% neg 0 invalid 762 tFOTS 8.0120 tGradient 1.5190 tsec 10.0970 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 618 dt 25.600000 rms 0.392 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5160 tsec 3.4740 #GCMRL# 619 dt 25.600000 rms 0.391 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5290 tsec 2.0660 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 620 dt 25.600000 rms 0.391 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5240 tsec 7.3990 iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 621 dt 25.600000 rms 0.391 0.111% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5280 tsec 7.9650 #GCMRL# 622 dt 25.600000 rms 0.390 0.164% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5330 tsec 2.0780 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 623 dt 25.600000 rms 0.389 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5620 tsec 6.2990 #GCMRL# 624 dt 25.600000 rms 0.389 0.127% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5480 tsec 2.0620 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 625 dt 25.600000 rms 0.389 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5400 tsec 3.4980 #GCMRL# 626 dt 25.600000 rms 0.388 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5770 tsec 2.1390 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.388106) vs oldopt=(dt=32,rms=0.388109) iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 627 dt 38.400000 rms 0.388 0.000% neg 0 invalid 762 tFOTS 7.7360 tGradient 1.5290 tsec 13.4890 #GCMRL# 628 dt 38.400000 rms 0.388 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5390 tsec 2.0600 #GCMRL# 629 dt 38.400000 rms 0.388 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5500 tsec 2.0840 #GCMRL# 630 dt 38.400000 rms 0.388 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5640 tsec 2.0950 #GCMRL# 631 dt 38.400000 rms 0.388 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5600 tsec 2.1000 #GCMRL# 632 dt 38.400000 rms 0.388 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5410 tsec 2.0840 #GCMRL# 633 dt 38.400000 rms 0.388 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5430 tsec 2.0700 #GCMRL# 634 dt 38.400000 rms 0.388 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5430 tsec 2.0700 #GCMRL# 635 dt 38.400000 rms 0.387 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5540 tsec 2.0790 #GCMRL# 636 dt 38.400000 rms 0.387 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5190 tsec 2.0560 #GCMRL# 637 dt 38.400000 rms 0.387 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.5440 tsec 2.0630 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 0.390249 #GCAMreg# pass 0 level1 2 level2 1 tsec 12.434 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 0.390249 #FOTS# QuadFit found better minimum quadopt=(dt=2.5,rms=0.390223) vs oldopt=(dt=2.88,rms=0.390223) #GCMRL# 640 dt 2.500000 rms 0.390 0.007% neg 0 invalid 762 tFOTS 7.8100 tGradient 1.4610 tsec 9.7880 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.390215) vs oldopt=(dt=0.72,rms=0.390217) #GCMRL# 641 dt 1.008000 rms 0.390 0.000% neg 0 invalid 762 tFOTS 7.4940 tGradient 1.4790 tsec 9.5550 #GCMRL# 642 dt 1.008000 rms 0.390 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.4700 tsec 2.0030 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 0.397142 #GCAMreg# pass 0 level1 1 level2 1 tsec 12.675 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 0.397142 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 0.385521 #FOTS# QuadFit found better minimum quadopt=(dt=1.28334,rms=0.375348) vs oldopt=(dt=1.28,rms=0.37535) iter 0, gcam->neg = 562 after 18 iterations, nbhd size=1, neg = 0 #GCMRL# 646 dt 1.283342 rms 0.378 1.894% neg 0 invalid 762 tFOTS 7.9210 tGradient 0.7060 tsec 20.6380 #FOTS# QuadFit found better minimum quadopt=(dt=2.34375e-05,rms=0.378219) vs oldopt=(dt=1.95313e-05,rms=0.378219) #GCMRL# 647 dt 0.000023 rms 0.378 0.000% neg 0 invalid 762 tFOTS 10.0530 tGradient 0.7250 tsec 11.3570 #GCAMreg# pass 0 level1 0 level2 1 tsec 36.26 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 0.378219 #FOTS# QuadFit found better minimum quadopt=(dt=0.096,rms=0.378015) vs oldopt=(dt=0.08,rms=0.378023) #GCMRL# 649 dt 0.096000 rms 0.378 0.054% neg 0 invalid 762 tFOTS 7.8260 tGradient 0.7310 tsec 9.0820 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.377966) vs oldopt=(dt=0.08,rms=0.377969) #GCMRL# 650 dt 0.064000 rms 0.378 0.000% neg 0 invalid 762 tFOTS 7.8160 tGradient 0.7150 tsec 9.0930 #GCMRL# 651 dt 0.064000 rms 0.378 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 0.6950 tsec 1.2180 GCAMregister done in 5.68243 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4871 tmin = 7.77988 Calls to gcamLabelEnergy 4359 tmin = 1.95425 Calls to gcamJacobianEnergy 4871 tmin = 3.79005 Calls to gcamSmoothnessEnergy 4871 tmin = 9.00287 Calls to gcamLogLikelihoodTerm 653 tmin = 1.68877 Calls to gcamLabelTerm 602 tmin = 9.41967 Calls to gcamJacobianTerm 653 tmin = 3.15327 Calls to gcamSmoothnessTerm 653 tmin = 1.03332 Calls to gcamComputeGradient 653 tmin = 28.204 Calls to gcamComputeMetricProperties 6627 tmin = 6.70877 mri_ca_register took 1 hours, 13 minutes and 52 seconds. #VMPC# mri_ca_register VmPeak 2308956 FSRUNTIME@ mri_ca_register 1.2310 hours 4 threads @#@FSTIME 2024:11:20:21:16:54 mri_ca_register N 9 e 4431.62 S 15.91 U 10935.50 P 247% M 1335236 F 1 R 20538088 W 0 c 986975 w 70200 I 0 O 63048 L 30.04 26.29 22.47 @#@FSLOADPOST 2024:11:20:22:30:46 mri_ca_register N 9 8.53 9.65 11.34 #-------------------------------------- #@# SubCort Seg Wed Nov 20 22:30:46 CST 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/PIB15-273_VYr9_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 5.70 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 = 0.13091 (23) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2450 voxels, overlap=0.888) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2450 voxels, peak = 20), gca=20.5 gca peak = 0.20380 (13) mri peak = 0.14212 (23) Right_Lateral_Ventricle (43): linear fit = 1.26 x + 0.0 (4355 voxels, overlap=0.456) Right_Lateral_Ventricle (43): linear fit = 1.26 x + 0.0 (4355 voxels, peak = 16), gca=16.4 gca peak = 0.26283 (96) mri peak = 0.10348 (92) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (481 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (481 voxels, peak = 93), gca=92.6 gca peak = 0.15814 (97) mri peak = 0.09256 (96) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (498 voxels, overlap=1.010) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (498 voxels, peak = 96), gca=95.5 gca peak = 0.27624 (56) mri peak = 0.11173 (67) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (893 voxels, overlap=0.017) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (893 voxels, peak = 65), gca=64.7 gca peak = 0.28723 (59) mri peak = 0.10489 (69) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (688 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (688 voxels, peak = 70), gca=69.9 gca peak = 0.07623 (103) mri peak = 0.13539 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (26675 voxels, overlap=0.618) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (26675 voxels, peak = 106), gca=105.6 gca peak = 0.07837 (105) mri peak = 0.13502 (108) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (29824 voxels, overlap=0.525) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (29824 voxels, peak = 109), gca=108.7 gca peak = 0.10165 (58) mri peak = 0.04123 (65) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (17180 voxels, overlap=0.449) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (17180 voxels, peak = 69), gca=68.7 gca peak = 0.11113 (58) mri peak = 0.04425 (75) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (16903 voxels, overlap=0.252) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (16903 voxels, peak = 69), gca=69.3 gca peak = 0.27796 (67) mri peak = 0.14482 (78) Right_Caudate (50): linear fit = 1.14 x + 0.0 (760 voxels, overlap=0.016) Right_Caudate (50): linear fit = 1.14 x + 0.0 (760 voxels, peak = 77), gca=76.7 gca peak = 0.14473 (69) mri peak = 0.11728 (78) Left_Caudate (11): linear fit = 1.07 x + 0.0 (800 voxels, overlap=0.573) Left_Caudate (11): linear fit = 1.07 x + 0.0 (800 voxels, peak = 73), gca=73.5 gca peak = 0.14301 (56) mri peak = 0.06095 (65) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (18270 voxels, overlap=0.641) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (18270 voxels, peak = 65), gca=64.7 gca peak = 0.14610 (55) mri peak = 0.06639 (65) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (19248 voxels, overlap=0.358) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (19248 voxels, peak = 64), gca=63.5 gca peak = 0.16309 (85) mri peak = 0.12912 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (5124 voxels, overlap=0.744) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (5124 voxels, peak = 88), gca=88.0 gca peak = 0.15172 (84) mri peak = 0.13317 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4900 voxels, overlap=0.761) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4900 voxels, peak = 87), gca=86.9 gca peak = 0.30461 (58) mri peak = 0.10998 (72) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (389 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (389 voxels, peak = 69), gca=69.3 gca peak = 0.32293 (57) mri peak = 0.11096 (71) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (333 voxels, overlap=0.047) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (333 voxels, peak = 70), gca=70.4 gca peak = 0.11083 (90) mri peak = 0.08245 (88) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (3514 voxels, overlap=0.917) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (3514 voxels, peak = 91), gca=91.3 gca peak = 0.11393 (83) mri peak = 0.08744 (87) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3600 voxels, overlap=0.922) Right_Thalamus (49): linear fit = 1.03 x + 0.0 (3600 voxels, peak = 86), gca=85.9 gca peak = 0.08575 (81) mri peak = 0.09449 (90) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1397 voxels, overlap=0.424) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1397 voxels, peak = 89), gca=88.7 gca peak = 0.08618 (78) mri peak = 0.10552 (87) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1428 voxels, overlap=0.638) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1428 voxels, peak = 84), gca=83.9 gca peak = 0.08005 (78) mri peak = 0.09950 (85) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11468 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11468 voxels, peak = 83), gca=83.1 gca peak = 0.12854 (88) mri peak = 0.07948 (92) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1132 voxels, overlap=0.682) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1132 voxels, peak = 94), gca=93.7 gca peak = 0.15703 (87) mri peak = 0.09150 (92) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1132 voxels, overlap=0.782) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1132 voxels, peak = 94), gca=93.5 gca peak = 0.17522 (25) mri peak = 0.22222 (22) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (108 voxels, overlap=0.919) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (108 voxels, peak = 21), gca=20.6 gca peak = 0.17113 (14) mri peak = 0.16465 (21) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (97 voxels, overlap=0.484) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (97 voxels, peak = 18), gca=17.9 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 1.19 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.10 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16757 (19) mri peak = 0.13091 (23) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (2450 voxels, overlap=0.854) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (2450 voxels, peak = 18), gca=17.8 gca peak = 0.17681 (16) mri peak = 0.14212 (23) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (4355 voxels, overlap=0.654) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (4355 voxels, peak = 18), gca=17.5 gca peak = 0.23675 (91) mri peak = 0.10348 (92) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (481 voxels, overlap=1.010) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (481 voxels, peak = 91), gca=90.5 gca peak = 0.18120 (95) mri peak = 0.09256 (96) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (498 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (498 voxels, peak = 96), gca=96.4 gca peak = 0.24329 (64) mri peak = 0.11173 (67) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (893 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (893 voxels, peak = 65), gca=65.0 gca peak = 0.33055 (67) mri peak = 0.10489 (69) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (688 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (688 voxels, peak = 68), gca=68.0 gca peak = 0.07763 (106) mri peak = 0.13539 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26675 voxels, overlap=0.695) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26675 voxels, peak = 106), gca=106.0 gca peak = 0.07610 (108) mri peak = 0.13502 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29824 voxels, overlap=0.681) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29824 voxels, peak = 107), gca=107.5 gca peak = 0.08573 (69) mri peak = 0.04123 (65) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17180 voxels, overlap=0.974) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17180 voxels, peak = 68), gca=68.0 gca peak = 0.09479 (70) mri peak = 0.04425 (75) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (16903 voxels, overlap=0.957) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (16903 voxels, peak = 72), gca=72.4 gca peak = 0.21882 (76) mri peak = 0.14482 (78) Right_Caudate (50): linear fit = 1.00 x + 0.0 (760 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (760 voxels, peak = 76), gca=76.0 gca peak = 0.12153 (73) mri peak = 0.11728 (78) Left_Caudate (11): linear fit = 1.00 x + 0.0 (800 voxels, overlap=0.959) Left_Caudate (11): linear fit = 1.00 x + 0.0 (800 voxels, peak = 73), gca=73.0 gca peak = 0.11930 (65) mri peak = 0.06095 (65) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (18270 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (18270 voxels, peak = 64), gca=64.0 gca peak = 0.13445 (64) mri peak = 0.06639 (65) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (19248 voxels, overlap=0.972) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (19248 voxels, peak = 64), gca=64.0 gca peak = 0.16129 (88) mri peak = 0.12912 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5124 voxels, overlap=0.901) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5124 voxels, peak = 88), gca=88.0 gca peak = 0.14603 (87) mri peak = 0.13317 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4900 voxels, overlap=0.908) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4900 voxels, peak = 87), gca=87.0 gca peak = 0.29204 (69) mri peak = 0.10998 (72) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (389 voxels, overlap=1.019) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (389 voxels, peak = 69), gca=69.0 gca peak = 0.30121 (71) mri peak = 0.11096 (71) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (333 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (333 voxels, peak = 70), gca=69.9 gca peak = 0.11272 (90) mri peak = 0.08245 (88) Left_Thalamus (10): linear fit = 0.99 x + 0.0 (3514 voxels, overlap=0.951) Left_Thalamus (10): linear fit = 0.99 x + 0.0 (3514 voxels, peak = 89), gca=88.7 gca peak = 0.10629 (86) mri peak = 0.08744 (87) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3600 voxels, overlap=0.969) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3600 voxels, peak = 86), gca=85.6 gca peak = 0.07543 (85) mri peak = 0.09449 (90) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1397 voxels, overlap=0.853) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1397 voxels, peak = 85), gca=84.6 gca peak = 0.08572 (83) mri peak = 0.10552 (87) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1428 voxels, overlap=0.910) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1428 voxels, peak = 83), gca=83.0 gca peak = 0.07396 (86) mri peak = 0.09950 (85) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11468 voxels, overlap=0.738) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11468 voxels, peak = 86), gca=85.6 gca peak = 0.12327 (95) mri peak = 0.07948 (92) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1132 voxels, overlap=0.824) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1132 voxels, peak = 96), gca=96.4 gca peak = 0.14478 (92) mri peak = 0.09150 (92) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1132 voxels, overlap=0.932) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1132 voxels, peak = 91), gca=90.6 gca peak = 0.21075 (21) mri peak = 0.22222 (22) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (108 voxels, overlap=1.005) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (108 voxels, peak = 21), gca=21.0 gca peak = 0.14790 (19) mri peak = 0.16465 (21) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (97 voxels, overlap=0.732) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (97 voxels, peak = 19), gca=18.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.15385 (33) gca peak CSF = 0.19204 (34) gca peak Left_Accumbens_area = 0.49340 (66) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.11538 (35) gca peak Right_Inf_Lat_Vent = 0.24870 (27) gca peak Right_Accumbens_area = 0.30899 (74) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (36) gca peak WM_hypointensities = 0.10282 (79) gca peak non_WM_hypointensities = 0.14635 (42) gca peak Optic_Chiasm = 0.51667 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 45741 voxels changed in iteration 0 of unlikely voxel relabeling 178 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 35310 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels) 297 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 54793 changed. image ll: -2.075, PF=0.500 pass 2: 13158 changed. image ll: -2.075, PF=0.500 pass 3: 3534 changed. 31739 voxels changed in iteration 0 of unlikely voxel relabeling 153 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6163 voxels changed in iteration 0 of unlikely voxel relabeling 80 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4972 voxels changed in iteration 0 of unlikely voxel relabeling 42 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 3676 voxels changed in iteration 0 of unlikely voxel relabeling 17 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 8647 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 156 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 12674 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 109 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 206 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2057.048477 mri_ca_label stimesec 5.781629 mri_ca_label ru_maxrss 2164404 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 6812254 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63040 mri_ca_label ru_oublock 632 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 530 mri_ca_label ru_nivcsw 181773 auto-labeling took 33 minutes and 27 seconds. @#@FSTIME 2024:11:20:22:30:46 mri_ca_label N 10 e 2006.77 S 5.90 U 2057.04 P 102% M 2164404 F 0 R 6812271 W 0 c 181785 w 531 I 63040 O 632 L 8.53 9.65 11.34 @#@FSLOADPOST 2024:11:20:23:04:13 mri_ca_label N 10 6.96 7.33 7.75 #-------------------------------------- #@# CC Seg Wed Nov 20 23:04:13 CST 2024 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/transforms/cc_up.lta PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/transforms/cc_up.lta reading aseg from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.auto_noCCseg.mgz reading norm from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/norm.mgz 33838 voxels in left wm, 53472 in right wm, xrange [121, 134] searching rotation angles z=[-10 4], y=[-11 3] searching scale 1 Z rot -10.2 searching scale 1 Z rot -10.0 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 global minimum found at slice 128.0, rotations (-3.90, -3.24) final transformation (x=128.0, yr=-3.899, zr=-3.237): 0.99609 0.05646 -0.06789 2.22078; -0.05633 0.99840 0.00384 19.92955; 0.06799 0.00000 0.99769 -1.42319; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 min_x_fornix = 123 min_x_fornix = 126 min_x_fornix = 127 min_x_fornix = 129 min_x_fornix = 130 cc center is found at 128 115 121 eigenvectors: -0.00721 -0.01730 0.99982; 0.01819 -0.99969 -0.01716; 0.99981 0.01806 0.00752; error in mid anterior detected - correcting... writing aseg with callosum to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #VMPC# mri_cc VmPeak 461924 mri_cc done @#@FSTIME 2024:11:20:23:04:13 mri_cc N 7 e 40.53 S 0.53 U 41.10 P 102% M 344908 F 0 R 472824 W 0 c 3662 w 82 I 0 O 616 L 6.96 7.33 7.75 @#@FSLOADPOST 2024:11:20:23:04:54 mri_cc N 7 6.99 7.30 7.72 #-------------------------------------- #@# Merge ASeg Wed Nov 20 23:04:54 CST 2024 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Nov 20 23:04:54 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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... 299 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 110 gm peak at 74 (74), valley at 46 (46) csf peak at 22, setting threshold to 56 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 77 (77), valley at 36 (36) csf peak at 23, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 17 seconds. @#@FSTIME 2024:11:20:23:04:54 mri_normalize N 9 e 138.26 S 1.62 U 150.08 P 109% M 1209420 F 0 R 1170017 W 0 c 13606 w 128 I 0 O 2400 L 6.99 7.30 7.72 @#@FSLOADPOST 2024:11:20:23:07:12 mri_normalize N 9 7.54 7.39 7.70 #-------------------------------------------- #@# Mask BFS Wed Nov 20 23:07:12 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1400195 voxels in mask (pct= 8.35) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:11:20:23:07:12 mri_mask N 5 e 0.88 S 0.03 U 1.29 P 149% M 74508 F 0 R 17273 W 0 c 123 w 93 I 0 O 2344 L 7.54 7.39 7.70 @#@FSLOADPOST 2024:11:20:23:07:13 mri_mask N 5 7.54 7.39 7.70 #-------------------------------------------- #@# WM Segmentation Wed Nov 20 23:07:13 CST 2024 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2024:11:20:23:07:13 AntsDenoiseImageFs N 4 e 37.47 S 0.27 U 37.44 P 100% M 351312 F 0 R 222571 W 0 c 3320 w 84 I 0 O 2392 L 7.54 7.39 7.70 @#@FSLOADPOST 2024:11:20:23:07:50 AntsDenoiseImageFs N 4 7.48 7.39 7.69 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): 100.8 +- 6.4 [79.0 --> 125.0] CCS GM (75.0) : 73.5 +- 11.0 [30.0 --> 95.0] white_mean 100.802 white_sigma 6.42253 gray_mean 73.4616 gray_sigma 10.9563 setting bottom of white matter range wm_low to 84.4 setting top of gray matter range gray_hi to 95.4 wm_low 84.418 wm_hi 125 gray_low 30 gray_hi 95.3743 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 84.418 wm_hi 125 gray_low 30 gray_hi 95.3743 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 95.3743, wm_low = 84.418 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=95.3743, wmlow=84.418 109779 voxels processed (0.65%) 51233 voxels white (0.31%) 58546 voxels non-white (0.35%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=79.418, gray_hi=95.3743, wsize=13 218789 voxels tested (1.30%) 41210 voxels changed (0.25%) 39355 multi-scale searches (0.23%) Recovering bright white MRIrecoverBrightWhite() wm_low 84.418 wm_hi 125 slack 6.42253 pct_thresh 0.33 intensity_thresh 131.423 nvox_thresh 8.58 79 voxels tested (0.00%) 62 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=79.418, hithr=95.3743 smoothing input volume with sigma = 0.250 90498 voxels tested (0.54%) 14183 voxels changed (0.08%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 1745 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1156 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 4236 filled MRIfindBrightNonWM(): 84 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.2 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:11:20:23:07:51 mri_segment N 5 e 70.08 S 0.31 U 70.58 P 101% M 146604 F 0 R 276661 W 0 c 6180 w 63 I 0 O 736 L 7.48 7.39 7.69 @#@FSLOADPOST 2024:11:20:23:09:01 mri_segment N 5 7.02 7.28 7.62 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 0.56 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2958 additional wm voxels added 0 additional wm voxels added SEG EDIT: 52077 voxels turned on, 31894 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:11:20:23:09:01 mri_edit_wm_with_aseg N 5 e 33.55 S 0.46 U 34.94 P 105% M 464320 F 0 R 456217 W 0 c 3136 w 141 I 0 O 680 L 7.02 7.28 7.62 @#@FSLOADPOST 2024:11:20:23:09:34 mri_edit_wm_with_aseg N 5 7.13 7.28 7.62 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 8 found - 8 modified | TOTAL: 8 pass 2 (xy+): 0 found - 8 modified | TOTAL: 8 pass 1 (xy-): 7 found - 7 modified | TOTAL: 15 pass 2 (xy-): 0 found - 7 modified | TOTAL: 15 pass 1 (yz+): 9 found - 9 modified | TOTAL: 24 pass 2 (yz+): 0 found - 9 modified | TOTAL: 24 pass 1 (yz-): 15 found - 15 modified | TOTAL: 39 pass 2 (yz-): 0 found - 15 modified | TOTAL: 39 pass 1 (xz+): 12 found - 12 modified | TOTAL: 51 pass 2 (xz+): 0 found - 12 modified | TOTAL: 51 pass 1 (xz-): 5 found - 5 modified | TOTAL: 56 pass 2 (xz-): 0 found - 5 modified | TOTAL: 56 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 5 found - 5 modified | TOTAL: 7 pass 2 (+++): 0 found - 5 modified | TOTAL: 7 pass 1 (+++): 4 found - 4 modified | TOTAL: 11 pass 2 (+++): 0 found - 4 modified | TOTAL: 11 pass 1 (+++): 8 found - 8 modified | TOTAL: 19 pass 2 (+++): 0 found - 8 modified | TOTAL: 19 Iteration Number : 1 pass 1 (++): 53 found - 53 modified | TOTAL: 53 pass 2 (++): 0 found - 53 modified | TOTAL: 53 pass 1 (+-): 22 found - 22 modified | TOTAL: 75 pass 2 (+-): 0 found - 22 modified | TOTAL: 75 pass 1 (--): 25 found - 25 modified | TOTAL: 100 pass 2 (--): 0 found - 25 modified | TOTAL: 100 pass 1 (-+): 18 found - 18 modified | TOTAL: 118 pass 2 (-+): 0 found - 18 modified | TOTAL: 118 Iteration Number : 2 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-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 3 found - 3 modified | TOTAL: 5 pass 2 (xz+): 0 found - 3 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 (++): 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-): 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 : 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 = 199 (out of 466883: 0.042623) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:20:23:09:34 mri_pretess N 4 e 3.89 S 0.04 U 4.27 P 110% M 57176 F 0 R 21520 W 0 c 395 w 60 I 0 O 680 L 7.13 7.28 7.62 @#@FSLOADPOST 2024:11:20:23:09:38 mri_pretess N 4 7.28 7.31 7.62 #-------------------------------------------- #@# Fill Wed Nov 20 23:09:38 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 1.10637 0.02814 -0.07074 -10.19952; -0.02003 1.19165 0.16130 -48.49336; 0.10446 -0.09728 1.04482 -24.91402; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.10637 0.02814 -0.07074 -10.19952; -0.02003 1.19165 0.16130 -48.49336; 0.10446 -0.09728 1.04482 -24.91402; 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] = 1304 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (126, 120, 155), TAL = (2.0, 27.0, 8.0) talairach voxel to voxel transform 0.89760 -0.01603 0.06325 9.95338; 0.02689 0.82825 -0.12605 37.29858; -0.08724 0.07872 0.93904 26.32262; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 120, 155) --> (2.0, 27.0, 8.0) done. filling took 1.1 minutes talairach cc position changed to (2.00, 27.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 27.00, 8.00) SRC: (114.77, 120.06, 171.90) search lh wm seed point around talairach space (-16.00, 27.00, 8.00), SRC: (147.09, 121.02, 168.76) 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 2024:11:20:23:09:38 mri_fill N 10 e 67.15 S 1.43 U 66.60 P 101% M 968764 F 0 R 1008019 W 0 c 6126 w 44 I 0 O 232 L 7.28 7.31 7.62 @#@FSLOADPOST 2024:11:20:23:10:45 mri_fill N 10 7.07 7.22 7.57 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Wed Nov 20 23:10:45 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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+): 5 found - 5 modified | TOTAL: 8 pass 2 (yz+): 0 found - 5 modified | TOTAL: 8 pass 1 (yz-): 3 found - 3 modified | TOTAL: 11 pass 2 (yz-): 0 found - 3 modified | TOTAL: 11 pass 1 (xz+): 0 found - 0 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 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 = 11 (out of 222203: 0.004950) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:20:23:10:45 mri_pretess N 4 e 1.66 S 0.03 U 2.11 P 129% M 40696 F 0 R 8832 W 0 c 198 w 56 I 0 O 224 L 7.07 7.22 7.57 @#@FSLOADPOST 2024:11:20:23:10:47 mri_pretess N 4 7.07 7.22 7.57 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.3.2 7.3.2 slice 50: 29 vertices, 38 faces slice 60: 2911 vertices, 3084 faces slice 70: 9116 vertices, 9349 faces slice 80: 17116 vertices, 17432 faces slice 90: 26159 vertices, 26448 faces slice 100: 35580 vertices, 35920 faces slice 110: 45148 vertices, 45507 faces slice 120: 54965 vertices, 55288 faces slice 130: 64468 vertices, 64808 faces slice 140: 73317 vertices, 73651 faces slice 150: 82113 vertices, 82384 faces slice 160: 89155 vertices, 89404 faces slice 170: 95370 vertices, 95599 faces slice 180: 101139 vertices, 101313 faces slice 190: 105493 vertices, 105642 faces slice 200: 108690 vertices, 108779 faces slice 210: 109174 vertices, 109184 faces slice 220: 109174 vertices, 109184 faces slice 230: 109174 vertices, 109184 faces slice 240: 109174 vertices, 109184 faces slice 250: 109174 vertices, 109184 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 2024:11:20:23:10:47 mri_tessellate N 3 e 1.65 S 0.02 U 1.85 P 113% M 35476 F 0 R 7821 W 0 c 171 w 162 I 0 O 5120 L 7.07 7.22 7.57 @#@FSLOADPOST 2024:11:20:23:10:49 mri_tessellate N 3 7.07 7.22 7.57 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 109174 voxel in cpt #1: X=-10 [v=109174,e=327552,f=218368] located at (-25.522112, -7.439683, 5.117372) For the whole surface: X=-10 [v=109174,e=327552,f=218368] One single component has been found nothing to do done @#@FSTIME 2024:11:20:23:10:49 mris_extract_main_component N 2 e 0.66 S 0.10 U 0.71 P 123% M 218372 F 4 R 57517 W 0 c 71 w 302 I 0 O 7680 L 7.07 7.22 7.57 @#@FSLOADPOST 2024:11:20:23:10:50 mris_extract_main_component N 2 7.07 7.22 7.57 #-------------------------------------------- #@# Tessellate rh Wed Nov 20 23:10:50 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 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+): 4 found - 4 modified | TOTAL: 5 pass 2 (yz+): 0 found - 4 modified | TOTAL: 5 pass 1 (yz-): 5 found - 5 modified | TOTAL: 10 pass 2 (yz-): 0 found - 5 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 2 found - 2 modified | TOTAL: 13 pass 2 (xz-): 0 found - 2 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 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 = 15 (out of 226918: 0.006610) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:20:23:10:50 mri_pretess N 4 e 1.80 S 0.03 U 2.26 P 127% M 40712 F 0 R 8834 W 0 c 211 w 38 I 0 O 224 L 7.22 7.25 7.57 @#@FSLOADPOST 2024:11:20:23:10:51 mri_pretess N 4 7.22 7.25 7.57 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 60: 1612 vertices, 1745 faces slice 70: 6957 vertices, 7159 faces slice 80: 13569 vertices, 13848 faces slice 90: 22752 vertices, 23066 faces slice 100: 31476 vertices, 31786 faces slice 110: 40743 vertices, 41083 faces slice 120: 50807 vertices, 51164 faces slice 130: 60581 vertices, 60909 faces slice 140: 70008 vertices, 70339 faces slice 150: 78710 vertices, 79004 faces slice 160: 86985 vertices, 87231 faces slice 170: 93710 vertices, 93931 faces slice 180: 99485 vertices, 99678 faces slice 190: 104338 vertices, 104515 faces slice 200: 108502 vertices, 108628 faces slice 210: 109816 vertices, 109828 faces slice 220: 109816 vertices, 109828 faces slice 230: 109816 vertices, 109828 faces slice 240: 109816 vertices, 109828 faces slice 250: 109816 vertices, 109828 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 2024:11:20:23:10:52 mri_tessellate N 3 e 1.65 S 0.01 U 1.86 P 113% M 35548 F 0 R 7834 W 0 c 167 w 160 I 0 O 5152 L 7.22 7.25 7.57 @#@FSLOADPOST 2024:11:20:23:10:53 mri_tessellate N 3 7.22 7.25 7.57 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 109816 voxel in cpt #1: X=-12 [v=109816,e=329484,f=219656] located at (26.278776, -3.246248, 8.856888) For the whole surface: X=-12 [v=109816,e=329484,f=219656] One single component has been found nothing to do done @#@FSTIME 2024:11:20:23:10:53 mris_extract_main_component N 2 e 0.71 S 0.11 U 0.75 P 121% M 219552 F 1 R 57851 W 0 c 86 w 284 I 0 O 7728 L 7.22 7.25 7.57 @#@FSLOADPOST 2024:11:20:23:10:54 mris_extract_main_component N 2 7.22 7.25 7.57 #-------------------------------------------- #@# Smooth1 lh Wed Nov 20 23:10:54 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Wed Nov 20 23:10:54 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 2845594 of (2845594 2845598) to complete... Waiting for PID 2845598 of (2845594 2845598) 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 (2845594 2845598) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Wed Nov 20 23:10:56 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Wed Nov 20 23:10:56 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 2845686 of (2845686 2845689) to complete... Waiting for PID 2845689 of (2845686 2845689) 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 = 43.9 mm, total surface area = 58617 mm^2 step 000: RMS=0.147 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.034 (target=0.015) step 050: RMS=0.033 (target=0.015) step 055: RMS=0.032 (target=0.015) step 060: RMS=0.032 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 27.128412 mris_inflate stimesec 1.257873 mris_inflate ru_maxrss 175016 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 595745 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7696 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5249 mris_inflate ru_nivcsw 2454 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 43.9 mm, total surface area = 59256 mm^2 step 000: RMS=0.146 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.078 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.053 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 27.645692 mris_inflate stimesec 0.327262 mris_inflate ru_maxrss 176580 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 145701 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7744 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 6264 mris_inflate ru_nivcsw 2403 PIDs (2845686 2845689) completed and logs appended. #-------------------------------------------- #@# QSphere lh Wed Nov 20 23:11:10 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Wed Nov 20 23:11:10 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 2845892 of (2845892 2845895) to complete... Waiting for PID 2845895 of (2845892 2845895) 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 0.341... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.60 (0.00-->7.47) (max @ vno 38097 --> 38923) face area 0.03 +- 0.04 (-0.06-->0.90) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.819, avgs=0 005/300: dt: 0.9000, rms radial error=176.559, avgs=0 010/300: dt: 0.9000, rms radial error=176.003, avgs=0 015/300: dt: 0.9000, rms radial error=175.273, avgs=0 020/300: dt: 0.9000, rms radial error=174.441, avgs=0 025/300: dt: 0.9000, rms radial error=173.550, avgs=0 030/300: dt: 0.9000, rms radial error=172.627, avgs=0 035/300: dt: 0.9000, rms radial error=171.687, avgs=0 040/300: dt: 0.9000, rms radial error=170.739, avgs=0 045/300: dt: 0.9000, rms radial error=169.789, avgs=0 050/300: dt: 0.9000, rms radial error=168.844, avgs=0 055/300: dt: 0.9000, rms radial error=167.900, avgs=0 060/300: dt: 0.9000, rms radial error=166.961, avgs=0 065/300: dt: 0.9000, rms radial error=166.026, avgs=0 070/300: dt: 0.9000, rms radial error=165.095, avgs=0 075/300: dt: 0.9000, rms radial error=164.169, avgs=0 080/300: dt: 0.9000, rms radial error=163.248, avgs=0 085/300: dt: 0.9000, rms radial error=162.333, avgs=0 090/300: dt: 0.9000, rms radial error=161.422, avgs=0 095/300: dt: 0.9000, rms radial error=160.516, avgs=0 100/300: dt: 0.9000, rms radial error=159.615, avgs=0 105/300: dt: 0.9000, rms radial error=158.719, avgs=0 110/300: dt: 0.9000, rms radial error=157.827, avgs=0 115/300: dt: 0.9000, rms radial error=156.940, avgs=0 120/300: dt: 0.9000, rms radial error=156.058, avgs=0 125/300: dt: 0.9000, rms radial error=155.181, avgs=0 130/300: dt: 0.9000, rms radial error=154.309, avgs=0 135/300: dt: 0.9000, rms radial error=153.441, avgs=0 140/300: dt: 0.9000, rms radial error=152.578, avgs=0 145/300: dt: 0.9000, rms radial error=151.720, avgs=0 150/300: dt: 0.9000, rms radial error=150.866, avgs=0 155/300: dt: 0.9000, rms radial error=150.017, avgs=0 160/300: dt: 0.9000, rms radial error=149.172, avgs=0 165/300: dt: 0.9000, rms radial error=148.332, avgs=0 170/300: dt: 0.9000, rms radial error=147.497, avgs=0 175/300: dt: 0.9000, rms radial error=146.666, avgs=0 180/300: dt: 0.9000, rms radial error=145.840, avgs=0 185/300: dt: 0.9000, rms radial error=145.018, avgs=0 190/300: dt: 0.9000, rms radial error=144.201, avgs=0 195/300: dt: 0.9000, rms radial error=143.388, avgs=0 200/300: dt: 0.9000, rms radial error=142.580, avgs=0 205/300: dt: 0.9000, rms radial error=141.776, avgs=0 210/300: dt: 0.9000, rms radial error=140.977, avgs=0 215/300: dt: 0.9000, rms radial error=140.182, avgs=0 220/300: dt: 0.9000, rms radial error=139.392, avgs=0 225/300: dt: 0.9000, rms radial error=138.606, avgs=0 230/300: dt: 0.9000, rms radial error=137.824, avgs=0 235/300: dt: 0.9000, rms radial error=137.046, avgs=0 240/300: dt: 0.9000, rms radial error=136.273, avgs=0 245/300: dt: 0.9000, rms radial error=135.505, avgs=0 250/300: dt: 0.9000, rms radial error=134.740, avgs=0 255/300: dt: 0.9000, rms radial error=133.980, avgs=0 260/300: dt: 0.9000, rms radial error=133.224, avgs=0 265/300: dt: 0.9000, rms radial error=132.472, avgs=0 270/300: dt: 0.9000, rms radial error=131.725, avgs=0 275/300: dt: 0.9000, rms radial error=130.981, avgs=0 280/300: dt: 0.9000, rms radial error=130.242, avgs=0 285/300: dt: 0.9000, rms radial error=129.507, avgs=0 290/300: dt: 0.9000, rms radial error=128.777, avgs=0 295/300: dt: 0.9000, rms radial error=128.050, avgs=0 300/300: dt: 0.9000, rms radial error=127.327, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12292.84 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 = 1833.30 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00061 epoch 3 (K=160.0), pass 1, starting sse = 135.46 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/18 = 0.01064 epoch 4 (K=640.0), pass 1, starting sse = 4.11 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/15 = 0.00498 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0216 hours FSRUNTIME@ mris_sphere 0.0216 hours 4 threads #VMPC# mris_sphere VmPeak 769680 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 0.337... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.59 (0.00-->7.77) (max @ vno 45527 --> 46440) face area 0.03 +- 0.03 (-0.01-->0.86) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.856, avgs=0 005/300: dt: 0.9000, rms radial error=176.597, avgs=0 010/300: dt: 0.9000, rms radial error=176.042, avgs=0 015/300: dt: 0.9000, rms radial error=175.311, avgs=0 020/300: dt: 0.9000, rms radial error=174.483, avgs=0 025/300: dt: 0.9000, rms radial error=173.596, avgs=0 030/300: dt: 0.9000, rms radial error=172.676, avgs=0 035/300: dt: 0.9000, rms radial error=171.740, avgs=0 040/300: dt: 0.9000, rms radial error=170.796, avgs=0 045/300: dt: 0.9000, rms radial error=169.850, avgs=0 050/300: dt: 0.9000, rms radial error=168.904, avgs=0 055/300: dt: 0.9000, rms radial error=167.961, avgs=0 060/300: dt: 0.9000, rms radial error=167.021, avgs=0 065/300: dt: 0.9000, rms radial error=166.085, avgs=0 070/300: dt: 0.9000, rms radial error=165.154, avgs=0 075/300: dt: 0.9000, rms radial error=164.228, avgs=0 080/300: dt: 0.9000, rms radial error=163.307, avgs=0 085/300: dt: 0.9000, rms radial error=162.390, avgs=0 090/300: dt: 0.9000, rms radial error=161.478, avgs=0 095/300: dt: 0.9000, rms radial error=160.571, avgs=0 100/300: dt: 0.9000, rms radial error=159.669, avgs=0 105/300: dt: 0.9000, rms radial error=158.772, avgs=0 110/300: dt: 0.9000, rms radial error=157.880, avgs=0 115/300: dt: 0.9000, rms radial error=156.992, avgs=0 120/300: dt: 0.9000, rms radial error=156.109, avgs=0 125/300: dt: 0.9000, rms radial error=155.232, avgs=0 130/300: dt: 0.9000, rms radial error=154.358, avgs=0 135/300: dt: 0.9000, rms radial error=153.490, avgs=0 140/300: dt: 0.9000, rms radial error=152.626, avgs=0 145/300: dt: 0.9000, rms radial error=151.767, avgs=0 150/300: dt: 0.9000, rms radial error=150.913, avgs=0 155/300: dt: 0.9000, rms radial error=150.063, avgs=0 160/300: dt: 0.9000, rms radial error=149.218, avgs=0 165/300: dt: 0.9000, rms radial error=148.378, avgs=0 170/300: dt: 0.9000, rms radial error=147.542, avgs=0 175/300: dt: 0.9000, rms radial error=146.711, avgs=0 180/300: dt: 0.9000, rms radial error=145.885, avgs=0 185/300: dt: 0.9000, rms radial error=145.063, avgs=0 190/300: dt: 0.9000, rms radial error=144.245, avgs=0 195/300: dt: 0.9000, rms radial error=143.432, avgs=0 200/300: dt: 0.9000, rms radial error=142.624, avgs=0 205/300: dt: 0.9000, rms radial error=141.820, avgs=0 210/300: dt: 0.9000, rms radial error=141.021, avgs=0 215/300: dt: 0.9000, rms radial error=140.226, avgs=0 220/300: dt: 0.9000, rms radial error=139.435, avgs=0 225/300: dt: 0.9000, rms radial error=138.649, avgs=0 230/300: dt: 0.9000, rms radial error=137.867, avgs=0 235/300: dt: 0.9000, rms radial error=137.089, avgs=0 240/300: dt: 0.9000, rms radial error=136.316, avgs=0 245/300: dt: 0.9000, rms radial error=135.547, avgs=0 250/300: dt: 0.9000, rms radial error=134.782, avgs=0 255/300: dt: 0.9000, rms radial error=134.021, avgs=0 260/300: dt: 0.9000, rms radial error=133.265, avgs=0 265/300: dt: 0.9000, rms radial error=132.513, avgs=0 270/300: dt: 0.9000, rms radial error=131.766, avgs=0 275/300: dt: 0.9000, rms radial error=131.022, avgs=0 280/300: dt: 0.9000, rms radial error=130.283, avgs=0 285/300: dt: 0.9000, rms radial error=129.548, avgs=0 290/300: dt: 0.9000, rms radial error=128.817, avgs=0 295/300: dt: 0.9000, rms radial error=128.090, avgs=0 300/300: dt: 0.9000, rms radial error=127.367, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12381.94 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00045 epoch 2 (K=40.0), pass 1, starting sse = 1837.94 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00068 epoch 3 (K=160.0), pass 1, starting sse = 141.72 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.24/18 = 0.01324 epoch 4 (K=640.0), pass 1, starting sse = 3.12 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/27 = 0.00862 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0228 hours FSRUNTIME@ mris_sphere 0.0228 hours 4 threads #VMPC# mris_sphere VmPeak 770128 mris_sphere done PIDs (2845892 2845895) completed and logs appended. #@# Fix Topology lh Wed Nov 20 23:12:32 CST 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_Bay3prisma lh #@# Fix Topology rh Wed Nov 20 23:12:32 CST 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_Bay3prisma rh Waiting for PID 2846772 of (2846772 2846775) to complete... Waiting for PID 2846775 of (2846772 2846775) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_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=-10 (nv=109174, nf=218368, ne=327552, g=6) 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... 1651 ambiguous faces found in tessellation segmenting defects... 11 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 11 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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: -9.1072 (-4.5536) -vertex loglikelihood: -6.3527 (-3.1764) -normal dot loglikelihood: -3.6681 (-3.6681) -quad curv loglikelihood: -6.1794 (-3.0897) Total Loglikelihood : -25.3075 CORRECTING DEFECT 0 (vertices=15, convex hull=23, v0=19797) After retessellation of defect 0 (v0=19797), euler #=-8 (108197,324290,216085) : difference with theory (-8) = 0 CORRECTING DEFECT 1 (vertices=131, convex hull=72, v0=60283) After retessellation of defect 1 (v0=60283), euler #=-7 (108215,324376,216154) : difference with theory (-7) = 0 CORRECTING DEFECT 2 (vertices=6, convex hull=22, v0=67739) After retessellation of defect 2 (v0=67739), euler #=-6 (108217,324387,216164) : difference with theory (-6) = 0 CORRECTING DEFECT 3 (vertices=111, convex hull=57, v0=71395) After retessellation of defect 3 (v0=71395), euler #=-5 (108237,324470,216228) : difference with theory (-5) = 0 CORRECTING DEFECT 4 (vertices=45, convex hull=76, v0=75120) After retessellation of defect 4 (v0=75120), euler #=-4 (108264,324581,216313) : difference with theory (-4) = 0 CORRECTING DEFECT 5 (vertices=62, convex hull=85, v0=76078) After retessellation of defect 5 (v0=76078), euler #=-3 (108292,324703,216408) : difference with theory (-3) = 0 CORRECTING DEFECT 6 (vertices=324, convex hull=68, v0=80149) After retessellation of defect 6 (v0=80149), euler #=-2 (108302,324765,216461) : difference with theory (-2) = 0 CORRECTING DEFECT 7 (vertices=5, convex hull=40, v0=87600) After retessellation of defect 7 (v0=87600), euler #=-1 (108304,324783,216478) : difference with theory (-1) = 0 CORRECTING DEFECT 8 (vertices=36, convex hull=38, v0=88188) After retessellation of defect 8 (v0=88188), euler #=0 (108312,324820,216508) : difference with theory (0) = 0 CORRECTING DEFECT 9 (vertices=209, convex hull=173, v0=89020) After retessellation of defect 9 (v0=89020), euler #=1 (108364,325063,216700) : difference with theory (1) = 0 CORRECTING DEFECT 10 (vertices=34, convex hull=65, v0=100161) After retessellation of defect 10 (v0=100161), euler #=2 (108376,325122,216748) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.16-->6.70) (max @ vno 88394 --> 109085) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.16-->6.70) (max @ vno 88394 --> 109085) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 50 mutations (36.8%), 86 crossovers (63.2%), 70 vertices were eliminated building final representation... 798 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=108376, nf=216748, ne=325122, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 52 intersecting 001: 2 intersecting terminating search with 0 intersecting topology fixing took 0.7 minutes FSRUNTIME@ mris_fix_topology lh 0.0125 hours 4 threads #VMPC# mris_fix_topology VmPeak 946184 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_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=-12 (nv=109816, nf=219656, ne=329484, g=7) 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 8 iterations marking ambiguous vertices... 565 ambiguous faces found in tessellation segmenting defects... 13 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 13 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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: -9.0274 (-4.5137) -vertex loglikelihood: -6.3387 (-3.1694) -normal dot loglikelihood: -3.6360 (-3.6360) -quad curv loglikelihood: -6.0543 (-3.0272) Total Loglikelihood : -25.0564 CORRECTING DEFECT 0 (vertices=11, convex hull=16, v0=30405) After retessellation of defect 0 (v0=30405), euler #=-10 (109416,327994,218568) : difference with theory (-10) = 0 CORRECTING DEFECT 1 (vertices=14, convex hull=28, v0=31382) After retessellation of defect 1 (v0=31382), euler #=-9 (109418,328008,218581) : difference with theory (-9) = 0 CORRECTING DEFECT 2 (vertices=15, convex hull=26, v0=50508) After retessellation of defect 2 (v0=50508), euler #=-8 (109421,328022,218593) : difference with theory (-8) = 0 CORRECTING DEFECT 3 (vertices=87, convex hull=57, v0=73417) After retessellation of defect 3 (v0=73417), euler #=-7 (109446,328121,218668) : difference with theory (-7) = 0 CORRECTING DEFECT 4 (vertices=15, convex hull=25, v0=75036) After retessellation of defect 4 (v0=75036), euler #=-6 (109449,328137,218682) : difference with theory (-6) = 0 CORRECTING DEFECT 5 (vertices=34, convex hull=30, v0=84527) After retessellation of defect 5 (v0=84527), euler #=-5 (109461,328184,218718) : difference with theory (-5) = 0 CORRECTING DEFECT 6 (vertices=28, convex hull=55, v0=101053) After retessellation of defect 6 (v0=101053), euler #=-4 (109470,328232,218758) : difference with theory (-4) = 0 CORRECTING DEFECT 7 (vertices=61, convex hull=103, v0=101067) After retessellation of defect 7 (v0=101067), euler #=-3 (109508,328394,218883) : difference with theory (-3) = 0 CORRECTING DEFECT 8 (vertices=34, convex hull=68, v0=105444) After retessellation of defect 8 (v0=105444), euler #=-2 (109529,328486,218955) : difference with theory (-2) = 0 CORRECTING DEFECT 9 (vertices=21, convex hull=63, v0=106427) After retessellation of defect 9 (v0=106427), euler #=-1 (109538,328539,219000) : difference with theory (-1) = 0 CORRECTING DEFECT 10 (vertices=17, convex hull=68, v0=107136) After retessellation of defect 10 (v0=107136), euler #=0 (109547,328590,219043) : difference with theory (0) = 0 CORRECTING DEFECT 11 (vertices=15, convex hull=42, v0=108488) After retessellation of defect 11 (v0=108488), euler #=1 (109554,328625,219072) : difference with theory (1) = 0 CORRECTING DEFECT 12 (vertices=49, convex hull=79, v0=108768) After retessellation of defect 12 (v0=108768), euler #=2 (109575,328719,219146) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.09-->5.11) (max @ vno 105179 --> 107217) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.09-->5.11) (max @ vno 105179 --> 107217) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 40 mutations (33.3%), 80 crossovers (66.7%), 15 vertices were eliminated building final representation... 241 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=109575, nf=219146, ne=328719, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 31 intersecting 001: 3 intersecting terminating search with 0 intersecting topology fixing took 0.5 minutes FSRUNTIME@ mris_fix_topology rh 0.0083 hours 4 threads #VMPC# mris_fix_topology VmPeak 946756 PIDs (2846772 2846775) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 108376 - 325122 + 216748 = 2 --> 0 holes F =2V-4: 216748 = 216752-4 (0) 2E=3F: 650244 = 650244 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 109575 - 328719 + 219146 = 2 --> 0 holes F =2V-4: 219146 = 219150-4 (0) 2E=3F: 657438 = 657438 (0) total defect index = 0 Wed Nov 20 23:13:18 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/defect2seg --s PIB15-273_VYr9_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 2847138 mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 12 non-cortical segments detected only using segment with 7185 vertices erasing segment 0 (vno[0] = 25107) erasing segment 2 (vno[0] = 57963) erasing segment 3 (vno[0] = 60796) erasing segment 4 (vno[0] = 70142) erasing segment 5 (vno[0] = 79343) erasing segment 6 (vno[0] = 80320) erasing segment 7 (vno[0] = 80994) erasing segment 8 (vno[0] = 81898) erasing segment 9 (vno[0] = 82603) erasing segment 10 (vno[0] = 84014) erasing segment 11 (vno[0] = 87721) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz 1000 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 525064 mris_defects_pointset done mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 6 non-cortical segments detected only using segment with 6969 vertices erasing segment 1 (vno[0] = 72455) erasing segment 2 (vno[0] = 79229) erasing segment 3 (vno[0] = 80107) erasing segment 4 (vno[0] = 81089) erasing segment 5 (vno[0] = 83714) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz 2000 1 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 525512 mris_defects_pointset done Started at Wed Nov 20 23:13:18 CST 2024 Ended at Wed Nov 20 23:13:53 CST 2024 Defect2seg-Run-Time-Sec 35 Defect2seg-Run-Time-Min 0.70 Defect2seg-Run-Time-Hours 0.01 tkmeditfv PIB15-273_VYr9_Bay3prisma brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2024:11:20:23:13:18 defect2seg N 3 e 35.11 S 0.88 U 37.89 P 110% M 314744 F 11 R 492885 W 0 c 3465 w 1402 I 0 O 18104 L 14.41 10.14 8.61 @#@FSLOADPOST 2024:11:20:23:13:53 defect2seg N 3 13.68 10.43 8.76 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.708434 remeshing to edge length 0.708434 with 3 iterations avg qual before : 0.894398 after: 0.971078 Removing intersections Remeshed surface quality stats nv0 = 108376 nv = 113658 1.04874 Area 227312 0.30039 0.03346 0.077857 0.4607 Corner 681936 60.00000 8.81785 19.897039 139.6269 Edge 340968 0.84086 0.08216 0.446136 1.2339 Hinge 340968 9.69876 9.77303 0.000005 127.4428 mris_remesh done @#@FSTIME 2024:11:20:23:13:53 mris_remesh N 7 e 27.13 S 0.85 U 27.66 P 105% M 636772 F 1 R 755771 W 0 c 2551 w 546 I 0 O 8000 L 13.68 10.43 8.76 @#@FSLOADPOST 2024:11:20:23:14:20 mris_remesh N 7 13.97 10.82 8.94 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.70859 remeshing to edge length 0.70859 with 3 iterations avg qual before : 0.892196 after: 0.971272 Removing intersections Remeshed surface quality stats nv0 = 109575 nv = 114515 1.04508 Area 229026 0.30093 0.03346 0.072749 0.4621 Corner 687078 60.00000 8.78905 16.970577 144.8488 Edge 343539 0.84157 0.08200 0.475928 1.3395 Hinge 343539 9.54798 9.86708 0.000017 131.1021 mris_remesh done @#@FSTIME 2024:11:20:23:14:20 mris_remesh N 7 e 28.16 S 0.87 U 28.71 P 105% M 641240 F 2 R 771789 W 0 c 2648 w 479 I 0 O 8056 L 13.97 10.82 8.94 @#@FSLOADPOST 2024:11:20:23:14:49 mris_remesh N 7 13.30 10.90 9.02 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:20:23:14:49 mris_remove_intersection N 2 e 2.51 S 0.24 U 2.49 P 108% M 287316 F 1 R 134943 W 0 c 252 w 344 I 0 O 8000 L 13.30 10.90 9.02 @#@FSLOADPOST 2024:11:20:23:14:51 mris_remove_intersection N 2 13.36 10.95 9.05 rm -f ../surf/lh.inflated /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:20:23:14:51 mris_remove_intersection N 2 e 2.62 S 0.21 U 2.70 P 111% M 290664 F 2 R 136358 W 0 c 254 w 300 I 0 O 8056 L 13.36 10.95 9.05 @#@FSLOADPOST 2024:11:20:23:14:54 mris_remove_intersection N 2 13.36 10.95 9.05 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Wed Nov 20 23:14:54 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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: 206385 voxels (1.23%) border gray 222908 voxels (1.33%) 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=22972, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 99.4 +- 7.5 [70.0 --> 110.0] CCS GM (77.0) : 75.9 +- 11.3 [30.0 --> 110.0] white_mean = 99.3662 +/- 7.49111, gray_mean = 75.9356 +/- 11.319 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=157 nbins=158 intensity peaks found at WM=102+-4.3, GM=73+-8.7 white_mode = 102, gray_mode = 73 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 61.7 (was 70.000000) setting MAX_BORDER_WHITE to 109.5 (was 105.000000) setting MIN_BORDER_WHITE to 73.0 (was 85.000000) setting MAX_CSF to 50.4 (was 40.000000) setting MAX_GRAY to 94.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 61.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40.000000) When placing the white surface white_border_hi = 109.491; white_border_low = 73; white_outside_low = 61.681; white_inside_hi = 120; white_outside_hi = 109.491; When placing the pial surface pial_border_hi = 61.681; pial_border_low = 39.043; pial_outside_low = 10; pial_inside_hi = 94.5089; pial_outside_hi = 56.0215; #VMPC# mris_autodet_gwstats VmPeak 563432 mris_autodet_gwstats done @#@FSTIME 2024:11:20:23:14:54 mris_autodet_gwstats N 8 e 4.21 S 0.20 U 4.97 P 122% M 204772 F 2 R 114639 W 0 c 468 w 102 I 0 O 8 L 13.36 10.95 9.05 @#@FSLOADPOST 2024:11:20:23:14:58 mris_autodet_gwstats N 8 13.33 10.99 9.07 #-------------------------------------------- #@# AutoDetGWStats rh Wed Nov 20 23:14:58 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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: 206385 voxels (1.23%) border gray 222908 voxels (1.33%) 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=22972, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 99.4 +- 7.5 [70.0 --> 110.0] CCS GM (77.0) : 75.9 +- 11.3 [30.0 --> 110.0] white_mean = 99.3662 +/- 7.49111, gray_mean = 75.9356 +/- 11.319 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=157 nbins=158 intensity peaks found at WM=103+-5.2, GM=74+-7.8 white_mode = 103, gray_mode = 74 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70.000000) setting MAX_BORDER_WHITE to 110.5 (was 105.000000) setting MIN_BORDER_WHITE to 74.0 (was 85.000000) setting MAX_CSF to 51.4 (was 40.000000) setting MAX_GRAY to 95.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 40.0 (was 40.000000) When placing the white surface white_border_hi = 110.491; white_border_low = 74; white_outside_low = 62.681; white_inside_hi = 120; white_outside_hi = 110.491; When placing the pial surface pial_border_hi = 62.681; pial_border_low = 40.043; pial_outside_low = 10; pial_inside_hi = 95.5089; pial_outside_hi = 57.0215; #VMPC# mris_autodet_gwstats VmPeak 564420 mris_autodet_gwstats done @#@FSTIME 2024:11:20:23:14:58 mris_autodet_gwstats N 8 e 4.13 S 0.17 U 4.94 P 123% M 206572 F 3 R 99258 W 0 c 462 w 91 I 0 O 8 L 13.33 10.99 9.07 @#@FSLOADPOST 2024:11:20:23:15:02 mris_autodet_gwstats N 8 13.06 10.97 9.08 #-------------------------------------------- #@# WhitePreAparc lh Wed Nov 20 23:15:02 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 227312 0.26559 0.06120 0.001000 0.5553 Corner 681936 60.00000 9.35877 2.959644 154.8319 Edge 340968 0.78704 0.11157 0.021755 1.2880 Hinge 340968 6.43123 6.21473 0.000039 147.7438 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=22972, wmmin=5, clip=110 MRIfindBrightNonWM(): 454 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 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6302, nmarked2=6, nripped=6302 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56829: xyz = (-32.5819,2.49646,0.626795) oxyz = (-32.5819,2.49646,0.626795) wxzy = (-32.5819,2.49646,0.626795) pxyz = (0,0,0) CBVO Creating mask 113658 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=6302 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6302, nmarked2=6, nripped=6302 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 = 109.4911120; border_low = 73.0000000; outside_low = 61.6810150; outside_hi = 109.4911120; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=2 had to be increased for 44 vertices, nripped=6302 mean border=83.0, 127 (127) missing vertices, mean dist 0.3 [0.8 (%35.3)->0.9 (%64.7))] %49 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0398 min Finding expansion regions mean absolute distance = 0.87 +- 1.05 3312 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=2421884.8, rms=10.356 001: dt: 0.5000, sse=1369130.4, rms=7.634 (26.278%) 002: dt: 0.5000, sse=833348.1, rms=5.773 (24.387%) 003: dt: 0.5000, sse=550406.2, rms=4.484 (22.327%) 004: dt: 0.5000, sse=400563.5, rms=3.616 (19.350%) 005: dt: 0.5000, sse=326061.2, rms=3.091 (14.526%) 006: dt: 0.5000, sse=292746.7, rms=2.819 (8.781%) 007: dt: 0.5000, sse=278428.4, rms=2.692 (4.536%) 008: dt: 0.5000, sse=272331.3, rms=2.633 (2.164%) rms = 2.6079/2.6333, sse=270884.5/272331.3, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=270884.5, rms=2.608 (0.963%) 010: dt: 0.2500, sse=176238.8, rms=1.513 (41.992%) 011: dt: 0.2500, sse=164941.8, rms=1.291 (14.659%) rms = 1.2424/1.2910, sse=162557.3/164941.8, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=162557.3, rms=1.242 (3.765%) rms = 1.2021/1.2424, sse=160088.0/162557.3, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=160088.0, rms=1.202 (3.244%) maximum number of reductions reached, breaking from loop positioning took 1.0 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=6302 removing 4 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=6424, nmarked2=7, nripped=6424 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 = 109.4911120; border_low = 73.0000000; outside_low = 61.6810150; outside_hi = 109.4911120; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=1 had to be increased for 64 vertices, nripped=6424 mean border=85.8, 110 (57) missing vertices, mean dist -0.3 [0.5 (%68.5)->0.2 (%31.5))] %59 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0300 min Finding expansion regions mean absolute distance = 0.43 +- 0.76 3432 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=573082.7, rms=4.327 014: dt: 0.5000, sse=328636.9, rms=2.724 (37.039%) 015: dt: 0.5000, sse=287404.2, rms=2.364 (13.232%) 016: dt: 0.5000, sse=276711.2, rms=2.256 (4.572%) rms = 2.3628/2.2557, sse=287278.4/276711.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=222967.7, rms=1.590 (29.496%) 018: dt: 0.2500, sse=200929.8, rms=1.219 (23.360%) 019: dt: 0.2500, sse=195491.7, rms=1.105 (9.335%) rms = 1.0712/1.1051, sse=194014.0/195491.7, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=194014.0, rms=1.071 (3.071%) rms = 1.0379/1.0712, sse=192628.7/194014.0, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=192628.7, rms=1.038 (3.109%) 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=6424 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 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6475, nmarked2=7, nripped=6475 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 = 109.4911120; border_low = 73.0000000; outside_low = 61.6810150; outside_hi = 109.4911120; 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=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 88 vertices, nripped=6475 mean border=88.5, 88 (32) missing vertices, mean dist -0.2 [0.4 (%71.4)->0.2 (%28.6))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0167 min Finding expansion regions mean absolute distance = 0.35 +- 0.48 3584 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=447658.6, rms=3.635 022: dt: 0.5000, sse=275660.4, rms=2.236 (38.479%) 023: dt: 0.5000, sse=260791.8, rms=2.118 (5.281%) rms = 2.1908/2.1183, sse=268489.0/260791.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=210096.2, rms=1.447 (31.675%) 025: dt: 0.2500, sse=189872.6, rms=1.066 (26.339%) 026: dt: 0.2500, sse=186447.8, rms=0.989 (7.194%) rms = 0.9755/0.9894, sse=185777.2/186447.8, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=185777.2, rms=0.976 (1.404%) rms = 0.9426/0.9755, sse=184387.6/185777.2, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=184387.6, rms=0.943 (3.376%) 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=6475 removing 2 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 removing 1 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=6484, nmarked2=8, nripped=6484 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 = 109.4911120; border_low = 73.0000000; outside_low = 61.6810150; outside_hi = 109.4911120; 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=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 94 vertices, nripped=6484 mean border=89.6, 81 (27) missing vertices, mean dist -0.1 [0.3 (%59.5)->0.2 (%40.5))] %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0113 min Finding expansion regions mean absolute distance = 0.27 +- 0.36 3009 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=229184.7, rms=1.784 029: dt: 0.5000, sse=202198.1, rms=1.347 (24.522%) rms = 1.6811/1.3467, sse=222411.8/202198.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=180857.7, rms=0.916 (32.016%) 031: dt: 0.2500, sse=175540.4, rms=0.784 (14.419%) rms = 0.7371/0.7835, sse=173635.9/175540.4, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=173635.9, rms=0.737 (5.922%) rms = 0.7206/0.7371, sse=172855.6/173635.9, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=172855.6, rms=0.721 (2.246%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 2.62 minutes #VMPC# mris_place_surfaces VmPeak 2047148 mris_place_surface done @#@FSTIME 2024:11:20:23:15:02 mris_place_surface N 18 e 164.16 S 2.14 U 324.10 P 198% M 1610548 F 3 R 1657987 W 0 c 28638 w 3078 I 0 O 8000 L 13.06 10.97 9.08 @#@FSLOADPOST 2024:11:20:23:17:47 mris_place_surface N 18 8.86 10.20 9.11 #-------------------------------------------- #@# WhitePreAparc rh Wed Nov 20 23:17:47 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 229026 0.26637 0.06204 0.000897 0.5493 Corner 687078 60.00000 9.40254 5.937467 136.2656 Edge 343539 0.78813 0.11265 0.036639 1.2535 Hinge 343539 6.34887 6.31928 0.000040 144.1164 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=22972, wmmin=5, clip=110 MRIfindBrightNonWM(): 454 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 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6074, nmarked2=0, nripped=6074 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57258: xyz = (43.4197,7.97479,40.6787) oxyz = (43.4197,7.97479,40.6787) wxzy = (43.4197,7.97479,40.6787) pxyz = (0,0,0) CBVO Creating mask 114515 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=6074 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6074, nmarked2=0, nripped=6074 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 = 110.4911120; border_low = 74.0000000; outside_low = 62.6810150; outside_hi = 110.4911120; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=2 had to be increased for 41 vertices, nripped=6074 mean border=83.6, 157 (157) missing vertices, mean dist 0.2 [0.9 (%36.3)->0.9 (%63.7))] %44 local maxima, %50 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0483 min Finding expansion regions mean absolute distance = 0.91 +- 1.17 3731 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=2387615.5, rms=10.224 001: dt: 0.5000, sse=1304208.4, rms=7.392 (27.698%) 002: dt: 0.5000, sse=778102.7, rms=5.511 (25.447%) 003: dt: 0.5000, sse=519968.2, rms=4.293 (22.107%) 004: dt: 0.5000, sse=389369.5, rms=3.512 (18.191%) 005: dt: 0.5000, sse=325579.4, rms=3.047 (13.225%) 006: dt: 0.5000, sse=292787.3, rms=2.792 (8.392%) 007: dt: 0.5000, sse=279539.8, rms=2.675 (4.192%) 008: dt: 0.5000, sse=272684.8, rms=2.606 (2.562%) rms = 2.5681/2.6060, sse=269287.8/272684.8, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=269287.8, rms=2.568 (1.456%) 010: dt: 0.2500, sse=180037.3, rms=1.541 (39.994%) 011: dt: 0.2500, sse=168963.0, rms=1.346 (12.636%) rms = 1.3026/1.3463, sse=166827.7/168963.0, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=166827.8, rms=1.303 (3.249%) rms = 1.2687/1.3026, sse=164739.9/166827.7, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=164739.9, rms=1.269 (2.601%) 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=6074 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 #FML# MRISripMidline(): nmarked=6261, nmarked2=0, nripped=6261 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 = 110.4911120; border_low = 74.0000000; outside_low = 62.6810150; outside_hi = 110.4911120; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=1 had to be increased for 91 vertices, nripped=6261 mean border=86.1, 160 (98) missing vertices, mean dist -0.3 [0.5 (%65.8)->0.2 (%34.2))] %56 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0329 min Finding expansion regions mean absolute distance = 0.44 +- 0.81 3479 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=543295.9, rms=4.148 014: dt: 0.5000, sse=318314.8, rms=2.624 (36.745%) 015: dt: 0.5000, sse=280882.9, rms=2.282 (13.025%) 016: dt: 0.5000, sse=269953.1, rms=2.170 (4.908%) rms = 2.2830/2.1702, sse=281258.4/269953.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=221134.5, rms=1.546 (28.763%) 018: dt: 0.2500, sse=201800.9, rms=1.213 (21.563%) 019: dt: 0.2500, sse=197444.8, rms=1.127 (7.098%) rms = 1.1005/1.1266, sse=196121.3/197444.8, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=196121.3, rms=1.100 (2.318%) rms = 1.0727/1.1005, sse=194905.6/196121.3, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=194905.6, rms=1.073 (2.519%) 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=6261 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 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6326, nmarked2=0, nripped=6326 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 = 110.4911120; border_low = 74.0000000; outside_low = 62.6810150; outside_hi = 110.4911120; 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=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 96 vertices, nripped=6326 mean border=88.9, 153 (90) missing vertices, mean dist -0.2 [0.4 (%72.2)->0.2 (%27.8))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0182 min Finding expansion regions mean absolute distance = 0.34 +- 0.49 3043 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=473833.8, rms=3.772 022: dt: 0.5000, sse=272143.1, rms=2.197 (41.754%) 023: dt: 0.5000, sse=261994.7, rms=2.091 (4.801%) rms = 2.1532/2.0914, sse=267340.0/261994.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=212675.1, rms=1.440 (31.141%) 025: dt: 0.2500, sse=193421.4, rms=1.082 (24.885%) 026: dt: 0.2500, sse=190681.6, rms=1.009 (6.736%) rms = 0.9965/1.0089, sse=193337.2/190681.6, time step reduction 2 of 3 to 0.125 0 1 1 027: dt: 0.2500, sse=193337.2, rms=0.997 (1.220%) rms = 0.9698/0.9965, sse=188835.7/193337.2, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=188835.7, rms=0.970 (2.684%) 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=6326 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=6365, nmarked2=0, nripped=6365 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 = 110.4911120; border_low = 74.0000000; outside_low = 62.6810150; outside_hi = 110.4911120; 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=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 100 vertices, nripped=6365 mean border=90.0, 163 (83) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0125 min Finding expansion regions mean absolute distance = 0.25 +- 0.37 2536 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=228373.1, rms=1.716 029: dt: 0.5000, sse=211594.1, rms=1.381 (19.571%) rms = 1.6965/1.3805, sse=229557.9/211594.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=187703.4, rms=0.930 (32.638%) 031: dt: 0.2500, sse=182852.8, rms=0.795 (14.522%) 032: dt: 0.2500, sse=177163.2, rms=0.745 (6.330%) rms = 0.7666/0.7446, sse=177366.2/177163.2, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.7365/0.7446, sse=176841.9/177163.2, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=176841.9, rms=0.736 (1.094%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.66 minutes #VMPC# mris_place_surfaces VmPeak 2086252 mris_place_surface done @#@FSTIME 2024:11:20:23:17:47 mris_place_surface N 18 e 166.44 S 2.29 U 318.71 P 192% M 1649380 F 1 R 2080386 W 0 c 28212 w 2162 I 0 O 8056 L 8.86 10.20 9.11 @#@FSLOADPOST 2024:11:20:23:20:33 mris_place_surface N 18 9.01 9.67 9.08 #-------------------------------------------- #@# CortexLabel lh Wed Nov 20 23:20:33 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 6 non-cortical segments detected only using segment with 7791 vertices erasing segment 1 (vno[0] = 52476) erasing segment 2 (vno[0] = 67711) erasing segment 3 (vno[0] = 70359) erasing segment 4 (vno[0] = 70997) erasing segment 5 (vno[0] = 72878) @#@FSTIME 2024:11:20:23:20:33 mri_label2label N 5 e 16.61 S 0.23 U 17.47 P 106% M 293968 F 2 R 163344 W 0 c 1521 w 333 I 0 O 9168 L 9.01 9.67 9.08 @#@FSLOADPOST 2024:11:20:23:20:50 mri_label2label N 5 8.86 9.60 9.07 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Wed Nov 20 23:20:50 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 8 non-cortical segments detected only using segment with 5636 vertices erasing segment 1 (vno[0] = 42143) erasing segment 2 (vno[0] = 52476) erasing segment 3 (vno[0] = 60886) erasing segment 4 (vno[0] = 64501) erasing segment 5 (vno[0] = 70359) erasing segment 6 (vno[0] = 70997) erasing segment 7 (vno[0] = 72878) @#@FSTIME 2024:11:20:23:20:50 mri_label2label N 5 e 16.62 S 0.22 U 17.47 P 106% M 302408 F 2 R 145069 W 0 c 1529 w 348 I 0 O 9360 L 8.86 9.60 9.07 @#@FSLOADPOST 2024:11:20:23:21:06 mri_label2label N 5 9.42 9.68 9.11 #-------------------------------------------- #@# CortexLabel rh Wed Nov 20 23:21:06 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2 non-cortical segments detected only using segment with 7607 vertices erasing segment 1 (vno[0] = 70083) @#@FSTIME 2024:11:20:23:21:07 mri_label2label N 5 e 16.87 S 0.23 U 17.56 P 105% M 279424 F 2 R 160519 W 0 c 1580 w 402 I 0 O 9040 L 9.42 9.68 9.11 @#@FSLOADPOST 2024:11:20:23:21:23 mri_label2label N 5 9.46 9.68 9.11 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Wed Nov 20 23:21:23 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 7 non-cortical segments detected only using segment with 5658 vertices erasing segment 1 (vno[0] = 41913) erasing segment 2 (vno[0] = 44597) erasing segment 3 (vno[0] = 46391) erasing segment 4 (vno[0] = 64850) erasing segment 5 (vno[0] = 64862) erasing segment 6 (vno[0] = 70083) @#@FSTIME 2024:11:20:23:21:23 mri_label2label N 5 e 17.00 S 0.22 U 17.71 P 105% M 299164 F 3 R 164619 W 0 c 1575 w 452 I 0 O 9200 L 9.46 9.68 9.11 @#@FSLOADPOST 2024:11:20:23:21:40 mri_label2label N 5 8.83 9.52 9.07 #-------------------------------------------- #@# Smooth2 lh Wed Nov 20 23:21:41 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Wed Nov 20 23:21:41 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 2850714 of (2850714 2850717) to complete... Waiting for PID 2850717 of (2850714 2850717) 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 (2850714 2850717) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Wed Nov 20 23:21:43 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Wed Nov 20 23:21:43 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 2850799 of (2850799 2850803) to complete... Waiting for PID 2850803 of (2850799 2850803) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 43.8 mm, total surface area = 68536 mm^2 step 000: RMS=0.168 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.019 (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 34.230638 mris_inflate stimesec 1.186843 mris_inflate ru_maxrss 176180 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 606180 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8904 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 12479 mris_inflate ru_nivcsw 3078 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 43.8 mm, total surface area = 69614 mm^2 step 000: RMS=0.168 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 29.345509 mris_inflate stimesec 0.240274 mris_inflate ru_maxrss 177612 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 212331 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8968 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3068 mris_inflate ru_nivcsw 2538 PIDs (2850799 2850803) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Wed Nov 20 23:22:00 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Nov 20 23:22:00 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf reconbatchjobs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2851001 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851004 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851007 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851010 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851014 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851017 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851020 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851023 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851026 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851030 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851033 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... Waiting for PID 2851036 of (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 18.193*4pi (228.621) --> -17 handles ICI = 135.2, FI = 1197.9, variation=19338.836 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 168 vertices thresholded to be in k1 ~ [-0.18 4.43], k2 ~ [-0.10 0.05] total integrated curvature = 0.709*4pi (8.905) --> 0 handles ICI = 1.5, FI = 7.7, variation=137.773 102 vertices thresholded to be in [-0.17 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 105 vertices thresholded to be in [-0.12 1.20] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.023 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 19.182*4pi (241.053) --> -18 handles ICI = 131.7, FI = 1215.6, variation=19412.595 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 212 vertices thresholded to be in k1 ~ [-0.19 0.33], k2 ~ [-0.10 0.07] total integrated curvature = 0.692*4pi (8.700) --> 0 handles ICI = 1.5, FI = 7.1, variation=130.697 119 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 146 vertices thresholded to be in [-0.13 0.16] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.021 done. PIDs (2851001 2851004 2851007 2851010 2851014 2851017 2851020 2851023 2851026 2851030 2851033 2851036) completed and logs appended. #-------------------------------------------- #@# Sphere lh Wed Nov 20 23:22:42 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Wed Nov 20 23:22:42 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 2851543 of (2851543 2851546) to complete... Waiting for PID 2851546 of (2851543 2851546) 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 0.313... 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 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 %18.90 pass 1: epoch 2 of 3 starting distance error %18.92 unfolding complete - removing small folds... starting distance error %18.88 removing remaining folds... final distance error %18.91 MRISunfold() return, current seed 1234 -01: dt=0.0000, 15 negative triangles VmPeak 772956 182: dt=0.9900, 15 negative triangles 183: dt=0.9900, 7 negative triangles 184: dt=0.9900, 6 negative triangles 185: dt=0.9900, 4 negative triangles 186: dt=0.9900, 2 negative triangles 187: dt=0.9900, 3 negative triangles 188: dt=0.9900, 2 negative triangles 189: dt=0.9900, 1 negative triangles 190: dt=0.9900, 4 negative triangles 191: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.0780 hours FSRUNTIME@ mris_sphere 0.0780 hours 4 threads #VMPC# mris_sphere VmPeak 772956 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 0.310... 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.35 pass 1: epoch 2 of 3 starting distance error %19.30 unfolding complete - removing small folds... starting distance error %19.29 removing remaining folds... final distance error %19.31 MRISunfold() return, current seed 1234 -01: dt=0.0000, 8 negative triangles VmPeak 773696 187: dt=0.9900, 8 negative triangles 188: dt=0.9900, 1 negative triangles 189: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.0799 hours FSRUNTIME@ mris_sphere 0.0799 hours 4 threads #VMPC# mris_sphere VmPeak 773696 mris_sphere done PIDs (2851543 2851546) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Wed Nov 20 23:27:30 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Nov 20 23:27:30 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2853457 of (2853457 2853460) to complete... Waiting for PID 2853460 of (2853457 2853460) 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/PIB15-273_VYr9_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 = 5.429 curvature mean = 0.032, std = 0.818 curvature mean = 0.012, std = 0.886 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (5.50, -11.50, -2.00) sse = 190530.1, elapsed since starting=0.1290 min MRISrigidBodyAlignGlobal() done 0.13 min curvature mean = 0.004, std = 0.853 curvature mean = 0.004, std = 0.958 curvature mean = 0.003, std = 0.866 curvature mean = 0.002, std = 0.984 curvature mean = 0.002, std = 0.869 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.020, std = 0.252 curvature mean = 0.040, std = 0.251 curvature mean = 0.050, std = 0.426 curvature mean = 0.037, std = 0.311 curvature mean = 0.020, std = 0.642 curvature mean = 0.036, std = 0.338 curvature mean = 0.008, std = 0.782 curvature mean = 0.036, std = 0.350 curvature mean = 0.001, std = 0.875 MRISregister() return, current seed 0 -01: dt=0.0000, 7 negative triangles VmPeak 772992 101: dt=0.9900, 7 negative triangles 102: dt=0.9900, 5 negative triangles 103: dt=0.9900, 7 negative triangles 104: dt=0.9900, 5 negative triangles 105: dt=0.9900, 4 negative triangles 106: dt=0.9900, 4 negative triangles 107: dt=0.9900, 2 negative triangles 108: dt=0.9900, 3 negative triangles 109: dt=0.9900, 2 negative triangles 110: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.06 hours #VMPC# mris_register VmPeak 772992 FSRUNTIME@ mris_register 0.0647 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/PIB15-273_VYr9_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 = 5.459 curvature mean = 0.034, std = 0.813 curvature mean = 0.014, std = 0.881 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (16.00, -9.00, 1.00) sse = 234548.1, elapsed since starting=0.1351 min MRISrigidBodyAlignGlobal() done 0.14 min curvature mean = 0.026, std = 0.842 curvature mean = 0.005, std = 0.956 curvature mean = 0.025, std = 0.855 curvature mean = 0.001, std = 0.983 curvature mean = 0.025, std = 0.858 curvature mean = -0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.022, std = 0.260 curvature mean = 0.040, std = 0.243 curvature mean = 0.054, std = 0.413 curvature mean = 0.036, std = 0.303 curvature mean = 0.024, std = 0.616 curvature mean = 0.035, std = 0.330 curvature mean = 0.010, std = 0.756 curvature mean = 0.035, std = 0.342 curvature mean = 0.001, std = 0.855 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... -01: dt=0.0000, 0 negative triangles VmPeak 694052 registration took 0.07 hours #VMPC# mris_register VmPeak 694052 FSRUNTIME@ mris_register 0.0669 hours 4 threads PIDs (2853457 2853460) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Wed Nov 20 23:31:31 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Wed Nov 20 23:31:31 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 2854703 of (2854703 2854706) to complete... Waiting for PID 2854706 of (2854703 2854706) 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 (2854703 2854706) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Wed Nov 20 23:31:32 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Nov 20 23:31:32 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2854782 of (2854782 2854785) to complete... Waiting for PID 2854785 of (2854782 2854785) 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 (2854782 2854785) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Wed Nov 20 23:31:33 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Nov 20 23:31:33 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 2854854 of (2854854 2854857) to complete... Waiting for PID 2854857 of (2854854 2854857) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 908 labels changed using aseg relabeling using gibbs priors... 000: 2709 changed, 113658 examined... 001: 632 changed, 11533 examined... 002: 166 changed, 3623 examined... 003: 63 changed, 1008 examined... 004: 25 changed, 380 examined... 005: 14 changed, 149 examined... 006: 8 changed, 83 examined... 007: 0 changed, 52 examined... 250 labels changed using aseg 000: 98 total segments, 58 labels (126 vertices) changed 001: 40 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... 1587 vertices marked for relabeling... 1587 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 10 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 1010 labels changed using aseg relabeling using gibbs priors... 000: 2481 changed, 114515 examined... 001: 557 changed, 10906 examined... 002: 124 changed, 3198 examined... 003: 38 changed, 779 examined... 004: 14 changed, 228 examined... 005: 6 changed, 90 examined... 006: 2 changed, 40 examined... 007: 0 changed, 14 examined... 157 labels changed using aseg 000: 85 total segments, 41 labels (84 vertices) changed 001: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1573 vertices marked for relabeling... 1573 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 10 seconds. PIDs (2854854 2854857) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Wed Nov 20 23:31:43 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 227312 0.33212 0.11335 0.001000 2.2547 Corner 681936 60.00000 13.71786 0.778107 178.3705 Edge 340968 0.88607 0.18924 0.018142 2.9485 Hinge 340968 10.83066 10.82606 0.000015 179.8548 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=22972, wmmin=5, clip=110 MRIfindBrightNonWM(): 454 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 8001/113658 vertices (105657 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 455 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56829: xyz = (-33.1412,2.41889,0.690203) oxyz = (-33.1412,2.41889,0.690203) wxzy = (-33.1412,2.41889,0.690203) pxyz = (0,0,0) CBVO Creating mask 113658 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4911120; border_low = 73.0000000; outside_low = 61.6810150; outside_hi = 109.4911120; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=2 had to be increased for 106 vertices, nripped=8456 mean border=83.1, 76 (76) missing vertices, mean dist 0.4 [1.5 (%12.7)->0.7 (%87.3))] %46 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0373 min Finding expansion regions mean absolute distance = 0.78 +- 1.02 2683 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=1462338.0, rms=7.879 001: dt: 0.5000, sse=641569.4, rms=4.817 (38.863%) 002: dt: 0.5000, sse=375891.2, rms=3.253 (32.469%) 003: dt: 0.5000, sse=301262.8, rms=2.652 (18.469%) 004: dt: 0.5000, sse=273448.2, rms=2.383 (10.164%) rms = 2.3741/2.3825, sse=273475.2/273448.2, time step reduction 1 of 3 to 0.250 0 1 1 005: dt: 0.5000, sse=273475.2, rms=2.374 (0.352%) 006: dt: 0.2500, sse=198262.2, rms=1.401 (40.979%) 007: dt: 0.2500, sse=188275.3, rms=1.212 (13.517%) rms = 1.1720/1.2118, sse=186012.4/188275.3, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=186012.4, rms=1.172 (3.286%) rms = 1.1410/1.1720, sse=184611.2/186012.4, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=184611.2, rms=1.141 (2.650%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4911120; border_low = 73.0000000; outside_low = 61.6810150; outside_hi = 109.4911120; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=1 had to be increased for 54 vertices, nripped=8456 mean border=85.6, 27 (6) missing vertices, mean dist -0.3 [0.5 (%64.6)->0.2 (%35.4))] %57 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0290 min Finding expansion regions mean absolute distance = 0.42 +- 0.77 3050 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=496670.8, rms=3.940 010: dt: 0.5000, sse=301797.9, rms=2.503 (36.465%) 011: dt: 0.5000, sse=267330.3, rms=2.162 (13.635%) 012: dt: 0.5000, sse=260786.0, rms=2.090 (3.318%) rms = 2.2156/2.0903, sse=271971.7/260786.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=213959.3, rms=1.445 (30.857%) 014: dt: 0.2500, sse=195477.0, rms=1.094 (24.327%) 015: dt: 0.2500, sse=191604.8, rms=1.002 (8.396%) rms = 0.9846/1.0019, sse=190893.9/191604.8, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=190893.9, rms=0.985 (1.722%) rms = 0.9620/0.9846, sse=189932.1/190893.9, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=189932.0, rms=0.962 (2.298%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4911120; border_low = 73.0000000; outside_low = 61.6810150; outside_hi = 109.4911120; 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=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 50 vertices, nripped=8456 mean border=88.4, 34 (3) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %74 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0170 min Finding expansion regions mean absolute distance = 0.35 +- 0.49 3711 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=446483.2, rms=3.659 018: dt: 0.5000, sse=270687.2, rms=2.211 (39.554%) 019: dt: 0.5000, sse=255875.8, rms=2.057 (6.995%) rms = 2.1177/2.0568, sse=261384.6/255875.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=208645.0, rms=1.400 (31.913%) 021: dt: 0.2500, sse=189408.8, rms=1.015 (27.494%) 022: dt: 0.2500, sse=185972.6, rms=0.932 (8.184%) rms = 0.9212/0.9323, sse=185235.7/185972.6, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=185235.7, rms=0.921 (1.194%) rms = 0.8960/0.9212, sse=184147.2/185235.7, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=184147.2, rms=0.896 (2.729%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4911120; border_low = 73.0000000; outside_low = 61.6810150; outside_hi = 109.4911120; 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=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 88 vertices, nripped=8456 mean border=89.6, 57 (3) missing vertices, mean dist -0.1 [0.3 (%59.8)->0.2 (%40.2))] %81 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0115 min Finding expansion regions mean absolute distance = 0.27 +- 0.37 3109 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=230174.2, rms=1.791 025: dt: 0.5000, sse=205583.1, rms=1.317 (26.456%) rms = 1.6283/1.3170, sse=222087.5/205583.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=184594.4, rms=0.892 (32.254%) 027: dt: 0.2500, sse=178027.6, rms=0.745 (16.553%) rms = 0.6981/0.7445, sse=176220.3/178027.6, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=176220.3, rms=0.698 (6.241%) rms = 0.6907/0.6981, sse=175286.0/176220.3, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=175286.0, rms=0.691 (1.063%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 2.09 minutes #VMPC# mris_place_surfaces VmPeak 2021764 mris_place_surface done @#@FSTIME 2024:11:20:23:31:43 mris_place_surface N 25 e 133.03 S 1.67 U 246.18 P 186% M 1596580 F 2 R 1607575 W 0 c 21821 w 1687 I 0 O 8000 L 13.31 14.21 11.90 @#@FSLOADPOST 2024:11:20:23:33:56 mris_place_surface N 25 9.66 12.45 11.56 #-------------------------------------------- #@# WhiteSurfs rh Wed Nov 20 23:33:56 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 229026 0.33439 0.11614 0.001031 1.8533 Corner 687078 60.00000 13.81964 0.356563 177.6776 Edge 343539 0.88916 0.19205 0.037272 3.0030 Hinge 343539 10.60221 10.96782 0.000011 179.8856 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=22972, wmmin=5, clip=110 MRIfindBrightNonWM(): 454 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 7852/114515 vertices (106663 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 390 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57258: xyz = (43.7407,7.61474,41.1068) oxyz = (43.7407,7.61474,41.1068) wxzy = (43.7407,7.61474,41.1068) pxyz = (0,0,0) CBVO Creating mask 114515 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4911120; border_low = 74.0000000; outside_low = 62.6810150; outside_hi = 110.4911120; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=2 had to be increased for 108 vertices, nripped=8242 mean border=83.6, 72 (72) missing vertices, mean dist 0.3 [2.1 (%11.7)->0.7 (%88.3))] %41 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0438 min Finding expansion regions mean absolute distance = 0.82 +- 1.11 3229 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=1406451.6, rms=7.657 001: dt: 0.5000, sse=580891.1, rms=4.467 (41.659%) 002: dt: 0.5000, sse=338781.4, rms=2.920 (34.636%) 003: dt: 0.5000, sse=283662.7, rms=2.442 (16.378%) 004: dt: 0.5000, sse=265132.9, rms=2.248 (7.939%) rms = 2.3153/2.2479, sse=271875.0/265132.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=219502.6, rms=1.689 (24.859%) 006: dt: 0.2500, sse=201575.7, rms=1.405 (16.817%) 007: dt: 0.2500, sse=198077.7, rms=1.331 (5.279%) rms = 1.3224/1.3309, sse=198685.8/198077.7, time step reduction 2 of 3 to 0.125 0 1 1 008: dt: 0.2500, sse=198685.8, rms=1.322 (0.639%) rms = 1.3050/1.3224, sse=198358.7/198685.8, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=198358.7, rms=1.305 (1.311%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4911120; border_low = 74.0000000; outside_low = 62.6810150; outside_hi = 110.4911120; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=1 had to be increased for 81 vertices, nripped=8242 mean border=85.9, 50 (15) missing vertices, mean dist -0.3 [0.6 (%62.1)->0.2 (%37.9))] %54 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0318 min Finding expansion regions mean absolute distance = 0.43 +- 0.81 3219 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=473604.3, rms=3.763 010: dt: 0.5000, sse=292289.2, rms=2.395 (36.357%) 011: dt: 0.5000, sse=263761.8, rms=2.092 (12.641%) 012: dt: 0.5000, sse=258909.2, rms=2.034 (2.786%) rms = 2.1692/2.0339, sse=270891.5/258909.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=217312.8, rms=1.457 (28.352%) 014: dt: 0.2500, sse=201527.5, rms=1.172 (19.575%) 015: dt: 0.2500, sse=198863.3, rms=1.113 (5.063%) rms = 1.1022/1.1127, sse=197372.6/198863.3, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=197372.6, rms=1.102 (0.937%) rms = 1.0823/1.1022, sse=196480.5/197372.6, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=196480.5, rms=1.082 (1.812%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4911120; border_low = 74.0000000; outside_low = 62.6810150; outside_hi = 110.4911120; 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=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 81 vertices, nripped=8242 mean border=88.8, 60 (12) missing vertices, mean dist -0.2 [0.4 (%72.3)->0.2 (%27.7))] %74 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0183 min Finding expansion regions mean absolute distance = 0.35 +- 0.50 2710 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=475794.7, rms=3.808 018: dt: 0.5000, sse=273785.1, rms=2.207 (42.046%) 019: dt: 0.5000, sse=258173.9, rms=2.049 (7.167%) rms = 2.1102/2.0489, sse=263754.8/258173.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=212067.2, rms=1.420 (30.713%) 021: dt: 0.2500, sse=193623.8, rms=1.067 (24.806%) 022: dt: 0.2500, sse=190162.6, rms=0.993 (6.980%) rms = 0.9782/0.9930, sse=189411.0/190162.6, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=189411.0, rms=0.978 (1.492%) rms = 0.9518/0.9782, sse=188297.8/189411.0, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=188297.8, rms=0.952 (2.697%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4911120; border_low = 74.0000000; outside_low = 62.6810150; outside_hi = 110.4911120; 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=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 82 vertices, nripped=8242 mean border=89.9, 79 (10) missing vertices, mean dist -0.1 [0.3 (%59.7)->0.2 (%40.3))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0121 min Finding expansion regions mean absolute distance = 0.25 +- 0.37 2403 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=228551.1, rms=1.727 025: dt: 0.5000, sse=216296.1, rms=1.371 (20.587%) rms = 1.6545/1.3714, sse=226315.5/216296.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=188526.9, rms=0.927 (32.400%) 027: dt: 0.2500, sse=181059.2, rms=0.775 (16.423%) 028: dt: 0.2500, sse=179156.0, rms=0.716 (7.607%) rms = 0.7315/0.7159, sse=179181.4/179156.0, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.7104/0.7159, sse=178748.8/179156.0, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=178748.8, rms=0.710 (0.765%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 2.15 minutes #VMPC# mris_place_surfaces VmPeak 2035576 mris_place_surface done @#@FSTIME 2024:11:20:23:33:56 mris_place_surface N 25 e 135.28 S 2.03 U 252.60 P 188% M 1610804 F 4 R 2276684 W 0 c 22359 w 1637 I 0 O 8056 L 9.66 12.45 11.56 @#@FSLOADPOST 2024:11:20:23:36:11 mris_place_surface N 25 9.36 11.24 11.22 #-------------------------------------------- #@# T1PialSurf lh Wed Nov 20 23:36:11 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 227312 0.33404 0.12786 0.001000 1.9739 Corner 681936 60.00000 15.27935 1.288687 176.1224 Edge 340968 0.89043 0.21075 0.021755 3.1205 Hinge 340968 10.95773 11.12188 0.000016 179.8779 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=22972, wmmin=5, clip=110 MRIfindBrightNonWM(): 454 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 66.776 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 5874/113658 vertices (107784 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 56829: xyz = (-33.4728,2.4141,0.867072) oxyz = (-33.4728,2.4141,0.867072) wxzy = (-33.4728,2.4141,0.867072) pxyz = (-33.4728,2.4141,0.867072) CBVO Creating mask 113658 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.5088880; border_hi = 61.6810150; border_low = 39.0430490; outside_low = 10.0000000; outside_hi = 56.0215230; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=2 had to be increased for 101 vertices, nripped=5874 mean border=58.8, 138 (138) missing vertices, mean dist 2.0 [0.4 (%0.0)->2.6 (%100.0))] %23 local maxima, %47 large gradients and %24 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0382 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=21333082.0, rms=31.360 001: dt: 0.5000, sse=15869712.0, rms=27.013 (13.863%) 002: dt: 0.5000, sse=11695060.0, rms=23.146 (14.314%) 003: dt: 0.5000, sse=8691297.0, rms=19.904 (14.009%) 004: dt: 0.5000, sse=6588090.5, rms=17.273 (13.215%) 005: dt: 0.5000, sse=5034477.0, rms=15.037 (12.947%) 006: dt: 0.5000, sse=3764771.8, rms=12.924 (14.052%) 007: dt: 0.5000, sse=2741760.0, rms=10.927 (15.449%) 008: dt: 0.5000, sse=1947883.2, rms=9.079 (16.913%) 009: dt: 0.5000, sse=1394347.5, rms=7.525 (17.116%) 010: dt: 0.5000, sse=1036091.3, rms=6.318 (16.048%) 011: dt: 0.5000, sse=837634.9, rms=5.535 (12.387%) 012: dt: 0.5000, sse=718255.0, rms=5.004 (9.595%) 013: dt: 0.5000, sse=664809.1, rms=4.745 (5.167%) 014: dt: 0.5000, sse=624705.4, rms=4.541 (4.311%) 015: dt: 0.5000, sse=611810.6, rms=4.471 (1.542%) 016: dt: 0.5000, sse=590870.2, rms=4.357 (2.541%) rms = 4.3394/4.3573, sse=588111.0/590870.2, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=588111.0, rms=4.339 (0.411%) 018: dt: 0.2500, sse=403848.3, rms=3.175 (26.842%) 019: dt: 0.2500, sse=362855.0, rms=2.855 (10.068%) 020: dt: 0.2500, sse=352408.9, rms=2.766 (3.117%) 021: dt: 0.2500, sse=345733.6, rms=2.708 (2.095%) rms = 2.6816/2.7081, sse=342835.0/345733.6, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=342835.0, rms=2.682 (0.979%) 023: dt: 0.1250, sse=327998.3, rms=2.546 (5.044%) rms = 2.5212/2.5463, sse=325373.2/327998.3, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=325373.2, rms=2.521 (0.984%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.5088880; border_hi = 61.6810150; border_low = 39.0430490; outside_low = 10.0000000; outside_hi = 56.0215230; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=1 had to be increased for 4819 vertices, nripped=5874 mean border=56.7, 760 (10) missing vertices, mean dist 0.2 [0.1 (%43.0)->0.4 (%57.0))] %40 local maxima, %36 large gradients and %19 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0126 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=592239.2, rms=4.150 025: dt: 0.5000, sse=535065.9, rms=3.811 (8.174%) rms = 3.9987/3.8108, sse=563280.2/535066.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=419759.4, rms=3.026 (20.590%) 027: dt: 0.2500, sse=377878.2, rms=2.689 (11.154%) 028: dt: 0.2500, sse=367152.5, rms=2.592 (3.579%) rms = 2.5535/2.5924, sse=362869.0/367152.5, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=362869.0, rms=2.554 (1.501%) 030: dt: 0.1250, sse=349907.1, rms=2.429 (4.876%) rms = 2.4049/2.4290, sse=347448.3/349907.1, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=347448.3, rms=2.405 (0.994%) 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 = 94.5088880; border_hi = 61.6810150; border_low = 39.0430490; outside_low = 10.0000000; outside_hi = 56.0215230; 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=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 5425 vertices, nripped=5874 mean border=55.4, 1031 (4) missing vertices, mean dist 0.1 [0.1 (%44.8)->0.3 (%55.2))] %51 local maxima, %24 large gradients and %19 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0077 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=422946.9, rms=3.023 rms = 3.6612/3.0225, sse=515444.3/422946.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=371826.1, rms=2.596 (14.099%) 033: dt: 0.2500, sse=358268.1, rms=2.471 (4.831%) rms = 2.4373/2.4709, sse=354486.2/358268.1, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=354486.2, rms=2.437 (1.360%) 035: dt: 0.1250, sse=345510.8, rms=2.348 (3.678%) rms = 2.3279/2.3477, sse=343515.6/345510.7, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=343515.7, rms=2.328 (0.841%) 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 = 94.5088880; border_hi = 61.6810150; border_low = 39.0430490; outside_low = 10.0000000; outside_hi = 56.0215230; 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=113658 Gdiag_no=-1 vno start=0, stop=113658 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 4776 vertices, nripped=5874 mean border=54.7, 2132 (4) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.3 (%51.7))] %56 local maxima, %19 large gradients and %18 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=370940.3, rms=2.586 rms = 3.1341/2.5855, sse=438031.1/370940.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=350956.5, rms=2.397 (7.276%) rms = 2.3484/2.3974, sse=345629.4/350956.5, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=345629.4, rms=2.348 (2.044%) 039: dt: 0.1250, sse=339636.2, rms=2.287 (2.607%) rms = 2.2641/2.2872, sse=337255.7/339636.2, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=337255.7, rms=2.264 (1.010%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 8 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 2.31 minutes #VMPC# mris_place_surfaces VmPeak 1414548 mris_place_surface done @#@FSTIME 2024:11:20:23:36:11 mris_place_surface N 28 e 144.98 S 1.27 U 286.77 P 198% M 977688 F 2 R 1397436 W 0 c 25274 w 1738 I 0 O 8000 L 9.36 11.24 11.22 @#@FSLOADPOST 2024:11:20:23:38:36 mris_place_surface N 28 9.81 10.70 11.01 #-------------------------------------------- #@# T1PialSurf rh Wed Nov 20 23:38:36 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 229026 0.33670 0.12978 0.001662 1.9268 Corner 687078 60.00000 15.10251 1.245151 175.9039 Edge 343539 0.89349 0.21129 0.033440 3.1976 Hinge 343539 10.68647 11.04108 0.000033 179.9625 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=22972, wmmin=5, clip=110 MRIfindBrightNonWM(): 454 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 67.776 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 5970/114515 vertices (108545 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 57258: xyz = (43.775,7.5033,41.0877) oxyz = (43.775,7.5033,41.0877) wxzy = (43.775,7.5033,41.0877) pxyz = (43.775,7.5033,41.0877) CBVO Creating mask 114515 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5088880; border_hi = 62.6810150; border_low = 40.0430490; outside_low = 10.0000000; outside_hi = 57.0215230; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=2 had to be increased for 145 vertices, nripped=5970 mean border=59.5, 134 (134) missing vertices, mean dist 2.0 [1.2 (%0.0)->2.5 (%100.0))] %24 local maxima, %51 large gradients and %20 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0380 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=20906800.0, rms=30.931 001: dt: 0.5000, sse=15428980.0, rms=26.535 (14.213%) 002: dt: 0.5000, sse=11287345.0, rms=22.651 (14.638%) 003: dt: 0.5000, sse=8324955.5, rms=19.400 (14.352%) 004: dt: 0.5000, sse=6257987.0, rms=16.761 (13.602%) 005: dt: 0.5000, sse=4758118.5, rms=14.549 (13.199%) 006: dt: 0.5000, sse=3536362.0, rms=12.459 (14.366%) 007: dt: 0.5000, sse=2574887.8, rms=10.525 (15.520%) 008: dt: 0.5000, sse=1848270.9, rms=8.784 (16.539%) 009: dt: 0.5000, sse=1353967.6, rms=7.367 (16.132%) 010: dt: 0.5000, sse=1025909.0, rms=6.250 (15.165%) 011: dt: 0.5000, sse=857840.2, rms=5.590 (10.553%) 012: dt: 0.5000, sse=749079.4, rms=5.117 (8.470%) 013: dt: 0.5000, sse=698475.4, rms=4.879 (4.644%) 014: dt: 0.5000, sse=652611.9, rms=4.653 (4.633%) 015: dt: 0.5000, sse=639079.8, rms=4.582 (1.531%) 016: dt: 0.5000, sse=613993.1, rms=4.450 (2.877%) rms = 4.4480/4.4501, sse=614009.2/613993.2, time step reduction 1 of 3 to 0.250 0 1 1 017: dt: 0.5000, sse=614009.2, rms=4.448 (0.048%) 018: dt: 0.2500, sse=403293.7, rms=3.143 (29.334%) 019: dt: 0.2500, sse=360028.7, rms=2.804 (10.792%) 020: dt: 0.2500, sse=349996.7, rms=2.718 (3.084%) rms = 2.6697/2.7176, sse=344539.7/349996.7, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=344539.7, rms=2.670 (1.760%) 022: dt: 0.1250, sse=321208.5, rms=2.456 (8.022%) rms = 2.4248/2.4556, sse=318035.1/321208.5, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=318035.1, rms=2.425 (1.254%) maximum number of reductions reached, breaking from loop positioning took 1.2 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5088880; border_hi = 62.6810150; border_low = 40.0430490; outside_low = 10.0000000; outside_hi = 57.0215230; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=1 had to be increased for 3563 vertices, nripped=5970 mean border=57.0, 658 (17) missing vertices, mean dist 0.2 [0.1 (%41.2)->0.4 (%58.8))] %43 local maxima, %36 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0131 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=667867.5, rms=4.520 024: dt: 0.5000, sse=581911.9, rms=4.051 (10.377%) rms = 4.1769/4.0508, sse=601029.9/581911.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=440500.2, rms=3.144 (22.396%) 026: dt: 0.2500, sse=392608.5, rms=2.774 (11.758%) 027: dt: 0.2500, sse=380523.6, rms=2.670 (3.738%) rms = 2.6218/2.6702, sse=374984.0/380523.6, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=374984.0, rms=2.622 (1.815%) 029: dt: 0.1250, sse=356745.9, rms=2.453 (6.441%) rms = 2.4223/2.4529, sse=353550.8/356745.9, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=353550.8, rms=2.422 (1.248%) 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 = 95.5088880; border_hi = 62.6810150; border_low = 40.0430490; outside_low = 10.0000000; outside_hi = 57.0215230; 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=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 4010 vertices, nripped=5970 mean border=55.4, 790 (10) missing vertices, mean dist 0.1 [0.1 (%39.1)->0.3 (%60.9))] %58 local maxima, %21 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0081 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=474622.4, rms=3.356 rms = 4.1431/3.3558, sse=603837.1/474622.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=392327.3, rms=2.728 (18.700%) 032: dt: 0.2500, sse=370646.4, rms=2.536 (7.053%) 033: dt: 0.2500, sse=363912.8, rms=2.477 (2.311%) rms = 2.4681/2.4773, sse=362794.7/363912.8, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=362794.7, rms=2.468 (0.368%) 035: dt: 0.1250, sse=350721.0, rms=2.350 (4.767%) rms = 2.3250/2.3505, sse=348085.9/350721.0, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=348085.8, rms=2.325 (1.086%) 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 = 95.5088880; border_hi = 62.6810150; border_low = 40.0430490; outside_low = 10.0000000; outside_hi = 57.0215230; 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=114515 Gdiag_no=-1 vno start=0, stop=114515 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 3576 vertices, nripped=5970 mean border=54.5, 1581 (10) missing vertices, mean dist 0.1 [0.2 (%45.6)->0.2 (%54.4))] %63 local maxima, %16 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0056 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=372042.6, rms=2.549 rms = 3.3385/2.5488, sse=472800.0/372042.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=349289.5, rms=2.331 (8.546%) rms = 2.2932/2.3310, sse=345233.6/349289.5, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=345233.6, rms=2.293 (1.622%) 039: dt: 0.1250, sse=339630.4, rms=2.235 (2.517%) rms = 2.2112/2.2354, sse=337152.7/339630.4, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=337152.7, rms=2.211 (1.085%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 31 intersecting 001: 8 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.29 minutes #VMPC# mris_place_surfaces VmPeak 1422720 mris_place_surface done @#@FSTIME 2024:11:20:23:38:36 mris_place_surface N 28 e 144.06 S 1.49 U 283.06 P 197% M 986048 F 2 R 1317706 W 0 c 25011 w 2003 I 0 O 8056 L 9.81 10.70 11.01 @#@FSLOADPOST 2024:11:20:23:41:00 mris_place_surface N 28 9.04 10.02 10.71 #@# white curv lh Wed Nov 20 23:41:00 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:20:23:41:00 mris_place_surface N 5 e 1.51 S 0.09 U 1.86 P 129% M 156988 F 1 R 42282 W 0 c 173 w 109 I 0 O 888 L 9.04 10.02 10.71 @#@FSLOADPOST 2024:11:20:23:41:02 mris_place_surface N 5 8.95 9.99 10.70 #@# white area lh Wed Nov 20 23:41:02 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2024:11:20:23:41:02 mris_place_surface N 3 e 0.70 S 0.10 U 0.97 P 154% M 157232 F 1 R 42287 W 0 c 104 w 113 I 0 O 888 L 8.95 9.99 10.70 @#@FSLOADPOST 2024:11:20:23:41:03 mris_place_surface N 3 8.95 9.99 10.70 #@# pial curv lh Wed Nov 20 23:41:03 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:20:23:41:03 mris_place_surface N 5 e 1.45 S 0.08 U 1.74 P 125% M 157372 F 3 R 42299 W 0 c 168 w 113 I 0 O 888 L 8.95 9.99 10.70 @#@FSLOADPOST 2024:11:20:23:41:04 mris_place_surface N 5 8.95 9.99 10.70 #@# pial area lh Wed Nov 20 23:41:04 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2024:11:20:23:41:04 mris_place_surface N 3 e 0.69 S 0.09 U 1.05 P 164% M 157040 F 1 R 42271 W 0 c 98 w 102 I 0 O 888 L 8.95 9.99 10.70 @#@FSLOADPOST 2024:11:20:23:41:05 mris_place_surface N 3 8.95 9.99 10.70 #@# thickness lh Wed Nov 20 23:41:05 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 113658 vertices processed 25000 of 113658 vertices processed 50000 of 113658 vertices processed 75000 of 113658 vertices processed 100000 of 113658 vertices processed 0 of 113658 vertices processed 25000 of 113658 vertices processed 50000 of 113658 vertices processed 75000 of 113658 vertices processed 100000 of 113658 vertices processed thickness calculation complete, 91:509 truncations. 54726 vertices at 0 distance 99687 vertices at 1 distance 48618 vertices at 2 distance 16056 vertices at 3 distance 5186 vertices at 4 distance 1844 vertices at 5 distance 705 vertices at 6 distance 261 vertices at 7 distance 90 vertices at 8 distance 42 vertices at 9 distance 26 vertices at 10 distance 13 vertices at 11 distance 12 vertices at 12 distance 9 vertices at 13 distance 13 vertices at 14 distance 6 vertices at 15 distance 5 vertices at 16 distance 3 vertices at 17 distance 5 vertices at 18 distance 2 vertices at 19 distance 7 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2024:11:20:23:41:05 mris_place_surface N 6 e 28.28 S 0.13 U 28.59 P 101% M 157432 F 2 R 141957 W 0 c 2554 w 112 I 0 O 888 L 8.95 9.99 10.70 @#@FSLOADPOST 2024:11:20:23:41:33 mris_place_surface N 6 8.39 9.75 10.59 #@# area and vertex vol lh Wed Nov 20 23:41:33 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Total face volume 189233 Total vertex volume 189022 (mask=0) #@# PIB15-273_VYr9_Bay3prisma lh 189022 vertexvol Done @#@FSTIME 2024:11:20:23:41:33 vertexvol N 4 e 1.55 S 0.15 U 2.03 P 139% M 261296 F 2 R 74459 W 0 c 203 w 347 I 0 O 2664 L 8.39 9.75 10.59 @#@FSLOADPOST 2024:11:20:23:41:35 vertexvol N 4 8.39 9.75 10.59 #@# white curv rh Wed Nov 20 23:41:35 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:20:23:41:35 mris_place_surface N 5 e 1.47 S 0.09 U 1.76 P 126% M 158368 F 3 R 42616 W 0 c 168 w 123 I 0 O 896 L 8.39 9.75 10.59 @#@FSLOADPOST 2024:11:20:23:41:37 mris_place_surface N 5 8.28 9.71 10.57 #@# white area rh Wed Nov 20 23:41:37 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2024:11:20:23:41:37 mris_place_surface N 3 e 0.68 S 0.11 U 1.00 P 164% M 158240 F 2 R 42539 W 0 c 96 w 116 I 0 O 896 L 8.28 9.71 10.57 @#@FSLOADPOST 2024:11:20:23:41:37 mris_place_surface N 3 8.28 9.71 10.57 #@# pial curv rh Wed Nov 20 23:41:37 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:20:23:41:37 mris_place_surface N 5 e 1.46 S 0.11 U 1.71 P 124% M 158300 F 1 R 42630 W 0 c 165 w 107 I 0 O 896 L 8.28 9.71 10.57 @#@FSLOADPOST 2024:11:20:23:41:39 mris_place_surface N 5 8.28 9.71 10.57 #@# pial area rh Wed Nov 20 23:41:39 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2024:11:20:23:41:39 mris_place_surface N 3 e 0.63 S 0.09 U 0.90 P 157% M 158408 F 2 R 42610 W 0 c 91 w 107 I 0 O 896 L 8.28 9.71 10.57 @#@FSLOADPOST 2024:11:20:23:41:40 mris_place_surface N 3 8.28 9.71 10.57 #@# thickness rh Wed Nov 20 23:41:40 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 114515 vertices processed 25000 of 114515 vertices processed 50000 of 114515 vertices processed 75000 of 114515 vertices processed 100000 of 114515 vertices processed 0 of 114515 vertices processed 25000 of 114515 vertices processed 50000 of 114515 vertices processed 75000 of 114515 vertices processed 100000 of 114515 vertices processed thickness calculation complete, 55:328 truncations. 60740 vertices at 0 distance 101852 vertices at 1 distance 46075 vertices at 2 distance 14175 vertices at 3 distance 4081 vertices at 4 distance 1280 vertices at 5 distance 447 vertices at 6 distance 146 vertices at 7 distance 71 vertices at 8 distance 47 vertices at 9 distance 32 vertices at 10 distance 13 vertices at 11 distance 12 vertices at 12 distance 13 vertices at 13 distance 15 vertices at 14 distance 10 vertices at 15 distance 8 vertices at 16 distance 5 vertices at 17 distance 5 vertices at 18 distance 2 vertices at 19 distance 1 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2024:11:20:23:41:40 mris_place_surface N 6 e 28.35 S 0.15 U 28.63 P 101% M 158456 F 1 R 158444 W 0 c 2584 w 108 I 0 O 896 L 8.28 9.71 10.57 @#@FSLOADPOST 2024:11:20:23:42:08 mris_place_surface N 6 7.76 9.43 10.45 #@# area and vertex vol rh Wed Nov 20 23:42:08 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Total face volume 189969 Total vertex volume 189767 (mask=0) #@# PIB15-273_VYr9_Bay3prisma rh 189767 vertexvol Done @#@FSTIME 2024:11:20:23:42:08 vertexvol N 4 e 1.45 S 0.17 U 1.75 P 133% M 263256 F 4 R 74934 W 0 c 178 w 321 I 0 O 2688 L 7.76 9.43 10.45 @#@FSLOADPOST 2024:11:20:23:42:10 vertexvol N 4 7.76 9.43 10.45 #----------------------------------------- #@# Curvature Stats lh Wed Nov 20 23:42:10 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PIB15-273_VYr9_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 [ PIB15-273_VYr9_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 [ 167 ] Gb_filter = 0 @#@FSTIME 2024:11:20:23:42:10 mris_curvature_stats N 11 e 2.37 S 0.11 U 2.66 P 116% M 157272 F 4 R 73709 W 0 c 261 w 311 I 0 O 7144 L 7.76 9.43 10.45 @#@FSLOADPOST 2024:11:20:23:42:12 mris_curvature_stats N 11 7.78 9.41 10.44 #----------------------------------------- #@# Curvature Stats rh Wed Nov 20 23:42:12 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PIB15-273_VYr9_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 [ PIB15-273_VYr9_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 @#@FSTIME 2024:11:20:23:42:12 mris_curvature_stats N 11 e 2.39 S 0.11 U 2.68 P 117% M 158308 F 1 R 74264 W 0 c 257 w 379 I 0 O 7208 L 7.78 9.41 10.44 @#@FSLOADPOST 2024:11:20:23:42:14 mris_curvature_stats N 11 7.78 9.41 10.44 #-------------------------------------------- #@# Cortical ribbon mask Wed Nov 20 23:42:14 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 = 24 writing volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz mris_volmask took 4.70 minutes writing ribbon files @#@FSTIME 2024:11:20:23:42:14 mris_volmask N 12 e 281.77 S 1.51 U 281.77 P 100% M 897680 F 1 R 1197554 W 0 c 25569 w 294 I 0 O 760 L 7.78 9.41 10.44 @#@FSLOADPOST 2024:11:20:23:46:56 mris_volmask N 12 7.09 7.89 9.51 #----------------------------------------- #@# Cortical Parc 2 lh Wed Nov 20 23:46:56 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Nov 20 23:46:56 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 2861603 of (2861603 2861606) to complete... Waiting for PID 2861606 of (2861603 2861606) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 76 labels changed using aseg relabeling using gibbs priors... 000: 7544 changed, 113658 examined... 001: 1795 changed, 29534 examined... 002: 540 changed, 9544 examined... 003: 221 changed, 3122 examined... 004: 95 changed, 1295 examined... 005: 49 changed, 552 examined... 006: 30 changed, 288 examined... 007: 11 changed, 181 examined... 008: 8 changed, 66 examined... 009: 8 changed, 55 examined... 010: 5 changed, 44 examined... 011: 5 changed, 30 examined... 012: 5 changed, 27 examined... 013: 6 changed, 30 examined... 014: 3 changed, 37 examined... 015: 2 changed, 18 examined... 016: 3 changed, 11 examined... 017: 2 changed, 16 examined... 018: 0 changed, 14 examined... 70 labels changed using aseg 000: 213 total segments, 130 labels (1117 vertices) changed 001: 91 total segments, 8 labels (17 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 25 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1140 vertices marked for relabeling... 1140 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 PIB15-273_VYr9_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... 32 labels changed using aseg relabeling using gibbs priors... 000: 7839 changed, 114515 examined... 001: 1730 changed, 30613 examined... 002: 506 changed, 9249 examined... 003: 205 changed, 2946 examined... 004: 106 changed, 1172 examined... 005: 53 changed, 600 examined... 006: 32 changed, 311 examined... 007: 19 changed, 189 examined... 008: 17 changed, 117 examined... 009: 4 changed, 84 examined... 010: 2 changed, 27 examined... 011: 1 changed, 13 examined... 012: 0 changed, 7 examined... 30 labels changed using aseg 000: 227 total segments, 137 labels (1519 vertices) changed 001: 92 total segments, 4 labels (9 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 21 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1152 vertices marked for relabeling... 1152 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 14 seconds. PIDs (2861603 2861606) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Wed Nov 20 23:47:10 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Nov 20 23:47:10 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 2861826 of (2861826 2861830) to complete... Waiting for PID 2861830 of (2861826 2861830) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 1201 labels changed using aseg relabeling using gibbs priors... 000: 1730 changed, 113658 examined... 001: 406 changed, 8094 examined... 002: 124 changed, 2304 examined... 003: 50 changed, 694 examined... 004: 34 changed, 273 examined... 005: 16 changed, 184 examined... 006: 11 changed, 94 examined... 007: 11 changed, 68 examined... 008: 12 changed, 65 examined... 009: 11 changed, 63 examined... 010: 4 changed, 48 examined... 011: 2 changed, 22 examined... 012: 1 changed, 10 examined... 013: 1 changed, 7 examined... 014: 1 changed, 6 examined... 015: 1 changed, 7 examined... 016: 2 changed, 8 examined... 017: 1 changed, 10 examined... 018: 1 changed, 8 examined... 019: 0 changed, 7 examined... 286 labels changed using aseg 000: 47 total segments, 14 labels (60 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 738 vertices marked for relabeling... 738 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 PIB15-273_VYr9_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... 1244 labels changed using aseg relabeling using gibbs priors... 000: 1774 changed, 114515 examined... 001: 409 changed, 8314 examined... 002: 117 changed, 2311 examined... 003: 52 changed, 669 examined... 004: 31 changed, 311 examined... 005: 24 changed, 174 examined... 006: 15 changed, 107 examined... 007: 9 changed, 75 examined... 008: 5 changed, 49 examined... 009: 4 changed, 33 examined... 010: 5 changed, 24 examined... 011: 3 changed, 31 examined... 012: 5 changed, 21 examined... 013: 1 changed, 22 examined... 014: 1 changed, 7 examined... 015: 0 changed, 7 examined... 303 labels changed using aseg 000: 43 total segments, 10 labels (42 vertices) changed 001: 33 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... 936 vertices marked for relabeling... 936 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. PIDs (2861826 2861830) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Wed Nov 20 23:47:20 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts pctsurfcon --s PIB15-273_VYr9_Bay3prisma --lh-only #----------------------------------------- #@# WM/GM Contrast rh Wed Nov 20 23:47:21 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts pctsurfcon --s PIB15-273_VYr9_Bay3prisma --rh-only Waiting for PID 2862007 of (2862007 2862014) to complete... Waiting for PID 2862014 of (2862007 2862014) to complete... pctsurfcon --s PIB15-273_VYr9_Bay3prisma --lh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts/pctsurfcon.log Wed Nov 20 23:47:21 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862007/lh.wm.mgh --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 72956 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862007/lh.wm.mgh Dim: 113658 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862007/lh.gm.mgh --projfrac 0.3 --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 86370 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862007/lh.gm.mgh Dim: 113658 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862007/lh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862007/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/stats/lh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Seg base 1000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh Vertex Area is 0.668064 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 PIB15-273_VYr9_Bay3prisma --rh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts/pctsurfcon.log Wed Nov 20 23:47:21 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862014/rh.wm.mgh --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 73772 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862014/rh.wm.mgh Dim: 114515 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862014/rh.gm.mgh --projfrac 0.3 --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 87669 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862014/rh.gm.mgh Dim: 114515 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862014/rh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.2862014/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/stats/rh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Seg base 2000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh Vertex Area is 0.673391 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 (2862007 2862014) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Wed Nov 20 23:47:25 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1179 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2013 voxels changed to hypointensity... 3179 hypointense voxels neighboring cortex changed @#@FSTIME 2024:11:20:23:47:25 mri_relabel_hypointensities N 3 e 18.61 S 0.93 U 19.51 P 109% M 444648 F 2 R 538784 W 0 c 1859 w 131 I 0 O 608 L 8.58 8.20 9.57 @#@FSLOADPOST 2024:11:20:23:47:44 mri_relabel_hypointensities N 3 8.65 8.24 9.55 #----------------------------------------- #@# APas-to-ASeg Wed Nov 20 23:47:44 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz --threads 4 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Done loading 0 128 64 192 1 65 193 2 66 194 129 3 67 195 4 5 196 68 6 197 69 7 198 70 8 9 199 130 71 10 200 72 11 201 12 13 202 73 14 203 131 15 74 204 16 17 205 75 18 206 19 207 20 132 76 21 208 22 209 23 77 210 24 25 211 133 26 78 212 27 213 28 29 79 214 30 215 134 31 80 32 216 33 217 34 135 81 218 35 36 219 37 82 220 38 136 221 39 40 83 222 41 223 42 43 224 84 137 44 225 45 226 46 85 47 227 48 228 138 49 86 50 229 51 230 52 87 231 53 139 54 232 55 88 233 56 57 234 58 235 59 89 236 60 140 61 237 62 238 90 63 239 240 241 91 141 242 243 244 92 245 246 142 247 93 248 249 250 143 94 251 252 253 95 144 254 255 96 145 146 97 147 98 148 149 99 150 100 151 152 101 153 154 102 155 103 156 157 104 158 105 159 106 160 161 107 162 108 163 164 109 165 110 166 111 167 168 112 169 170 113 171 172 173 174 114 175 176 177 178 115 179 180 181 182 183 116 184 185 186 187 188 117 189 190 191 118 119 120 121 122 123 124 125 126 127 nrelabeled = 92611 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 987092 mri_surf2volseg done @#@FSTIME 2024:11:20:23:47:44 mri_surf2volseg N 20 e 9.03 S 0.73 U 16.89 P 195% M 799804 F 3 R 455442 W 0 c 1620 w 1656 I 0 O 632 L 8.65 8.24 9.55 @#@FSLOADPOST 2024:11:20:23:47:53 mri_surf2volseg N 20 8.40 8.20 9.52 mri_brainvol_stats PIB15-273_VYr9_Bay3prisma ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1434259.0 #CBVS2 BrainSegVol 948600.0 #CBVS2 BrainSegVolNotVent 922179.0 #CBVS2 SupraTentVol 828586.0 #CBVS2 SupraTentVolNotVent 802165.0 #CBVS2 lhCtxGM 189307.0 #CBVS2 rhCtxGM 190006.6 #CBVS2 lhCerebralWM 188509.5 #CBVS2 rhCerebralWM 186738.5 #CBVS2 SubCortGMVol 48684.0 #CBVS2 CerebellumVol 120014.0 #CBVS2 CerebellumGMVol 96456.0 #CBVS2 VentChorVol 23413.0 #CBVS2 3rd4th5thCSF 3008.0 #CBVS2 AllCSF 26421.0 #CBVS2 CCVol 2775.0 @#@FSTIME 2024:11:20:23:47:53 mri_brainvol_stats N 1 e 3.90 S 0.33 U 7.12 P 190% M 208600 F 3 R 198513 W 0 c 675 w 159 I 0 O 8 L 8.40 8.20 9.52 @#@FSLOADPOST 2024:11:20:23:47:57 mri_brainvol_stats N 1 8.53 8.23 9.52 #----------------------------------------- #@# AParc-to-ASeg aparc Wed Nov 20 23:47:57 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8001 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7852 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Done loading 0 192 64 128 1 65 193 2 194 66 3 195 4 196 5 67 6 197 7 198 8 9 199 68 10 200 11 201 12 13 202 14 203 15 69 16 204 17 205 18 206 19 20 207 21 208 22 23 209 24 210 25 211 26 27 212 28 29 213 30 214 31 70 32 215 33 216 34 35 217 36 218 37 219 38 39 220 40 221 41 42 222 43 223 44 45 224 46 225 47 48 226 49 227 50 51 228 71 52 229 53 54 230 55 56 231 57 232 58 59 233 60 234 61 235 62 236 63 237 238 239 240 241 242 243 72 244 245 246 247 248 249 250 251 252 253 254 255 129 73 74 130 75 131 76 132 77 133 78 134 79 80 135 81 136 82 83 137 84 138 85 139 86 140 87 141 88 142 89 143 144 90 145 91 146 92 147 148 93 149 94 150 95 151 96 152 153 97 154 98 155 99 156 100 157 101 158 102 159 103 104 160 105 106 161 107 162 108 163 109 110 164 111 165 112 166 113 114 167 115 168 116 169 117 118 170 119 171 120 172 121 173 122 123 174 175 124 125 176 126 177 127 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 378208 ndotcheck = 13308 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 971104 mri_surf2volseg done @#@FSTIME 2024:11:20:23:47:57 mri_surf2volseg N 25 e 69.72 S 1.10 U 133.89 P 193% M 784880 F 1 R 1005830 W 0 c 12446 w 1739 I 0 O 728 L 8.53 8.23 9.52 @#@FSLOADPOST 2024:11:20:23:49:07 mri_surf2volseg N 25 8.94 8.42 9.49 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Wed Nov 20 23:49:07 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8001 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.a2009s.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7852 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.a2009s.annot Done loading 0 192 64 128 1 193 65 2 194 66 3 195 4 196 67 5 197 6 7 198 8 199 9 68 200 10 201 11 202 12 13 203 14 204 15 205 16 69 206 17 18 207 19 208 20 209 21 210 22 23 211 24 212 25 213 26 214 27 28 215 29 216 30 217 31 32 218 33 219 34 220 35 36 221 70 37 222 38 223 39 224 40 41 225 42 226 43 227 44 45 228 46 229 47 230 48 49 231 50 232 51 233 52 234 53 54 235 55 236 56 237 57 58 238 59 239 60 71 240 61 241 62 242 63 243 244 245 246 247 248 249 250 251 252 253 254 255 72 129 73 74 130 75 131 76 132 77 133 78 79 134 80 135 81 136 82 83 137 84 138 85 139 86 140 87 88 141 89 142 143 90 144 91 145 146 92 147 93 148 94 149 150 95 151 96 152 97 153 98 154 99 155 100 156 101 157 102 158 103 159 104 105 160 106 161 107 108 162 109 163 110 111 164 112 165 113 114 166 115 167 116 117 168 118 169 119 170 120 171 121 172 122 123 173 174 124 125 175 126 176 127 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 378208 ndotcheck = 13308 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 971188 mri_surf2volseg done @#@FSTIME 2024:11:20:23:49:07 mri_surf2volseg N 25 e 70.02 S 1.34 U 132.29 P 190% M 784988 F 1 R 778869 W 0 c 12275 w 4453 I 0 O 784 L 8.94 8.42 9.49 @#@FSLOADPOST 2024:11:20:23:50:17 mri_surf2volseg N 25 8.65 8.46 9.43 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Wed Nov 20 23:50:17 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8001 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.DKTatlas.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7852 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.DKTatlas.annot Done loading 0 192 128 64 1 193 65 2 194 66 3 195 4 196 67 5 197 6 198 7 199 8 200 9 68 201 10 202 11 203 12 204 13 205 14 206 69 15 207 16 208 17 209 18 210 19 211 20 212 21 213 22 214 23 215 24 216 25 217 26 218 27 219 28 220 29 70 221 30 222 31 223 32 224 33 34 225 35 226 36 227 37 228 38 229 39 230 40 231 41 232 42 233 43 234 44 235 45 236 46 237 47 238 48 71 49 239 50 240 51 241 52 242 53 243 54 244 55 245 56 246 57 247 58 248 59 249 60 250 61 251 62 252 63 253 254 255 72 129 73 74 130 75 131 76 132 77 133 78 79 134 80 135 81 82 136 83 84 137 85 138 86 87 139 88 140 89 141 90 142 91 143 144 92 145 93 146 147 94 148 95 149 150 96 151 97 152 98 153 99 154 100 155 101 156 102 157 103 158 104 159 105 106 160 107 161 108 109 162 110 111 163 112 164 113 114 165 115 166 116 117 167 118 168 119 169 120 170 121 171 122 172 123 173 124 174 125 126 175 127 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 378208 ndotcheck = 13308 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 971120 mri_surf2volseg done @#@FSTIME 2024:11:20:23:50:17 mri_surf2volseg N 25 e 61.51 S 1.35 U 115.76 P 190% M 784692 F 2 R 1163178 W 0 c 10923 w 675 I 0 O 720 L 8.65 8.46 9.43 @#@FSLOADPOST 2024:11:20:23:51:18 mri_surf2volseg N 25 8.81 8.55 9.40 #----------------------------------------- #@# WMParc Wed Nov 20 23:51:18 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot 3000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot 4000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8001 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7852 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Done loading 0 192 64 128 193 1 65 194 66 2 195 67 3 196 68 4 197 5 69 198 6 70 199 7 200 71 8 201 9 202 129 72 10 203 11 204 12 205 13 206 14 73 207 15 208 16 209 17 210 18 211 19 212 74 20 213 21 214 22 215 23 216 24 217 25 218 26 219 27 220 28 221 29 222 75 30 223 31 224 32 225 33 226 34 227 35 130 228 36 229 37 230 38 231 39 76 232 40 41 233 42 234 43 235 44 236 45 237 46 238 47 239 48 240 49 241 50 242 77 51 243 52 244 53 245 54 246 55 247 56 248 57 249 58 250 59 60 251 252 61 253 62 78 254 63 255 131 79 80 132 81 133 82 83 134 84 135 85 136 86 137 87 138 88 139 89 90 140 91 141 92 93 142 94 143 95 144 96 97 145 98 146 99 100 147 101 148 102 149 103 150 104 151 105 152 106 153 107 154 108 155 156 109 157 110 158 111 159 112 160 161 113 162 114 163 115 164 116 165 117 166 167 118 168 119 169 170 120 171 121 122 172 123 173 174 124 175 125 176 177 126 178 127 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 372473 ndotcheck = 3734 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 971120 mri_surf2volseg done @#@FSTIME 2024:11:20:23:51:18 mri_surf2volseg N 25 e 25.54 S 1.15 U 48.52 P 194% M 784892 F 1 R 669720 W 0 c 4575 w 5501 I 0 O 808 L 8.81 8.55 9.40 @#@FSLOADPOST 2024:11:20:23:51:44 mri_surf2volseg N 25 8.82 8.58 9.39 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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) = 1351565 mm^3 (det: 1.441370 ) 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 2024:11:20:23:51:44 mri_segstats N 24 e 247.16 S 1.01 U 507.92 P 205% M 239964 F 0 R 1574032 W 0 c 45778 w 680 I 0 O 24 L 8.82 8.58 9.39 @#@FSLOADPOST 2024:11:20:23:55:51 mri_segstats N 24 10.36 9.11 9.39 #----------------------------------------- #@# Parcellation Stats lh Wed Nov 20 23:55:51 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh pial #----------------------------------------- #@# Parcellation Stats rh Wed Nov 20 23:55:51 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh pial Waiting for PID 2865702 of (2865702 2865706 2865709 2865712) to complete... Waiting for PID 2865706 of (2865702 2865706 2865709 2865712) to complete... Waiting for PID 2865709 of (2865702 2865706 2865709 2865712) to complete... Waiting for PID 2865712 of (2865702 2865706 2865709 2865712) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189233 Total vertex volume 189022 (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) = 1351565 mm^3 (det: 1.441370 ) 1259 821 1786 2.268 0.413 0.085 0.014 6 0.8 bankssts 816 529 1370 2.503 0.620 0.125 0.021 10 0.7 caudalanteriorcingulate 2219 1469 3741 2.461 0.520 0.110 0.022 16 2.2 caudalmiddlefrontal 2072 1283 2672 1.913 0.413 0.142 0.036 31 3.1 cuneus 589 408 1798 3.367 0.714 0.104 0.024 4 0.6 entorhinal 3180 2307 7237 2.722 0.552 0.139 0.032 41 4.3 fusiform 4785 3248 8211 2.311 0.475 0.125 0.025 52 5.0 inferiorparietal 3801 2648 8019 2.674 0.537 0.129 0.030 46 4.9 inferiortemporal 1258 850 1847 1.943 0.734 0.125 0.033 19 1.8 isthmuscingulate 6091 3970 9626 2.139 0.578 0.138 0.032 76 7.8 lateraloccipital 3131 2191 6174 2.717 0.605 0.132 0.033 36 4.0 lateralorbitofrontal 4062 2677 5604 1.927 0.553 0.136 0.033 57 5.6 lingual 2454 1758 4257 2.311 0.585 0.136 0.032 39 3.2 medialorbitofrontal 3816 2512 7863 2.650 0.548 0.118 0.025 43 3.8 middletemporal 922 587 1841 2.628 0.733 0.091 0.019 6 0.7 parahippocampal 1838 1072 2810 2.408 0.527 0.090 0.018 10 1.4 paracentral 2103 1403 3927 2.563 0.462 0.114 0.026 20 2.3 parsopercularis 909 681 2143 2.667 0.573 0.147 0.037 14 1.6 parsorbitalis 1890 1288 3440 2.356 0.530 0.121 0.024 17 1.9 parstriangularis 1941 1296 2162 1.852 0.519 0.130 0.029 19 2.5 pericalcarine 5585 3499 7380 1.927 0.630 0.108 0.024 51 5.3 postcentral 1402 944 2388 2.286 0.639 0.121 0.025 16 1.5 posteriorcingulate 6735 4227 12002 2.578 0.589 0.110 0.026 51 7.2 precentral 4373 3060 7162 2.207 0.511 0.128 0.026 51 4.9 precuneus 858 629 2022 2.848 0.651 0.154 0.039 16 1.4 rostralanteriorcingulate 5680 4163 11035 2.348 0.517 0.144 0.036 77 8.4 rostralmiddlefrontal 8630 5943 17882 2.666 0.561 0.121 0.026 80 9.5 superiorfrontal 7210 4725 10550 2.065 0.479 0.114 0.022 66 6.5 superiorparietal 5283 3547 11062 2.756 0.607 0.114 0.026 50 5.7 superiortemporal 5844 3912 10036 2.365 0.533 0.121 0.025 57 6.0 supramarginal 332 281 1038 2.808 0.411 0.185 0.049 7 0.7 frontalpole 624 478 2510 3.558 0.662 0.126 0.032 8 0.7 temporalpole 724 415 1055 2.233 0.346 0.099 0.023 6 0.6 transversetemporal 3241 2259 6371 2.872 0.832 0.133 0.041 38 5.4 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 PIB15-273_VYr9_Bay3prisma lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189233 Total vertex volume 189022 (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) = 1351565 mm^3 (det: 1.441370 ) 1259 752 1786 2.268 0.413 0.090 0.019 17 1.0 bankssts 816 602 1370 2.503 0.620 0.159 0.059 53 1.7 caudalanteriorcingulate 2219 1546 3741 2.461 0.520 0.123 0.029 52 2.6 caudalmiddlefrontal 2072 1603 2672 1.913 0.413 0.132 0.031 43 2.5 cuneus 589 718 1798 3.367 0.714 0.238 0.058 19 1.6 entorhinal 3180 2969 7237 2.722 0.552 0.164 0.044 120 5.5 fusiform 4785 3777 8211 2.311 0.475 0.135 0.028 76 5.2 inferiorparietal 3801 3330 8019 2.674 0.537 0.155 0.041 104 5.9 inferiortemporal 1258 1109 1847 1.943 0.734 0.181 0.053 33 2.8 isthmuscingulate 6091 4890 9626 2.139 0.578 0.137 0.033 104 8.0 lateraloccipital 3131 2367 6174 2.717 0.605 0.132 0.036 65 4.0 lateralorbitofrontal 4062 3357 5604 1.927 0.553 0.145 0.037 110 6.0 lingual 2454 1990 4257 2.311 0.585 0.138 0.034 50 3.1 medialorbitofrontal 3816 3288 7863 2.650 0.548 0.142 0.030 98 4.8 middletemporal 922 821 1841 2.628 0.733 0.155 0.042 13 1.8 parahippocampal 1838 1274 2810 2.408 0.527 0.090 0.016 10 1.2 paracentral 2103 1688 3927 2.563 0.462 0.126 0.027 36 2.4 parsopercularis 909 902 2143 2.667 0.573 0.172 0.037 17 1.5 parsorbitalis 1890 1557 3440 2.356 0.530 0.142 0.028 25 2.3 parstriangularis 1941 1099 2162 1.852 0.519 0.105 0.028 27 2.1 pericalcarine 5585 4288 7380 1.927 0.630 0.117 0.023 65 5.1 postcentral 1402 1116 2388 2.286 0.639 0.140 0.032 25 1.8 posteriorcingulate 6735 4962 12002 2.578 0.589 0.109 0.023 80 6.0 precentral 4373 3427 7162 2.207 0.511 0.139 0.033 76 5.4 precuneus 858 797 2022 2.848 0.651 0.240 0.076 2317 2.9 rostralanteriorcingulate 5680 5136 11035 2.348 0.517 0.168 0.039 129 8.8 rostralmiddlefrontal 8630 7243 17882 2.666 0.561 0.139 0.032 134 10.1 superiorfrontal 7210 5456 10550 2.065 0.479 0.121 0.023 73 6.8 superiorparietal 5283 4300 11062 2.756 0.607 0.129 0.030 96 6.0 superiortemporal 5844 4511 10036 2.365 0.533 0.129 0.028 86 6.6 supramarginal 332 461 1038 2.808 0.411 0.208 0.038 4 0.6 frontalpole 624 920 2510 3.558 0.662 0.206 0.038 9 1.1 temporalpole 724 555 1055 2.233 0.346 0.100 0.019 4 0.6 transversetemporal 3241 2112 6371 2.872 0.832 0.154 0.048 114 6.2 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189969 Total vertex volume 189767 (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) = 1351565 mm^3 (det: 1.441370 ) 1017 671 1544 2.344 0.312 0.083 0.016 4 0.6 bankssts 969 674 1810 2.491 0.756 0.140 0.030 17 1.2 caudalanteriorcingulate 2798 1898 4830 2.322 0.450 0.118 0.022 25 2.6 caudalmiddlefrontal 2267 1400 2770 1.784 0.432 0.127 0.031 28 2.9 cuneus 582 417 2182 3.597 0.663 0.118 0.025 6 0.5 entorhinal 3531 2409 7210 2.607 0.577 0.126 0.031 44 4.3 fusiform 6741 4653 11538 2.304 0.403 0.121 0.024 70 6.7 inferiorparietal 3561 2542 7726 2.674 0.652 0.135 0.033 51 4.7 inferiortemporal 1297 833 1797 1.905 0.710 0.115 0.027 16 1.1 isthmuscingulate 6735 4424 10364 2.135 0.510 0.135 0.030 88 8.0 lateraloccipital 3285 2336 6185 2.538 0.610 0.143 0.039 44 5.5 lateralorbitofrontal 4315 2865 6283 2.056 0.578 0.135 0.034 54 6.1 lingual 2466 1747 4478 2.321 0.661 0.122 0.031 34 3.0 medialorbitofrontal 3846 2690 8152 2.597 0.485 0.122 0.024 44 3.8 middletemporal 935 596 1897 2.683 0.776 0.099 0.023 7 0.9 parahippocampal 1908 1068 2912 2.534 0.586 0.091 0.021 13 1.6 paracentral 1406 975 2632 2.544 0.391 0.112 0.025 13 1.4 parsopercularis 1051 781 2323 2.347 0.503 0.137 0.036 16 1.6 parsorbitalis 1651 1204 3242 2.339 0.510 0.127 0.028 17 2.0 parstriangularis 2285 1491 2321 1.660 0.381 0.117 0.026 23 2.4 pericalcarine 5078 3203 6721 1.913 0.511 0.101 0.019 38 4.0 postcentral 1421 973 2555 2.335 0.698 0.120 0.025 17 1.5 posteriorcingulate 6596 4169 11230 2.484 0.516 0.103 0.021 47 5.9 precentral 4268 2898 7035 2.280 0.537 0.124 0.026 44 4.5 precuneus 581 404 1165 2.791 0.711 0.110 0.024 5 0.6 rostralanteriorcingulate 6394 4965 13379 2.332 0.551 0.151 0.034 102 10.0 rostralmiddlefrontal 7869 5443 15935 2.610 0.575 0.126 0.028 78 9.4 superiorfrontal 8040 5238 11980 2.091 0.432 0.102 0.019 65 6.4 superiorparietal 4677 3123 9548 2.658 0.578 0.106 0.023 41 4.4 superiortemporal 4345 2948 7799 2.401 0.463 0.115 0.025 43 4.4 supramarginal 401 349 1245 2.796 0.522 0.199 0.050 10 0.9 frontalpole 633 463 2214 3.631 0.584 0.137 0.034 8 0.9 temporalpole 434 248 698 2.515 0.280 0.113 0.022 5 0.4 transversetemporal 3280 2229 6066 2.745 0.742 0.126 0.038 37 4.9 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 PIB15-273_VYr9_Bay3prisma rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189969 Total vertex volume 189767 (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) = 1351565 mm^3 (det: 1.441370 ) 1017 648 1544 2.344 0.312 0.093 0.022 7 0.9 bankssts 969 790 1810 2.491 0.756 0.175 0.048 35 2.0 caudalanteriorcingulate 2798 2190 4830 2.322 0.450 0.124 0.023 37 2.6 caudalmiddlefrontal 2267 1818 2770 1.784 0.432 0.130 0.026 27 2.6 cuneus 582 832 2182 3.597 0.663 0.323 0.160 371 2.1 entorhinal 3531 3083 7210 2.607 0.577 0.151 0.038 69 5.7 fusiform 6741 5280 11538 2.304 0.403 0.132 0.027 84 7.5 inferiorparietal 3561 3077 7726 2.674 0.652 0.146 0.036 66 5.3 inferiortemporal 1297 1074 1797 1.905 0.710 0.163 0.051 24 2.7 isthmuscingulate 6735 5310 10364 2.135 0.510 0.134 0.032 120 8.6 lateraloccipital 3285 2549 6185 2.538 0.610 0.145 0.042 73 5.5 lateralorbitofrontal 4315 3446 6283 2.056 0.578 0.136 0.036 64 5.9 lingual 2466 2149 4478 2.321 0.661 0.151 0.036 52 4.1 medialorbitofrontal 3846 3517 8152 2.597 0.485 0.144 0.028 54 4.4 middletemporal 935 805 1897 2.683 0.776 0.159 0.042 18 1.7 parahippocampal 1908 1230 2912 2.534 0.586 0.095 0.017 15 1.4 paracentral 1406 1113 2632 2.544 0.391 0.121 0.023 13 1.4 parsopercularis 1051 1207 2323 2.347 0.503 0.184 0.033 18 1.7 parsorbitalis 1651 1518 3242 2.339 0.510 0.154 0.032 22 2.2 parstriangularis 2285 1408 2321 1.660 0.381 0.107 0.025 39 2.0 pericalcarine 5078 3882 6721 1.913 0.511 0.110 0.019 38 3.8 postcentral 1421 1187 2555 2.335 0.698 0.157 0.046 103 2.6 posteriorcingulate 6596 4799 11230 2.484 0.516 0.103 0.019 75 4.9 precentral 4268 3238 7035 2.280 0.537 0.132 0.034 88 4.9 precuneus 581 454 1165 2.791 0.711 0.131 0.027 22 0.8 rostralanteriorcingulate 6394 6418 13379 2.332 0.551 0.179 0.040 128 10.6 rostralmiddlefrontal 7869 6677 15935 2.610 0.575 0.143 0.031 105 9.9 superiorfrontal 8040 6194 11980 2.091 0.432 0.114 0.020 76 6.5 superiorparietal 4677 3909 9548 2.658 0.578 0.126 0.024 83 4.6 superiortemporal 4345 3412 7799 2.401 0.463 0.123 0.024 44 4.4 supramarginal 401 545 1245 2.796 0.522 0.221 0.043 6 0.8 frontalpole 633 811 2214 3.631 0.584 0.188 0.030 9 1.0 temporalpole 434 311 698 2.515 0.280 0.095 0.018 2 0.3 transversetemporal 3280 2175 6066 2.745 0.742 0.143 0.045 77 5.1 insula PIDs (2865702 2865706 2865709 2865712) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Nov 20 23:56:04 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 2 rh Wed Nov 20 23:56:04 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh white Waiting for PID 2866025 of (2866025 2866028) to complete... Waiting for PID 2866028 of (2866025 2866028) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189233 Total vertex volume 189022 (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) = 1351565 mm^3 (det: 1.441370 ) 892 685 1723 2.399 0.441 0.157 0.036 14 1.3 G_and_S_frontomargin 1213 840 2426 2.463 0.471 0.147 0.030 16 1.6 G_and_S_occipital_inf 1549 864 2427 2.346 0.563 0.099 0.024 14 1.4 G_and_S_paracentral 1131 764 2313 2.661 0.458 0.127 0.027 12 1.2 G_and_S_subcentral 576 494 1649 2.642 0.549 0.202 0.058 13 1.6 G_and_S_transv_frontopol 1603 1165 3267 2.735 0.520 0.138 0.033 22 2.3 G_and_S_cingul-Ant 1067 706 1827 2.606 0.508 0.103 0.017 6 0.8 G_and_S_cingul-Mid-Ant 1150 776 1904 2.403 0.465 0.111 0.024 8 1.1 G_and_S_cingul-Mid-Post 465 319 1159 2.708 0.481 0.140 0.036 8 0.6 G_cingul-Post-dorsal 238 168 418 2.094 0.730 0.149 0.037 4 0.3 G_cingul-Post-ventral 2012 1207 2701 1.921 0.442 0.139 0.036 30 2.9 G_cuneus 1084 754 2519 2.605 0.350 0.135 0.032 16 1.4 G_front_inf-Opercular 451 312 1131 2.691 0.376 0.145 0.033 8 0.6 G_front_inf-Orbital 1106 739 2562 2.641 0.479 0.136 0.030 14 1.3 G_front_inf-Triangul 3128 2295 7271 2.501 0.527 0.146 0.037 47 4.7 G_front_middle 5792 3917 13665 2.815 0.553 0.126 0.028 63 6.9 G_front_sup 639 443 1473 3.115 0.777 0.134 0.047 10 1.2 G_Ins_lg_and_S_cent_ins 711 524 2144 3.274 0.858 0.154 0.048 13 1.3 G_insular_short 1473 951 2855 2.384 0.525 0.134 0.029 21 1.6 G_occipital_middle 1597 986 2489 2.138 0.527 0.133 0.031 21 2.0 G_occipital_sup 1211 861 2989 2.766 0.542 0.134 0.034 17 1.5 G_oc-temp_lat-fusifor 2707 1764 3923 1.939 0.570 0.151 0.041 46 4.4 G_oc-temp_med-Lingual 1016 659 2803 3.088 0.797 0.097 0.024 7 0.9 G_oc-temp_med-Parahip 1932 1437 4851 2.706 0.637 0.149 0.040 32 2.9 G_orbital 2231 1519 4953 2.559 0.512 0.141 0.031 33 2.9 G_pariet_inf-Angular 2679 1838 5352 2.452 0.533 0.128 0.029 31 3.1 G_pariet_inf-Supramar 2653 1786 4597 2.140 0.501 0.120 0.023 29 2.4 G_parietal_sup 2226 1296 3174 1.981 0.610 0.108 0.027 24 2.4 G_postcentral 2437 1393 5561 2.879 0.587 0.108 0.029 22 2.8 G_precentral 2079 1503 4175 2.304 0.485 0.143 0.033 36 2.7 G_precuneus 1064 772 2213 2.352 0.520 0.161 0.039 23 1.6 G_rectus 596 393 847 2.251 0.827 0.119 0.042 9 0.9 G_subcallosal 585 338 944 2.298 0.332 0.091 0.021 4 0.4 G_temp_sup-G_T_transv 1825 1230 5476 3.205 0.500 0.133 0.035 26 2.6 G_temp_sup-Lateral 543 364 1250 3.287 0.530 0.084 0.019 3 0.4 G_temp_sup-Plan_polar 767 502 1413 2.340 0.612 0.090 0.020 5 0.5 G_temp_sup-Plan_tempo 2037 1403 5319 2.831 0.567 0.136 0.037 35 3.1 G_temporal_inf 2021 1265 4957 2.787 0.524 0.122 0.027 29 2.1 G_temporal_middle 355 246 392 1.890 0.400 0.104 0.016 2 0.2 Lat_Fis-ant-Horizont 395 266 537 2.436 0.520 0.098 0.025 2 0.4 Lat_Fis-ant-Vertical 995 655 1225 2.339 0.546 0.116 0.025 6 1.1 Lat_Fis-post 1880 1209 2941 1.969 0.682 0.147 0.038 27 2.8 Pole_occipital 1273 991 4914 3.380 0.647 0.154 0.040 19 2.2 Pole_temporal 2387 1621 2715 1.904 0.558 0.126 0.027 21 2.9 S_calcarine 2979 2020 3422 1.945 0.669 0.107 0.022 16 3.1 S_central 985 641 1171 2.003 0.434 0.089 0.012 4 0.6 S_cingul-Marginalis 465 319 660 2.562 0.387 0.105 0.024 2 0.5 S_circular_insula_ant 1594 1046 2305 2.667 0.747 0.092 0.021 8 1.3 S_circular_insula_inf 1540 1050 2038 2.358 0.445 0.121 0.030 10 2.1 S_circular_insula_sup 774 514 1235 2.627 0.385 0.106 0.017 5 0.6 S_collat_transv_ant 468 317 484 1.933 0.379 0.136 0.030 4 0.7 S_collat_transv_post 1789 1188 2493 2.194 0.489 0.105 0.021 11 1.6 S_front_inf 947 653 1237 2.156 0.461 0.120 0.029 6 1.1 S_front_middle 1885 1306 3003 2.362 0.505 0.115 0.024 13 1.9 S_front_sup 667 440 758 2.149 0.270 0.101 0.018 4 0.5 S_interm_prim-Jensen 2820 1872 3313 1.995 0.416 0.106 0.018 17 2.3 S_intrapariet_and_P_trans 593 404 649 1.929 0.289 0.118 0.021 5 0.5 S_oc_middle_and_Lunatus 975 637 1248 2.133 0.350 0.115 0.022 7 0.9 S_oc_sup_and_transversal 530 355 768 2.230 0.314 0.121 0.022 6 0.5 S_occipital_ant 649 470 1072 2.486 0.374 0.139 0.033 7 1.0 S_oc-temp_lat 1965 1357 2953 2.331 0.520 0.116 0.021 17 1.7 S_oc-temp_med_and_Lingual 281 202 376 2.160 0.407 0.132 0.022 2 0.3 S_orbital_lateral 481 358 657 2.272 0.485 0.131 0.026 5 0.5 S_orbital_med-olfact 1134 783 2168 2.981 0.527 0.128 0.032 9 1.6 S_orbital-H_Shaped 1791 1197 2451 2.107 0.549 0.113 0.022 14 1.7 S_parieto_occipital 1165 722 872 1.590 0.581 0.121 0.027 21 1.5 S_pericallosal 2814 1833 3304 1.938 0.462 0.113 0.023 21 2.7 S_postcentral 1273 844 1871 2.530 0.387 0.097 0.018 6 1.0 S_precentral-inf-part 1474 961 2025 2.307 0.441 0.101 0.019 8 1.3 S_precentral-sup-part 566 386 721 2.313 0.497 0.114 0.019 4 0.4 S_suborbital 652 449 836 2.122 0.441 0.132 0.023 6 0.7 S_subparietal 1143 840 1674 2.433 0.445 0.129 0.022 9 1.2 S_temporal_inf 5126 3447 7354 2.310 0.454 0.105 0.018 35 4.1 S_temporal_sup 361 245 461 2.246 0.378 0.137 0.025 4 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189969 Total vertex volume 189767 (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) = 1351565 mm^3 (det: 1.441370 ) 873 702 1973 2.368 0.506 0.167 0.042 16 1.6 G_and_S_frontomargin 973 660 1595 2.318 0.447 0.139 0.029 14 1.1 G_and_S_occipital_inf 1139 588 1824 2.498 0.558 0.097 0.024 11 1.0 G_and_S_paracentral 1126 761 2238 2.453 0.457 0.124 0.021 12 1.0 G_and_S_subcentral 938 786 2539 2.607 0.581 0.179 0.047 18 2.0 G_and_S_transv_frontopol 2374 1695 4570 2.565 0.617 0.122 0.030 23 2.7 G_and_S_cingul-Ant 1246 861 2403 2.670 0.608 0.129 0.029 14 1.6 G_and_S_cingul-Mid-Ant 1069 706 1934 2.545 0.476 0.104 0.021 8 1.0 G_and_S_cingul-Mid-Post 438 305 1144 2.706 0.505 0.143 0.033 8 0.6 G_cingul-Post-dorsal 263 160 493 2.251 0.761 0.130 0.036 4 0.3 G_cingul-Post-ventral 2215 1352 2741 1.801 0.425 0.131 0.034 31 3.0 G_cuneus 986 705 2535 2.773 0.395 0.122 0.024 12 1.0 G_front_inf-Opercular 312 240 863 2.562 0.530 0.150 0.039 6 0.5 G_front_inf-Orbital 712 529 1781 2.534 0.524 0.155 0.034 12 1.2 G_front_inf-Triangul 3930 2964 9186 2.460 0.529 0.155 0.034 71 6.1 G_front_middle 5111 3464 11912 2.770 0.579 0.134 0.032 66 6.8 G_front_sup 534 356 1329 3.138 0.770 0.116 0.035 8 0.6 G_Ins_lg_and_S_cent_ins 609 457 1555 2.899 0.665 0.151 0.048 10 1.1 G_insular_short 1964 1370 4433 2.532 0.440 0.139 0.031 30 2.3 G_occipital_middle 1755 1134 2713 2.082 0.414 0.121 0.027 20 1.9 G_occipital_sup 1573 1011 3647 2.689 0.528 0.125 0.034 22 1.9 G_oc-temp_lat-fusifor 2685 1748 4439 2.190 0.632 0.145 0.037 40 4.1 G_oc-temp_med-Lingual 1245 838 3786 3.234 0.844 0.119 0.036 14 1.6 G_oc-temp_med-Parahip 2270 1641 5371 2.536 0.671 0.141 0.040 40 3.4 G_orbital 2521 1774 5662 2.515 0.389 0.141 0.032 41 3.4 G_pariet_inf-Angular 1843 1266 4067 2.632 0.455 0.126 0.028 23 2.0 G_pariet_inf-Supramar 2170 1384 3993 2.307 0.381 0.109 0.023 25 1.9 G_parietal_sup 1818 1049 2589 1.928 0.487 0.109 0.023 19 1.7 G_postcentral 2641 1485 5129 2.662 0.422 0.103 0.024 24 2.5 G_precentral 1870 1257 3887 2.431 0.497 0.125 0.029 24 2.1 G_precuneus 626 457 1192 2.144 0.537 0.122 0.037 13 0.8 G_rectus 422 291 710 2.595 0.779 0.141 0.046 5 0.9 G_subcallosal 338 181 599 2.546 0.297 0.112 0.024 5 0.3 G_temp_sup-G_T_transv 1616 1090 4493 2.994 0.495 0.135 0.032 23 2.2 G_temp_sup-Lateral 666 458 1497 3.256 0.724 0.075 0.015 2 0.4 G_temp_sup-Plan_polar 738 476 1346 2.481 0.512 0.095 0.020 5 0.5 G_temp_sup-Plan_tempo 2033 1476 5492 2.845 0.719 0.159 0.046 43 3.5 G_temporal_inf 2218 1548 5477 2.694 0.463 0.127 0.027 32 2.3 G_temporal_middle 377 253 427 1.936 0.286 0.090 0.014 1 0.2 Lat_Fis-ant-Horizont 186 132 319 2.590 0.425 0.110 0.021 1 0.1 Lat_Fis-ant-Vertical 1236 824 1552 2.234 0.388 0.106 0.020 7 1.1 Lat_Fis-post 3401 2143 4307 1.847 0.471 0.141 0.033 50 4.6 Pole_occipital 1516 1138 4761 3.169 0.602 0.144 0.035 25 2.2 Pole_temporal 2266 1568 2517 1.778 0.493 0.119 0.026 20 2.5 S_calcarine 2731 1888 3189 1.943 0.593 0.094 0.017 12 2.0 S_central 1073 715 1407 2.193 0.435 0.088 0.012 4 0.6 S_cingul-Marginalis 554 394 954 2.542 0.549 0.131 0.038 5 0.8 S_circular_insula_ant 1256 804 1701 2.475 0.708 0.082 0.017 7 1.0 S_circular_insula_inf 1225 798 1573 2.459 0.361 0.102 0.026 7 1.3 S_circular_insula_sup 1010 701 1550 2.452 0.424 0.099 0.017 4 0.8 S_collat_transv_ant 420 285 461 1.875 0.303 0.127 0.026 3 0.5 S_collat_transv_post 1231 884 1751 2.129 0.422 0.116 0.024 10 1.4 S_front_inf 1579 1163 2241 2.051 0.393 0.123 0.023 12 1.7 S_front_middle 1760 1192 2521 2.302 0.419 0.101 0.019 9 1.4 S_front_sup 297 210 356 2.110 0.433 0.131 0.019 2 0.3 S_interm_prim-Jensen 3801 2516 4766 1.988 0.385 0.093 0.015 20 2.5 S_intrapariet_and_P_trans 908 607 1092 2.020 0.417 0.118 0.023 6 1.0 S_oc_middle_and_Lunatus 1349 905 1742 2.074 0.392 0.113 0.020 9 1.2 S_oc_sup_and_transversal 508 356 674 2.167 0.405 0.126 0.031 4 0.7 S_occipital_ant 659 477 970 2.289 0.504 0.128 0.024 7 0.7 S_oc-temp_lat 1662 1112 2295 2.329 0.407 0.095 0.015 8 1.1 S_oc-temp_med_and_Lingual 274 202 390 1.997 0.455 0.129 0.040 2 0.4 S_orbital_lateral 761 579 1118 2.228 0.712 0.157 0.039 9 1.5 S_orbital_med-olfact 1225 846 1987 2.486 0.478 0.124 0.030 11 1.6 S_orbital-H_Shaped 1841 1200 2279 1.963 0.546 0.110 0.021 14 1.7 S_parieto_occipital 1334 861 1051 1.551 0.532 0.115 0.020 20 1.0 S_pericallosal 2331 1577 2711 1.875 0.351 0.099 0.018 14 1.9 S_postcentral 1411 943 1989 2.346 0.432 0.112 0.022 10 1.3 S_precentral-inf-part 1156 761 1512 2.272 0.491 0.092 0.016 5 0.8 S_precentral-sup-part 283 191 351 2.203 0.519 0.111 0.015 2 0.3 S_suborbital 760 550 1123 2.287 0.503 0.131 0.026 6 0.8 S_subparietal 950 662 1248 2.382 0.441 0.119 0.018 6 1.0 S_temporal_inf 5278 3523 7437 2.318 0.366 0.097 0.018 29 4.1 S_temporal_sup 194 138 307 2.273 0.294 0.126 0.022 2 0.2 S_temporal_transverse PIDs (2866025 2866028) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Nov 20 23:56:16 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 3 rh Wed Nov 20 23:56:16 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh white Waiting for PID 2866302 of (2866302 2866305) to complete... Waiting for PID 2866305 of (2866302 2866305) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189233 Total vertex volume 189022 (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) = 1351565 mm^3 (det: 1.441370 ) 1410 901 2330 2.574 0.535 0.118 0.021 15 1.2 caudalanteriorcingulate 2364 1565 4031 2.457 0.518 0.111 0.023 17 2.3 caudalmiddlefrontal 2808 1719 3615 1.913 0.441 0.133 0.033 38 3.7 cuneus 537 369 1598 3.359 0.729 0.101 0.022 3 0.5 entorhinal 3043 2164 6170 2.630 0.502 0.135 0.031 37 3.7 fusiform 5009 3390 8824 2.342 0.490 0.124 0.025 53 5.1 inferiorparietal 3789 2696 8999 2.738 0.607 0.131 0.031 49 5.2 inferiortemporal 1283 869 1893 1.962 0.730 0.126 0.033 19 1.8 isthmuscingulate 6062 3968 9633 2.136 0.580 0.138 0.031 75 7.8 lateraloccipital 3426 2458 7058 2.736 0.644 0.137 0.037 45 5.0 lateralorbitofrontal 4079 2683 5600 1.924 0.556 0.136 0.033 57 5.6 lingual 1994 1415 3479 2.300 0.586 0.136 0.032 32 2.3 medialorbitofrontal 4982 3281 9709 2.582 0.543 0.117 0.024 53 5.0 middletemporal 964 616 1929 2.660 0.732 0.092 0.019 6 0.7 parahippocampal 2172 1297 3408 2.445 0.518 0.091 0.019 12 1.6 paracentral 2020 1358 3709 2.529 0.436 0.114 0.025 19 2.2 parsopercularis 984 707 1956 2.478 0.485 0.131 0.028 12 1.3 parsorbitalis 2216 1490 4155 2.453 0.555 0.124 0.026 21 2.3 parstriangularis 1917 1285 2121 1.850 0.521 0.130 0.029 18 2.5 pericalcarine 6342 3999 8383 1.950 0.621 0.109 0.024 57 6.1 postcentral 1511 1017 2516 2.292 0.639 0.121 0.025 17 1.6 posteriorcingulate 6664 4169 11877 2.588 0.585 0.110 0.026 51 7.1 precentral 4286 2985 7198 2.238 0.493 0.130 0.027 52 4.9 precuneus 1210 878 2601 2.764 0.660 0.152 0.039 22 2.1 rostralanteriorcingulate 3981 2889 7412 2.330 0.555 0.143 0.036 51 5.7 rostralmiddlefrontal 9249 6558 20083 2.635 0.566 0.129 0.029 98 11.6 superiorfrontal 5781 3843 8419 2.054 0.474 0.114 0.021 51 5.1 superiorparietal 6891 4651 14826 2.770 0.663 0.112 0.025 63 7.2 superiortemporal 5217 3518 8921 2.355 0.530 0.123 0.026 52 5.6 supramarginal 703 405 1031 2.240 0.328 0.101 0.023 6 0.6 transversetemporal 2763 1936 5539 2.847 0.830 0.130 0.040 33 4.4 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189969 Total vertex volume 189767 (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) = 1351565 mm^3 (det: 1.441370 ) 1117 776 2140 2.488 0.776 0.138 0.030 20 1.4 caudalanteriorcingulate 2903 1965 4977 2.329 0.453 0.119 0.022 26 2.8 caudalmiddlefrontal 2727 1714 3244 1.746 0.419 0.125 0.030 32 3.2 cuneus 534 373 1923 3.559 0.677 0.112 0.025 5 0.5 entorhinal 3224 2168 6355 2.572 0.557 0.119 0.029 35 3.7 fusiform 6585 4548 11202 2.303 0.397 0.123 0.024 69 6.7 inferiorparietal 3885 2819 8906 2.713 0.656 0.140 0.035 60 5.4 inferiortemporal 1269 814 1774 1.904 0.707 0.114 0.026 15 1.1 isthmuscingulate 6752 4437 10256 2.119 0.510 0.135 0.030 88 8.0 lateraloccipital 3702 2670 7251 2.541 0.609 0.145 0.039 53 6.0 lateralorbitofrontal 4240 2826 6112 2.044 0.578 0.137 0.034 52 6.2 lingual 1904 1366 3433 2.320 0.653 0.135 0.037 32 2.9 medialorbitofrontal 4774 3298 9611 2.560 0.469 0.115 0.022 48 4.4 middletemporal 988 633 2013 2.690 0.791 0.100 0.023 8 0.9 parahippocampal 1993 1122 3041 2.521 0.584 0.092 0.021 13 1.7 paracentral 1646 1150 3064 2.533 0.417 0.113 0.025 15 1.5 parsopercularis 913 666 1976 2.432 0.514 0.124 0.031 11 1.2 parsorbitalis 1577 1156 2990 2.296 0.506 0.133 0.032 18 2.3 parstriangularis 2273 1474 2344 1.682 0.394 0.115 0.025 23 2.3 pericalcarine 5555 3520 7366 1.912 0.514 0.104 0.019 44 4.6 postcentral 1463 1005 2605 2.359 0.672 0.121 0.024 17 1.5 posteriorcingulate 6379 4028 10928 2.481 0.518 0.101 0.021 45 5.6 precentral 4452 3003 7474 2.303 0.517 0.124 0.026 47 4.8 precuneus 841 572 1643 2.725 0.712 0.105 0.023 7 0.8 rostralanteriorcingulate 4404 3403 8884 2.265 0.541 0.151 0.034 72 6.8 rostralmiddlefrontal 10297 7328 21422 2.572 0.581 0.131 0.030 114 13.3 superiorfrontal 6797 4421 10285 2.111 0.414 0.100 0.019 53 5.4 superiorparietal 6061 4071 12927 2.744 0.661 0.110 0.024 54 6.1 superiortemporal 4182 2835 7529 2.408 0.458 0.111 0.024 39 4.1 supramarginal 431 250 694 2.512 0.279 0.111 0.021 5 0.4 transversetemporal 2795 1915 5397 2.761 0.716 0.123 0.035 31 3.9 insula PIDs (2866302 2866305) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Wed Nov 20 23:56:28 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1351565 mm^3 (det: 1.441370 ) Computing euler number orig.nofix lheno = -10, rheno = -12 orig.nofix lhholes = 6, rhholes = 7 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 2024:11:20:23:56:28 mri_segstats N 32 e 88.45 S 0.93 U 327.06 P 370% M 280640 F 1 R 973414 W 0 c 30487 w 1442 I 0 O 24 L 12.10 9.78 9.60 @#@FSLOADPOST 2024:11:20:23:57:57 mri_segstats N 32 13.40 10.74 9.96 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed Nov 20 23:57:57 CST 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 2867944 of (2867944 2867948 2867951 2867954 2867957) to complete... Waiting for PID 2867948 of (2867944 2867948 2867951 2867954 2867957) to complete... Waiting for PID 2867951 of (2867944 2867948 2867951 2867954 2867957) to complete... Waiting for PID 2867954 of (2867944 2867948 2867951 2867954 2867957) to complete... Waiting for PID 2867957 of (2867944 2867948 2867951 2867954 2867957) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4217 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 136 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8045 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4103 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6063 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 117 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5901 mri_label2label: Done PIDs (2867944 2867948 2867951 2867954 2867957) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 2868188 of (2868188 2868192 2868195 2868198) to complete... Waiting for PID 2868192 of (2868188 2868192 2868195 2868198) to complete... Waiting for PID 2868195 of (2868188 2868192 2868195 2868198) to complete... Waiting for PID 2868198 of (2868188 2868192 2868195 2868198) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4127 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13836 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4245 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 233 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3655 mri_label2label: Done PIDs (2868188 2868192 2868195 2868198) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 2868438 of (2868438 2868442 2868445 2868448 2868451) to complete... Waiting for PID 2868442 of (2868438 2868442 2868445 2868448 2868451) to complete... Waiting for PID 2868445 of (2868438 2868442 2868445 2868448 2868451) to complete... Waiting for PID 2868448 of (2868438 2868442 2868445 2868448 2868451) to complete... Waiting for PID 2868451 of (2868438 2868442 2868445 2868448 2868451) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 916 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5557 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 1610 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9724 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2062 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1310 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1210 mri_label2label: Done PIDs (2868438 2868442 2868445 2868448 2868451) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 2868668 of (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) to complete... Waiting for PID 2868671 of (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) to complete... Waiting for PID 2868674 of (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) to complete... Waiting for PID 2868677 of (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) to complete... Waiting for PID 2868680 of (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) to complete... Waiting for PID 2868684 of (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) to complete... Waiting for PID 2868687 of (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) to complete... Waiting for PID 2868690 of (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 442 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 726 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1920 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2211 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 764 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4641 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 762 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3681 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 219 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1505 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1168 mri_label2label: Done PIDs (2868668 2868671 2868674 2868677 2868680 2868684 2868687 2868690) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 99907 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.mpm.vpnl.annot @#@FSTIME 2024:11:20:23:58:24 mris_label2annot N 26 e 0.72 S 0.10 U 0.90 P 139% M 133252 F 1 R 36197 W 0 c 96 w 181 I 0 O 1784 L 14.17 11.17 10.13 @#@FSLOADPOST 2024:11:20:23:58:25 mris_label2annot N 26 14.17 11.17 10.13 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 2869024 of (2869024 2869028 2869031 2869036 2869039) to complete... Waiting for PID 2869028 of (2869024 2869028 2869031 2869036 2869039) to complete... Waiting for PID 2869031 of (2869024 2869028 2869031 2869036 2869039) to complete... Waiting for PID 2869036 of (2869024 2869028 2869031 2869036 2869039) to complete... Waiting for PID 2869039 of (2869024 2869028 2869031 2869036 2869039) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1040 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2139 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1510 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2014 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2361 mri_label2label: Done PIDs (2869024 2869028 2869031 2869036 2869039) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 2869306 of (2869306 2869309 2869312 2869315) to complete... Waiting for PID 2869309 of (2869306 2869309 2869312 2869315) to complete... Waiting for PID 2869312 of (2869306 2869309 2869312 2869315) to complete... Waiting for PID 2869315 of (2869306 2869309 2869312 2869315) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1571 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 172 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7207 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1941 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 126 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1277 mri_label2label: Done PIDs (2869306 2869309 2869312 2869315) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 2869514 of (2869514 2869517 2869521 2869524 2869527) to complete... Waiting for PID 2869517 of (2869514 2869517 2869521 2869524 2869527) to complete... Waiting for PID 2869521 of (2869514 2869517 2869521 2869524 2869527) to complete... Waiting for PID 2869524 of (2869514 2869517 2869521 2869524 2869527) to complete... Waiting for PID 2869527 of (2869514 2869517 2869521 2869524 2869527) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 671 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 820 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 523 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 480 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113658 Number of reverse mapping hits = 2 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 452 mri_label2label: Done PIDs (2869514 2869517 2869521 2869524 2869527) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 77474 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.BA_exvivo.annot @#@FSTIME 2024:11:20:23:58:43 mris_label2annot N 38 e 0.73 S 0.11 U 0.94 P 143% M 133752 F 3 R 36329 W 0 c 104 w 293 I 0 O 1784 L 15.47 11.67 10.32 @#@FSLOADPOST 2024:11:20:23:58:44 mris_label2annot N 38 15.47 11.67 10.32 mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 91460 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2024:11:20:23:58:44 mris_label2annot N 38 e 0.70 S 0.08 U 0.93 P 145% M 133688 F 1 R 36297 W 0 c 96 w 277 I 0 O 1784 L 15.47 11.67 10.32 @#@FSLOADPOST 2024:11:20:23:58:45 mris_label2annot N 38 15.47 11.67 10.32 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189233 Total vertex volume 189022 (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) = 1351565 mm^3 (det: 1.441370 ) 1062 582 1685 2.173 0.662 0.118 0.030 15 1.1 BA1_exvivo 3639 2345 4827 2.006 0.506 0.110 0.022 28 3.6 BA2_exvivo 976 678 906 1.702 0.393 0.132 0.029 7 1.3 BA3a_exvivo 2174 1377 2585 1.728 0.551 0.101 0.023 18 1.9 BA3b_exvivo 1492 799 2636 2.736 0.537 0.090 0.023 10 1.4 BA4a_exvivo 1271 795 2095 2.720 0.515 0.102 0.025 7 1.5 BA4p_exvivo 7871 5067 15795 2.674 0.598 0.110 0.023 61 7.7 BA6_exvivo 1925 1293 3519 2.529 0.413 0.116 0.026 19 2.1 BA44_exvivo 2643 1794 5105 2.468 0.523 0.126 0.029 28 3.0 BA45_exvivo 3448 2164 4226 1.865 0.556 0.127 0.032 41 4.5 V1_exvivo 7220 4731 10012 1.950 0.531 0.146 0.036 102 10.6 V2_exvivo 1399 934 2728 2.481 0.421 0.126 0.026 16 1.4 MT_exvivo 543 392 1369 3.142 0.668 0.113 0.024 4 0.5 perirhinal_exvivo 521 346 1686 3.296 1.116 0.105 0.031 6 0.8 entorhinal_exvivo @#@FSTIME 2024:11:20:23:58:45 mris_anatomical_stats N 12 e 4.23 S 0.30 U 6.25 P 154% M 403128 F 1 R 192281 W 0 c 611 w 335 I 0 O 136 L 15.47 11.67 10.32 @#@FSLOADPOST 2024:11:20:23:58:49 mris_anatomical_stats N 12 14.71 11.58 10.29 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189233 Total vertex volume 189022 (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) = 1351565 mm^3 (det: 1.441370 ) 704 351 1098 2.199 0.683 0.134 0.041 12 1.0 BA1_exvivo 1401 889 1851 1.974 0.489 0.094 0.019 8 1.1 BA2_exvivo 817 576 757 1.699 0.381 0.136 0.031 6 1.2 BA3a_exvivo 1335 884 1291 1.432 0.337 0.094 0.018 8 1.1 BA3b_exvivo 1473 819 2660 2.759 0.527 0.090 0.026 9 1.6 BA4a_exvivo 1064 654 1651 2.650 0.519 0.098 0.023 6 1.1 BA4p_exvivo 4684 2960 9819 2.719 0.630 0.109 0.025 37 4.6 BA6_exvivo 1252 849 2311 2.553 0.407 0.123 0.030 14 1.6 BA44_exvivo 1111 737 2398 2.571 0.516 0.125 0.028 12 1.2 BA45_exvivo 3661 2302 4520 1.864 0.544 0.126 0.032 43 4.8 V1_exvivo 3748 2471 5050 1.882 0.534 0.158 0.041 59 6.5 V2_exvivo 396 270 585 2.364 0.358 0.111 0.018 2 0.3 MT_exvivo 230 163 475 2.977 0.543 0.093 0.017 1 0.2 perirhinal_exvivo 322 214 1169 3.755 0.577 0.085 0.015 2 0.2 entorhinal_exvivo @#@FSTIME 2024:11:20:23:58:49 mris_anatomical_stats N 12 e 3.59 S 0.28 U 4.94 P 145% M 402572 F 4 R 153946 W 0 c 483 w 264 I 0 O 136 L 14.71 11.58 10.29 @#@FSLOADPOST 2024:11:20:23:58:53 mris_anatomical_stats N 12 14.41 11.57 10.30 #-------------------------------------------- #@# BA_exvivo Labels rh Wed Nov 20 23:58:53 CST 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 2870122 of (2870122 2870125 2870128 2870131 2870135) to complete... Waiting for PID 2870125 of (2870122 2870125 2870128 2870131 2870135) to complete... Waiting for PID 2870128 of (2870122 2870125 2870128 2870131 2870135) to complete... Waiting for PID 2870131 of (2870122 2870125 2870128 2870131 2870135) to complete... Waiting for PID 2870135 of (2870122 2870125 2870128 2870131 2870135) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 3988 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6719 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 3995 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4534 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5793 mri_label2label: Done PIDs (2870122 2870125 2870128 2870131 2870135) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 2870320 of (2870320 2870323 2870326 2870329) to complete... Waiting for PID 2870323 of (2870320 2870323 2870326 2870329) to complete... Waiting for PID 2870326 of (2870320 2870323 2870326 2870329) to complete... Waiting for PID 2870329 of (2870320 2870323 2870326 2870329) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4514 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12346 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 6989 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 147 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5502 mri_label2label: Done PIDs (2870320 2870323 2870326 2870329) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 2870440 of (2870440 2870443 2870446 2870449 2870452) to complete... Waiting for PID 2870443 of (2870440 2870443 2870446 2870449 2870452) to complete... Waiting for PID 2870446 of (2870440 2870443 2870446 2870449 2870452) to complete... Waiting for PID 2870449 of (2870440 2870443 2870446 2870449 2870452) to complete... Waiting for PID 2870452 of (2870440 2870443 2870446 2870449 2870452) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 1259 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5986 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 1860 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9876 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2032 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1067 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 774 mri_label2label: Done PIDs (2870440 2870443 2870446 2870449 2870452) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 2870577 of (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) to complete... Waiting for PID 2870580 of (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) to complete... Waiting for PID 2870584 of (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) to complete... Waiting for PID 2870587 of (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) to complete... Waiting for PID 2870590 of (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) to complete... Waiting for PID 2870593 of (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) to complete... Waiting for PID 2870596 of (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) to complete... Waiting for PID 2870600 of (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 647 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 835 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1606 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1641 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 976 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4643 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 707 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3426 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 268 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1496 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 281 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1306 mri_label2label: Done PIDs (2870577 2870580 2870584 2870587 2870590 2870593 2870596 2870600) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 100718 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.mpm.vpnl.annot @#@FSTIME 2024:11:20:23:59:18 mris_label2annot N 26 e 0.59 S 0.07 U 0.76 P 142% M 134516 F 2 R 36558 W 0 c 85 w 207 I 0 O 1792 L 13.01 11.46 10.29 @#@FSLOADPOST 2024:11:20:23:59:18 mris_label2annot N 26 13.01 11.46 10.29 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 2870799 of (2870799 2870802 2870806 2870809 2870812) to complete... Waiting for PID 2870802 of (2870799 2870802 2870806 2870809 2870812) to complete... Waiting for PID 2870806 of (2870799 2870802 2870806 2870809 2870812) to complete... Waiting for PID 2870809 of (2870799 2870802 2870806 2870809 2870812) to complete... Waiting for PID 2870812 of (2870799 2870802 2870806 2870809 2870812) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 894 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 8 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2696 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1702 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2186 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1391 mri_label2label: Done PIDs (2870799 2870802 2870806 2870809 2870812) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 2870911 of (2870911 2870914 2870917 2870920) to complete... Waiting for PID 2870914 of (2870911 2870914 2870917 2870920) to complete... Waiting for PID 2870917 of (2870911 2870914 2870917 2870920) to complete... Waiting for PID 2870920 of (2870911 2870914 2870917 2870920) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1509 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7006 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1016 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 8 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1186 mri_label2label: Done PIDs (2870911 2870914 2870917 2870920) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 2871028 of (2871028 2871032 2871035 2871038 2871041) to complete... Waiting for PID 2871032 of (2871028 2871032 2871035 2871038 2871041) to complete... Waiting for PID 2871035 of (2871028 2871032 2871035 2871038 2871041) to complete... Waiting for PID 2871038 of (2871028 2871032 2871035 2871038 2871041) to complete... Waiting for PID 2871041 of (2871028 2871032 2871035 2871038 2871041) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 855 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4087 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 934 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4371 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 279 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 711 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114515 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 301 mri_label2label: Done PIDs (2871028 2871032 2871035 2871038 2871041) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 79977 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.BA_exvivo.annot @#@FSTIME 2024:11:20:23:59:34 mris_label2annot N 38 e 0.64 S 0.07 U 0.81 P 137% M 134740 F 2 R 36726 W 0 c 84 w 245 I 0 O 1792 L 12.41 11.40 10.29 @#@FSLOADPOST 2024:11:20:23:59:35 mris_label2annot N 38 12.41 11.40 10.29 mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 94545 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2024:11:20:23:59:35 mris_label2annot N 38 e 0.59 S 0.09 U 0.73 P 140% M 134552 F 2 R 36664 W 0 c 78 w 252 I 0 O 1792 L 12.41 11.40 10.29 @#@FSLOADPOST 2024:11:20:23:59:36 mris_label2annot N 38 12.41 11.40 10.29 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189969 Total vertex volume 189767 (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) = 1351565 mm^3 (det: 1.441370 ) 823 440 1341 2.151 0.504 0.133 0.031 12 1.2 BA1_exvivo 2612 1710 3165 1.882 0.415 0.101 0.019 17 2.1 BA2_exvivo 942 709 980 1.744 0.333 0.133 0.024 6 1.0 BA3a_exvivo 1613 1016 1905 1.717 0.493 0.087 0.015 9 1.0 BA3b_exvivo 1289 665 2168 2.760 0.455 0.078 0.024 8 1.1 BA4a_exvivo 1187 726 1804 2.559 0.467 0.074 0.015 4 0.7 BA4p_exvivo 6271 3925 11795 2.596 0.533 0.107 0.023 52 5.8 BA6_exvivo 2887 1974 5245 2.489 0.452 0.119 0.023 26 2.9 BA44_exvivo 2911 2188 6188 2.365 0.514 0.137 0.032 39 4.0 BA45_exvivo 3973 2505 4629 1.760 0.437 0.122 0.030 45 4.8 V1_exvivo 7538 4938 10470 1.980 0.519 0.144 0.035 105 10.9 V2_exvivo 1616 1093 2702 2.365 0.453 0.119 0.028 18 1.6 MT_exvivo 344 262 925 3.371 0.562 0.149 0.027 3 0.5 perirhinal_exvivo 532 363 2076 3.556 0.839 0.097 0.024 5 0.5 entorhinal_exvivo @#@FSTIME 2024:11:20:23:59:36 mris_anatomical_stats N 12 e 3.54 S 0.31 U 4.83 P 145% M 405156 F 1 R 155069 W 0 c 479 w 317 I 0 O 136 L 12.41 11.40 10.29 @#@FSLOADPOST 2024:11:20:23:59:39 mris_anatomical_stats N 12 11.82 11.30 10.26 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189969 Total vertex volume 189767 (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) = 1351565 mm^3 (det: 1.441370 ) 550 298 823 2.033 0.531 0.129 0.029 8 0.7 BA1_exvivo 1493 948 1873 1.862 0.386 0.087 0.015 8 0.9 BA2_exvivo 849 642 847 1.738 0.335 0.138 0.026 6 1.0 BA3a_exvivo 1280 842 1285 1.548 0.340 0.081 0.013 5 0.7 BA3b_exvivo 750 333 1226 2.861 0.493 0.091 0.035 8 0.9 BA4a_exvivo 984 614 1497 2.568 0.469 0.075 0.015 3 0.6 BA4p_exvivo 4065 2516 7631 2.613 0.544 0.108 0.023 34 3.7 BA6_exvivo 629 455 1361 2.728 0.330 0.129 0.031 7 0.7 BA44_exvivo 716 536 1790 2.649 0.430 0.140 0.031 9 0.9 BA45_exvivo 3800 2405 4328 1.744 0.431 0.120 0.030 41 4.4 V1_exvivo 4078 2666 5505 1.888 0.508 0.155 0.039 66 6.8 V2_exvivo 213 145 418 2.429 0.495 0.136 0.035 3 0.3 MT_exvivo 34 28 80 3.568 0.593 0.159 0.032 0 0.1 perirhinal_exvivo 529 354 1836 3.656 0.656 0.099 0.020 4 0.4 entorhinal_exvivo @#@FSTIME 2024:11:20:23:59:39 mris_anatomical_stats N 12 e 3.96 S 0.43 U 5.36 P 146% M 405376 F 2 R 198570 W 0 c 528 w 297 I 0 O 136 L 11.82 11.30 10.26 @#@FSLOADPOST 2024:11:20:23:59:43 mris_anatomical_stats N 12 11.27 11.19 10.24 Started at Wed Nov 20 20:58:10 CST 2024 Ended at Wed Nov 20 23:59:43 CST 2024 #@#%# recon-all-run-time-hours 3.026 recon-all -s PIB15-273_VYr9_Bay3prisma finished without error at Wed Nov 20 23:59:43 CST 2024 #New# invocation of recon-all Fri Nov 22 11:17:44 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma/ -autorecon2 -autorecon3 subjid PIB15-273_VYr9_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 143Gi 30Gi 8.0Mi 76Gi 104Gi Swap: 111Gi 230Mi 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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-17:17:44-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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 Fri Nov 22 11:17:45 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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=17.9 skull bounding box = (64, 72, 50) --> (190, 197, 210) finding center of left hemi white matter using (106, 114, 130) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (91,99,110) --> (121, 129,149) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 106 +- 4.5 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.341 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.157681 @ (-10.526, -10.526, -10.526) max log p = -3.958246 @ (5.263, 5.263, -5.263) max log p = -3.910158 @ (2.632, -7.895, -2.632) max log p = -3.891977 @ (-1.316, 1.316, -1.316) max log p = -3.879139 @ (0.658, 0.658, -1.974) max log p = -3.879139 @ (0.000, 0.000, 0.000) max log p = -3.879139 @ (0.000, 0.000, 0.000) max log p = -3.879139 @ (0.000, 0.000, 0.000) Found translation: (-3.3, -11.2, -21.7): log p = -3.879 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.666, old_max_log_p =-3.879 (thresh=-3.9) 1.05465 0.01348 -0.12032 3.13871; 0.00000 1.13509 0.16902 -42.79792; 0.16136 -0.11896 1.06209 -27.57447; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 22 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.666, old_max_log_p =-3.666 (thresh=-3.7) 1.05465 0.01348 -0.12032 3.13871; 0.00000 1.13509 0.16902 -42.79792; 0.16136 -0.11896 1.06209 -27.57447; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.448, old_max_log_p =-3.666 (thresh=-3.7) 1.12108 0.08444 -0.04168 -23.72408; -0.07385 1.15689 0.13951 -34.19447; 0.08803 -0.08093 1.05262 -25.39273; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.436, old_max_log_p =-3.448 (thresh=-3.4) 1.09826 0.04954 -0.08005 -11.64689; -0.03498 1.17757 0.17451 -46.14056; 0.12465 -0.11374 1.02596 -22.71021; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 21 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.436, old_max_log_p =-3.436 (thresh=-3.4) 1.09826 0.04954 -0.08005 -11.64689; -0.03498 1.17757 0.17451 -46.14056; 0.12465 -0.11374 1.02596 -22.71021; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 20 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.400, old_max_log_p =-3.436 (thresh=-3.4) 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09762 -0.10581 1.03262 -21.03091; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 19 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.392, old_max_log_p =-3.400 (thresh=-3.4) 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 19 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.392, old_max_log_p =-3.392 (thresh=-3.4) 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 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 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 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: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.392 (old=-4.341) transform before final EM align: 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 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 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 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: 012: -log(p) = 3.9 tol 0.000000 final transform: 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 798456 FSRUNTIME@ mri_em_register 0.0577 hours 4 threads registration took 3 minutes and 28 seconds. @#@FSTIME 2024:11:22:11:17:45 mri_em_register N 7 e 207.63 S 1.56 U 714.90 P 345% M 616672 F 0 R 1073220 W 0 c 66045 w 379 I 328 O 32 L 27.87 23.30 23.00 @#@FSLOADPOST 2024:11:22:11:21:12 mri_em_register N 7 28.57 25.95 24.13 #-------------------------------------- #@# CA Normalize Fri Nov 22 11:21:12 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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=17.9 skull bounding box = (64, 72, 48) --> (190, 197, 210) finding center of left hemi white matter using (106, 114, 129) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (91,99,109) --> (121, 129,148) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 106 +- 4.5 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246437 sample points... INFO: compute sample coordinates transform 1.09938 0.05633 -0.05324 -15.94840; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47582; 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 (124, 70, 47) --> (189, 168, 207) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 1423 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 71, 49) --> (133, 167, 210) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 2 of 1211 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 143, 70) --> (170, 184, 123) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 21 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (85, 143, 72) --> (126, 180, 127) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 55 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (112, 136, 106) --> (144, 195, 136) Brain_Stem: limiting intensities to 104.0 --> 132.0 18 of 34 (52.9%) samples deleted using 2744 total control points for intensity normalization... bias field = 0.966 +- 0.052 19 of 2724 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (124, 70, 47) --> (189, 168, 207) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 1725 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 71, 49) --> (133, 167, 210) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 2 of 1562 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 143, 70) --> (170, 184, 123) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 92 (10.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (85, 143, 72) --> (126, 180, 127) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 102 (2.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (112, 136, 106) --> (144, 195, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 22 of 122 (18.0%) samples deleted using 3603 total control points for intensity normalization... bias field = 1.014 +- 0.053 13 of 3543 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (124, 70, 47) --> (189, 168, 207) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 1765 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (69, 71, 49) --> (133, 167, 210) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 3 of 1593 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (127, 143, 70) --> (170, 184, 123) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 30 of 127 (23.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (85, 143, 72) --> (126, 180, 127) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 62 of 153 (40.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (112, 136, 106) --> (144, 195, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 112 of 208 (53.8%) samples deleted using 3846 total control points for intensity normalization... bias field = 1.012 +- 0.048 11 of 3563 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 2 seconds. @#@FSTIME 2024:11:22:11:21:12 mri_ca_normalize N 8 e 62.32 S 0.90 U 64.33 P 104% M 695620 F 0 R 781891 W 0 c 6071 w 349 I 0 O 3456 L 28.57 25.95 24.13 @#@FSLOADPOST 2024:11:22:11:22:15 mri_ca_normalize N 8 28.84 26.51 24.45 #-------------------------------------- #@# SubCort Seg Fri Nov 22 11:22:15 CST 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/PIB15-273_VYr9_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/PIB15-273_VYr9_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 5.70 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 = 0.13094 (23) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2443 voxels, overlap=0.888) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (2443 voxels, peak = 20), gca=20.5 gca peak = 0.20380 (13) mri peak = 0.14176 (23) Right_Lateral_Ventricle (43): linear fit = 1.26 x + 0.0 (4353 voxels, overlap=0.456) Right_Lateral_Ventricle (43): linear fit = 1.26 x + 0.0 (4353 voxels, peak = 16), gca=16.4 gca peak = 0.26283 (96) mri peak = 0.08190 (90) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (475 voxels, overlap=0.640) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (475 voxels, peak = 92), gca=91.7 gca peak = 0.15814 (97) mri peak = 0.10953 (97) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (494 voxels, overlap=0.973) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (494 voxels, peak = 96), gca=95.5 gca peak = 0.27624 (56) mri peak = 0.13102 (67) Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (892 voxels, overlap=0.017) Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (892 voxels, peak = 66), gca=65.8 gca peak = 0.28723 (59) mri peak = 0.09316 (68) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (687 voxels, overlap=0.022) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (687 voxels, peak = 71), gca=70.5 gca peak = 0.07623 (103) mri peak = 0.11563 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (26679 voxels, overlap=0.618) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (26679 voxels, peak = 106), gca=105.6 gca peak = 0.07837 (105) mri peak = 0.12235 (109) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (29849 voxels, overlap=0.525) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (29849 voxels, peak = 109), gca=108.7 gca peak = 0.10165 (58) mri peak = 0.04206 (67) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (17128 voxels, overlap=0.449) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (17128 voxels, peak = 69), gca=68.7 gca peak = 0.11113 (58) mri peak = 0.03902 (72) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (16758 voxels, overlap=0.252) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (16758 voxels, peak = 71), gca=71.1 gca peak = 0.27796 (67) mri peak = 0.14239 (78) Right_Caudate (50): linear fit = 1.14 x + 0.0 (759 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.14 x + 0.0 (759 voxels, peak = 77), gca=76.7 gca peak = 0.14473 (69) mri peak = 0.11626 (78) Left_Caudate (11): linear fit = 1.10 x + 0.0 (800 voxels, overlap=0.573) Left_Caudate (11): linear fit = 1.10 x + 0.0 (800 voxels, peak = 76), gca=75.6 gca peak = 0.14301 (56) mri peak = 0.06147 (65) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (18135 voxels, overlap=0.641) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (18135 voxels, peak = 65), gca=64.7 gca peak = 0.14610 (55) mri peak = 0.07038 (66) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (18880 voxels, overlap=0.358) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (18880 voxels, peak = 64), gca=63.5 gca peak = 0.16309 (85) mri peak = 0.12598 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5120 voxels, overlap=0.744) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5120 voxels, peak = 89), gca=88.8 gca peak = 0.15172 (84) mri peak = 0.12656 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4897 voxels, overlap=0.702) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4897 voxels, peak = 87), gca=86.9 gca peak = 0.30461 (58) mri peak = 0.11690 (72) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (389 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (389 voxels, peak = 69), gca=69.3 gca peak = 0.32293 (57) mri peak = 0.12059 (67) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (333 voxels, overlap=0.050) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (333 voxels, peak = 70), gca=69.8 gca peak = 0.11083 (90) mri peak = 0.07787 (89) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (3515 voxels, overlap=0.917) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (3515 voxels, peak = 91), gca=91.3 gca peak = 0.11393 (83) mri peak = 0.08780 (88) Right_Thalamus (49): linear fit = 1.04 x + 0.0 (3598 voxels, overlap=0.922) Right_Thalamus (49): linear fit = 1.04 x + 0.0 (3598 voxels, peak = 87), gca=86.7 gca peak = 0.08575 (81) mri peak = 0.10029 (89) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1396 voxels, overlap=0.507) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1396 voxels, peak = 90), gca=90.3 gca peak = 0.08618 (78) mri peak = 0.08965 (86) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1427 voxels, overlap=0.710) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1427 voxels, peak = 85), gca=84.6 gca peak = 0.08005 (78) mri peak = 0.10360 (86) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11463 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11463 voxels, peak = 82), gca=82.3 gca peak = 0.12854 (88) mri peak = 0.09888 (92) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1138 voxels, overlap=0.737) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1138 voxels, peak = 95), gca=94.6 gca peak = 0.15703 (87) mri peak = 0.12383 (93) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1143 voxels, overlap=0.656) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1143 voxels, peak = 92), gca=91.8 gca peak = 0.17522 (25) mri peak = 0.21818 (22) Third_Ventricle (14): linear fit = 0.86 x + 0.0 (110 voxels, overlap=0.919) Third_Ventricle (14): linear fit = 0.86 x + 0.0 (110 voxels, peak = 21), gca=21.4 gca peak = 0.17113 (14) mri peak = 0.15135 (19) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (96 voxels, overlap=0.632) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (96 voxels, peak = 18), gca=17.9 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 1.20 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.11 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16757 (19) mri peak = 0.13094 (23) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (2443 voxels, overlap=0.854) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (2443 voxels, peak = 18), gca=17.8 gca peak = 0.17681 (16) mri peak = 0.14176 (23) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (4353 voxels, overlap=0.654) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (4353 voxels, peak = 18), gca=17.5 gca peak = 0.24101 (91) mri peak = 0.08190 (90) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (475 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (475 voxels, peak = 91), gca=90.5 gca peak = 0.18120 (95) mri peak = 0.10953 (97) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (494 voxels, overlap=1.006) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (494 voxels, peak = 96), gca=96.4 gca peak = 0.25289 (65) mri peak = 0.13102 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (892 voxels, overlap=1.001) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (892 voxels, peak = 65), gca=65.0 gca peak = 0.24140 (67) mri peak = 0.09316 (68) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (687 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (687 voxels, peak = 66), gca=66.0 gca peak = 0.07763 (106) mri peak = 0.11563 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26679 voxels, overlap=0.695) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26679 voxels, peak = 106), gca=106.0 gca peak = 0.07610 (108) mri peak = 0.12235 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29849 voxels, overlap=0.681) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29849 voxels, peak = 108), gca=108.0 gca peak = 0.08555 (69) mri peak = 0.04206 (67) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17128 voxels, overlap=0.979) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17128 voxels, peak = 68), gca=68.0 gca peak = 0.09254 (71) mri peak = 0.03902 (72) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16758 voxels, overlap=0.963) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16758 voxels, peak = 70), gca=69.9 gca peak = 0.21911 (76) mri peak = 0.14239 (78) Right_Caudate (50): linear fit = 1.00 x + 0.0 (759 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (759 voxels, peak = 76), gca=76.0 gca peak = 0.14711 (85) mri peak = 0.11626 (78) Left_Caudate (11): linear fit = 0.98 x + 0.0 (800 voxels, overlap=0.999) Left_Caudate (11): linear fit = 0.98 x + 0.0 (800 voxels, peak = 83), gca=82.9 gca peak = 0.11930 (65) mri peak = 0.06147 (65) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18135 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18135 voxels, peak = 65), gca=65.0 gca peak = 0.13448 (64) mri peak = 0.07038 (66) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (18880 voxels, overlap=0.983) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (18880 voxels, peak = 66), gca=65.6 gca peak = 0.15128 (88) mri peak = 0.12598 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5120 voxels, overlap=0.934) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5120 voxels, peak = 88), gca=88.0 gca peak = 0.14534 (87) mri peak = 0.12656 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4897 voxels, overlap=0.866) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4897 voxels, peak = 87), gca=87.0 gca peak = 0.29204 (69) mri peak = 0.11690 (72) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (389 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (389 voxels, peak = 71), gca=70.7 gca peak = 0.25432 (70) mri peak = 0.12059 (67) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (333 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (333 voxels, peak = 70), gca=70.0 gca peak = 0.11196 (90) mri peak = 0.07787 (89) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3515 voxels, overlap=0.946) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3515 voxels, peak = 90), gca=89.6 gca peak = 0.09468 (86) mri peak = 0.08780 (88) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3598 voxels, overlap=0.940) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3598 voxels, peak = 86), gca=85.6 gca peak = 0.08292 (84) mri peak = 0.10029 (89) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1396 voxels, overlap=0.867) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1396 voxels, peak = 83), gca=82.7 gca peak = 0.09419 (82) mri peak = 0.08965 (86) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1427 voxels, overlap=0.909) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1427 voxels, peak = 81), gca=80.8 gca peak = 0.08462 (83) mri peak = 0.10360 (86) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11463 voxels, overlap=0.723) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11463 voxels, peak = 83), gca=82.6 gca peak = 0.12652 (96) mri peak = 0.09888 (92) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1138 voxels, overlap=0.860) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1138 voxels, peak = 95), gca=94.6 gca peak = 0.15305 (90) mri peak = 0.12383 (93) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1143 voxels, overlap=0.888) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1143 voxels, peak = 90), gca=89.6 gca peak = 0.19686 (22) mri peak = 0.21818 (22) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (110 voxels, overlap=1.005) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (110 voxels, peak = 21), gca=21.5 gca peak = 0.14790 (19) mri peak = 0.15135 (19) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (96 voxels, overlap=0.735) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (96 voxels, peak = 19), gca=19.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.18489 (33) gca peak CSF = 0.21360 (34) gca peak Left_Accumbens_area = 0.75247 (68) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.11538 (35) gca peak Right_Inf_Lat_Vent = 0.21842 (27) gca peak Right_Accumbens_area = 0.30880 (74) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (36) gca peak WM_hypointensities = 0.10318 (79) gca peak non_WM_hypointensities = 0.14635 (42) gca peak Optic_Chiasm = 0.51667 (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 1.00 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 46134 voxels changed in iteration 0 of unlikely voxel relabeling 199 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 36224 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels) 297 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 54467 changed. image ll: -2.077, PF=0.500 pass 2: 13123 changed. image ll: -2.076, PF=0.500 pass 3: 3411 changed. 32257 voxels changed in iteration 0 of unlikely voxel relabeling 141 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 5605 voxels changed in iteration 0 of unlikely voxel relabeling 59 voxels changed in iteration 1 of unlikely voxel relabeling 17 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 5095 voxels changed in iteration 0 of unlikely voxel relabeling 45 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 3686 voxels changed in iteration 0 of unlikely voxel relabeling 23 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 0 with volume 8642 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 143 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 12692 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 223 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2246.476288 mri_ca_label stimesec 8.403347 mri_ca_label ru_maxrss 2099108 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 8537184 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 688 mri_ca_label ru_oublock 632 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 803 mri_ca_label ru_nivcsw 209509 auto-labeling took 36 minutes and 34 seconds. @#@FSTIME 2024:11:22:11:22:20 mri_ca_label N 10 e 2193.78 S 8.56 U 2246.47 P 102% M 2099108 F 0 R 8537201 W 0 c 209524 w 804 I 688 O 632 L 28.61 26.50 24.46 @#@FSLOADPOST 2024:11:22:11:58:54 mri_ca_label N 10 20.08 25.17 26.58 #-------------------------------------- #@# CC Seg Fri Nov 22 11:58:54 CST 2024 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/transforms/cc_up.lta PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/transforms/cc_up.lta reading aseg from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.auto_noCCseg.mgz reading norm from /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/norm.mgz 33732 voxels in left wm, 54090 in right wm, xrange [121, 134] searching rotation angles z=[-10 4], y=[-11 3] searching scale 1 Z rot -10.3 searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 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 global minimum found at slice 128.0, rotations (-3.92, -3.32) final transformation (x=128.0, yr=-3.916, zr=-3.320): 0.99599 0.05792 -0.06818 2.22840; -0.05778 0.99832 0.00396 21.10494; 0.06829 0.00000 0.99767 -2.45672; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 min_x_fornix = 126 min_x_fornix = 127 min_x_fornix = 126 min_x_fornix = 125 min_x_fornix = 129 cc center is found at 128 114 122 eigenvectors: -0.00017 -0.00095 1.00000; 0.00211 -1.00000 -0.00095; 1.00000 0.00211 0.00018; error in mid anterior detected - correcting... writing aseg with callosum to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #VMPC# mri_cc VmPeak 461936 mri_cc done @#@FSTIME 2024:11:22:11:58:54 mri_cc N 7 e 43.33 S 0.49 U 44.27 P 103% M 345436 F 0 R 434913 W 0 c 4156 w 70 I 0 O 616 L 20.08 25.17 26.58 @#@FSLOADPOST 2024:11:22:11:59:37 mri_cc N 7 21.63 24.90 26.43 #-------------------------------------- #@# Merge ASeg Fri Nov 22 11:59:37 CST 2024 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Nov 22 11:59:38 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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... 478 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 110 gm peak at 75 (75), valley at 42 (42) csf peak at 17, setting threshold to 55 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 76 (76), valley at 36 (36) csf peak at 22, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 26 seconds. @#@FSTIME 2024:11:22:11:59:38 mri_normalize N 9 e 147.04 S 1.98 U 159.05 P 109% M 1209052 F 1 R 1255149 W 0 c 15075 w 211 I 0 O 2400 L 21.63 24.90 26.43 @#@FSLOADPOST 2024:11:22:12:02:05 mri_normalize N 9 23.49 24.52 26.07 #-------------------------------------------- #@# Mask BFS Fri Nov 22 12:02:05 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1392486 voxels in mask (pct= 8.30) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:11:22:12:02:05 mri_mask N 5 e 1.31 S 0.03 U 2.33 P 179% M 74504 F 0 R 17270 W 0 c 226 w 121 I 0 O 2344 L 23.49 24.52 26.07 @#@FSLOADPOST 2024:11:22:12:02:06 mri_mask N 5 23.94 24.59 26.09 #-------------------------------------------- #@# WM Segmentation Fri Nov 22 12:02:06 CST 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/PIB15-273_VYr9_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/PIB15-273_VYr9_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 2024:11:22:12:02:10 AntsDenoiseImageFs N 4 e 38.62 S 0.24 U 39.09 P 101% M 351336 F 0 R 225232 W 0 c 3633 w 67 I 0 O 2392 L 23.94 24.59 26.09 @#@FSLOADPOST 2024:11:22:12:02:49 AntsDenoiseImageFs N 4 24.93 24.78 26.09 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): 100.7 +- 6.4 [79.0 --> 125.0] CCS GM (75.0) : 73.4 +- 10.9 [30.0 --> 95.0] white_mean 100.74 white_sigma 6.40031 gray_mean 73.4404 gray_sigma 10.9072 setting bottom of white matter range wm_low to 84.3 setting top of gray matter range gray_hi to 95.3 wm_low 84.3476 wm_hi 125 gray_low 30 gray_hi 95.2548 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 84.3476 wm_hi 125 gray_low 30 gray_hi 95.2548 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 95.2548, wm_low = 84.3476 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=95.2548, wmlow=84.3476 108419 voxels processed (0.65%) 51244 voxels white (0.31%) 57175 voxels non-white (0.34%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=79.3476, gray_hi=95.2548, wsize=13 216268 voxels tested (1.29%) 40738 voxels changed (0.24%) 38580 multi-scale searches (0.23%) Recovering bright white MRIrecoverBrightWhite() wm_low 84.3476 wm_hi 125 slack 6.40031 pct_thresh 0.33 intensity_thresh 131.4 nvox_thresh 8.58 72 voxels tested (0.00%) 56 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=79.3476, hithr=95.2548 smoothing input volume with sigma = 0.250 91138 voxels tested (0.54%) 14330 voxels changed (0.09%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 1687 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1266 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 3729 filled MRIfindBrightNonWM(): 101 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.2 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:11:22:12:02:49 mri_segment N 6 e 70.51 S 0.34 U 71.70 P 102% M 146388 F 0 R 324705 W 0 c 6627 w 94 I 0 O 736 L 24.93 24.78 26.09 @#@FSLOADPOST 2024:11:22:12:04:00 mri_segment N 6 27.57 25.55 26.26 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 0.59 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2842 additional wm voxels added 0 additional wm voxels added SEG EDIT: 51985 voxels turned on, 30633 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:11:22:12:04:00 mri_edit_wm_with_aseg N 5 e 35.67 S 0.57 U 38.04 P 108% M 464116 F 0 R 453025 W 0 c 3574 w 128 I 0 O 680 L 27.57 25.55 26.26 @#@FSLOADPOST 2024:11:22:12:04:35 mri_edit_wm_with_aseg N 5 26.86 25.60 26.25 mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 8 found - 8 modified | TOTAL: 14 pass 2 (xy-): 0 found - 8 modified | TOTAL: 14 pass 1 (yz+): 12 found - 12 modified | TOTAL: 26 pass 2 (yz+): 0 found - 12 modified | TOTAL: 26 pass 1 (yz-): 12 found - 12 modified | TOTAL: 38 pass 2 (yz-): 0 found - 12 modified | TOTAL: 38 pass 1 (xz+): 11 found - 11 modified | TOTAL: 49 pass 2 (xz+): 0 found - 11 modified | TOTAL: 49 pass 1 (xz-): 6 found - 6 modified | TOTAL: 55 pass 2 (xz-): 0 found - 6 modified | TOTAL: 55 Iteration Number : 1 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 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 pass 1 (+++): 6 found - 6 modified | TOTAL: 12 pass 2 (+++): 0 found - 6 modified | TOTAL: 12 Iteration Number : 1 pass 1 (++): 42 found - 42 modified | TOTAL: 42 pass 2 (++): 0 found - 42 modified | TOTAL: 42 pass 1 (+-): 23 found - 23 modified | TOTAL: 65 pass 2 (+-): 0 found - 23 modified | TOTAL: 65 pass 1 (--): 31 found - 31 modified | TOTAL: 96 pass 2 (--): 0 found - 31 modified | TOTAL: 96 pass 1 (-+): 24 found - 24 modified | TOTAL: 120 pass 2 (-+): 0 found - 24 modified | TOTAL: 120 Iteration Number : 2 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+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 3 found - 3 modified | TOTAL: 6 pass 2 (xz+): 0 found - 3 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 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-): 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 : 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 = 195 (out of 467244: 0.041734) 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 2024:11:22:12:04:35 mri_pretess N 5 e 4.49 S 0.06 U 5.47 P 123% M 57644 F 1 R 30075 W 0 c 525 w 60 I 8 O 680 L 26.86 25.60 26.25 @#@FSLOADPOST 2024:11:22:12:04:40 mri_pretess N 5 26.87 25.62 26.25 #-------------------------------------------- #@# Fill Fri Nov 22 12:04:40 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 1.09938 0.05633 -0.05324 -15.94841; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47585; 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 1.09938 0.05633 -0.05324 -15.94841; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47585; 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] = 1273 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) no need to search using seed (126, 120, 155), TAL = (2.0, 27.0, 8.0) talairach voxel to voxel transform 0.90335 -0.03841 0.05260 13.82314; 0.04583 0.83382 -0.13192 35.09698; -0.08070 0.08907 0.94653 23.01431; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 120, 155) --> (2.0, 27.0, 8.0) done. filling took 1.3 minutes talairach cc position changed to (2.00, 27.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 27.00, 8.00) SRC: (114.93, 119.66, 171.70) search lh wm seed point around talairach space (-16.00, 27.00, 8.00), SRC: (147.45, 121.31, 168.79) 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 2024:11:22:12:04:40 mri_fill N 14 e 78.16 S 1.38 U 78.79 P 102% M 968960 F 0 R 942009 W 0 c 7423 w 99 I 0 O 232 L 26.87 25.62 26.25 @#@FSLOADPOST 2024:11:22:12:05:58 mri_fill N 14 28.73 26.47 26.50 #-------------------------------------------- #@# Tessellate lh Fri Nov 22 12:05:58 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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+): 10 found - 10 modified | TOTAL: 12 pass 2 (yz+): 0 found - 10 modified | TOTAL: 12 pass 1 (yz-): 4 found - 4 modified | TOTAL: 16 pass 2 (yz-): 0 found - 4 modified | TOTAL: 16 pass 1 (xz+): 1 found - 1 modified | TOTAL: 17 pass 2 (xz+): 0 found - 1 modified | TOTAL: 17 pass 1 (xz-): 2 found - 2 modified | TOTAL: 19 pass 2 (xz-): 0 found - 2 modified | TOTAL: 19 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 = 19 (out of 223041: 0.008519) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:22:12:05:58 mri_pretess N 4 e 1.96 S 0.02 U 3.06 P 157% M 40792 F 1 R 8836 W 0 c 288 w 50 I 0 O 224 L 28.73 26.47 26.50 @#@FSLOADPOST 2024:11:22:12:06:00 mri_pretess N 4 28.73 26.47 26.50 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.3.2 7.3.2 slice 50: 23 vertices, 31 faces slice 60: 2868 vertices, 3040 faces slice 70: 9063 vertices, 9298 faces slice 80: 17115 vertices, 17433 faces slice 90: 26164 vertices, 26450 faces slice 100: 35581 vertices, 35919 faces slice 110: 45187 vertices, 45543 faces slice 120: 55012 vertices, 55336 faces slice 130: 64527 vertices, 64863 faces slice 140: 73433 vertices, 73760 faces slice 150: 82230 vertices, 82496 faces slice 160: 89290 vertices, 89537 faces slice 170: 95540 vertices, 95760 faces slice 180: 101258 vertices, 101428 faces slice 190: 105627 vertices, 105766 faces slice 200: 108781 vertices, 108862 faces slice 210: 109270 vertices, 109276 faces slice 220: 109270 vertices, 109276 faces slice 230: 109270 vertices, 109276 faces slice 240: 109270 vertices, 109276 faces slice 250: 109270 vertices, 109276 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 2024:11:22:12:06:00 mri_tessellate N 3 e 1.82 S 0.02 U 2.35 P 130% M 35504 F 0 R 7829 W 0 c 231 w 208 I 0 O 5128 L 28.73 26.47 26.50 @#@FSLOADPOST 2024:11:22:12:06:02 mri_tessellate N 3 28.91 26.55 26.52 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 109270 voxel in cpt #1: X=-6 [v=109270,e=327828,f=218552] located at (-25.468838, -7.456163, 5.226558) For the whole surface: X=-6 [v=109270,e=327828,f=218552] One single component has been found nothing to do done @#@FSTIME 2024:11:22:12:06:02 mris_extract_main_component N 2 e 0.82 S 0.12 U 0.91 P 125% M 218384 F 2 R 57493 W 0 c 109 w 258 I 0 O 7688 L 28.91 26.55 26.52 @#@FSLOADPOST 2024:11:22:12:06:03 mris_extract_main_component N 2 28.91 26.55 26.52 #-------------------------------------------- #@# Tessellate rh Fri Nov 22 12:06:03 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 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+): 11 found - 11 modified | TOTAL: 12 pass 2 (yz+): 0 found - 11 modified | TOTAL: 12 pass 1 (yz-): 8 found - 8 modified | TOTAL: 20 pass 2 (yz-): 0 found - 8 modified | TOTAL: 20 pass 1 (xz+): 1 found - 1 modified | TOTAL: 21 pass 2 (xz+): 0 found - 1 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 (+++): 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 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 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 = 27 (out of 226666: 0.011912) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:22:12:06:03 mri_pretess N 4 e 2.65 S 0.04 U 3.61 P 137% M 40688 F 0 R 13160 W 0 c 340 w 41 I 0 O 224 L 28.91 26.55 26.52 @#@FSLOADPOST 2024:11:22:12:06:06 mri_pretess N 4 28.91 26.55 26.52 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 60: 1646 vertices, 1781 faces slice 70: 7005 vertices, 7206 faces slice 80: 13570 vertices, 13845 faces slice 90: 22719 vertices, 23033 faces slice 100: 31437 vertices, 31746 faces slice 110: 40651 vertices, 40994 faces slice 120: 50732 vertices, 51085 faces slice 130: 60512 vertices, 60840 faces slice 140: 69912 vertices, 70242 faces slice 150: 78562 vertices, 78854 faces slice 160: 86901 vertices, 87146 faces slice 170: 93665 vertices, 93890 faces slice 180: 99443 vertices, 99648 faces slice 190: 104336 vertices, 104517 faces slice 200: 108512 vertices, 108641 faces slice 210: 109766 vertices, 109782 faces slice 220: 109766 vertices, 109782 faces slice 230: 109766 vertices, 109782 faces slice 240: 109766 vertices, 109782 faces slice 250: 109766 vertices, 109782 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 2024:11:22:12:06:06 mri_tessellate N 3 e 1.80 S 0.01 U 2.29 P 128% M 35636 F 0 R 7830 W 0 c 223 w 100 I 0 O 5152 L 28.91 26.55 26.52 @#@FSLOADPOST 2024:11:22:12:06:07 mri_tessellate N 3 29.32 26.67 26.56 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 109766 voxel in cpt #1: X=-16 [v=109766,e=329346,f=219564] located at (26.311928, -3.224860, 8.883297) For the whole surface: X=-16 [v=109766,e=329346,f=219564] One single component has been found nothing to do done @#@FSTIME 2024:11:22:12:06:08 mris_extract_main_component N 2 e 0.85 S 0.16 U 0.91 P 126% M 219344 F 2 R 57863 W 0 c 99 w 371 I 0 O 7720 L 29.32 26.67 26.56 @#@FSLOADPOST 2024:11:22:12:06:08 mris_extract_main_component N 2 29.32 26.67 26.56 #-------------------------------------------- #@# Smooth1 lh Fri Nov 22 12:06:08 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Fri Nov 22 12:06:08 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 3801082 of (3801082 3801086) to complete... Waiting for PID 3801086 of (3801082 3801086) 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 (3801082 3801086) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Fri Nov 22 12:06:11 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Fri Nov 22 12:06:11 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 3801179 of (3801179 3801183) to complete... Waiting for PID 3801183 of (3801179 3801183) 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 = 43.8 mm, total surface area = 58710 mm^2 step 000: RMS=0.147 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.054 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.033 (target=0.015) step 055: RMS=0.032 (target=0.015) step 060: RMS=0.031 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 30.391869 mris_inflate stimesec 0.256100 mris_inflate ru_maxrss 175940 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 244697 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7704 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3970 mris_inflate ru_nivcsw 2672 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 43.9 mm, total surface area = 59264 mm^2 step 000: RMS=0.146 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.078 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.053 (target=0.015) step 025: RMS=0.045 (target=0.015) step 030: RMS=0.039 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.025 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 31.748369 mris_inflate stimesec 1.253803 mris_inflate ru_maxrss 175724 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 611952 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7744 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5299 mris_inflate ru_nivcsw 2866 PIDs (3801179 3801183) completed and logs appended. #-------------------------------------------- #@# QSphere lh Fri Nov 22 12:06:27 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Fri Nov 22 12:06:27 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 3801326 of (3801326 3801329) to complete... Waiting for PID 3801329 of (3801326 3801329) 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 0.340... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.60 (0.00-->7.23) (max @ vno 38094 --> 38916) face area 0.03 +- 0.03 (-0.03-->0.82) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.823, avgs=0 005/300: dt: 0.9000, rms radial error=176.564, avgs=0 010/300: dt: 0.9000, rms radial error=176.008, avgs=0 015/300: dt: 0.9000, rms radial error=175.277, avgs=0 020/300: dt: 0.9000, rms radial error=174.444, avgs=0 025/300: dt: 0.9000, rms radial error=173.553, avgs=0 030/300: dt: 0.9000, rms radial error=172.630, avgs=0 035/300: dt: 0.9000, rms radial error=171.690, avgs=0 040/300: dt: 0.9000, rms radial error=170.742, avgs=0 045/300: dt: 0.9000, rms radial error=169.795, avgs=0 050/300: dt: 0.9000, rms radial error=168.849, avgs=0 055/300: dt: 0.9000, rms radial error=167.906, avgs=0 060/300: dt: 0.9000, rms radial error=166.966, avgs=0 065/300: dt: 0.9000, rms radial error=166.031, avgs=0 070/300: dt: 0.9000, rms radial error=165.100, avgs=0 075/300: dt: 0.9000, rms radial error=164.174, avgs=0 080/300: dt: 0.9000, rms radial error=163.252, avgs=0 085/300: dt: 0.9000, rms radial error=162.335, avgs=0 090/300: dt: 0.9000, rms radial error=161.423, avgs=0 095/300: dt: 0.9000, rms radial error=160.516, avgs=0 100/300: dt: 0.9000, rms radial error=159.614, avgs=0 105/300: dt: 0.9000, rms radial error=158.717, avgs=0 110/300: dt: 0.9000, rms radial error=157.825, avgs=0 115/300: dt: 0.9000, rms radial error=156.938, avgs=0 120/300: dt: 0.9000, rms radial error=156.055, avgs=0 125/300: dt: 0.9000, rms radial error=155.178, avgs=0 130/300: dt: 0.9000, rms radial error=154.305, avgs=0 135/300: dt: 0.9000, rms radial error=153.436, avgs=0 140/300: dt: 0.9000, rms radial error=152.573, avgs=0 145/300: dt: 0.9000, rms radial error=151.714, avgs=0 150/300: dt: 0.9000, rms radial error=150.859, avgs=0 155/300: dt: 0.9000, rms radial error=150.009, avgs=0 160/300: dt: 0.9000, rms radial error=149.165, avgs=0 165/300: dt: 0.9000, rms radial error=148.324, avgs=0 170/300: dt: 0.9000, rms radial error=147.488, avgs=0 175/300: dt: 0.9000, rms radial error=146.657, avgs=0 180/300: dt: 0.9000, rms radial error=145.831, avgs=0 185/300: dt: 0.9000, rms radial error=145.009, avgs=0 190/300: dt: 0.9000, rms radial error=144.191, avgs=0 195/300: dt: 0.9000, rms radial error=143.378, avgs=0 200/300: dt: 0.9000, rms radial error=142.570, avgs=0 205/300: dt: 0.9000, rms radial error=141.766, avgs=0 210/300: dt: 0.9000, rms radial error=140.966, avgs=0 215/300: dt: 0.9000, rms radial error=140.171, avgs=0 220/300: dt: 0.9000, rms radial error=139.380, avgs=0 225/300: dt: 0.9000, rms radial error=138.594, avgs=0 230/300: dt: 0.9000, rms radial error=137.812, avgs=0 235/300: dt: 0.9000, rms radial error=137.034, avgs=0 240/300: dt: 0.9000, rms radial error=136.261, avgs=0 245/300: dt: 0.9000, rms radial error=135.492, avgs=0 250/300: dt: 0.9000, rms radial error=134.727, avgs=0 255/300: dt: 0.9000, rms radial error=133.967, avgs=0 260/300: dt: 0.9000, rms radial error=133.211, avgs=0 265/300: dt: 0.9000, rms radial error=132.459, avgs=0 270/300: dt: 0.9000, rms radial error=131.711, avgs=0 275/300: dt: 0.9000, rms radial error=130.967, avgs=0 280/300: dt: 0.9000, rms radial error=130.228, avgs=0 285/300: dt: 0.9000, rms radial error=129.493, avgs=0 290/300: dt: 0.9000, rms radial error=128.762, avgs=0 295/300: dt: 0.9000, rms radial error=128.035, avgs=0 300/300: dt: 0.9000, rms radial error=127.312, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12302.73 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00040 epoch 2 (K=40.0), pass 1, starting sse = 1831.03 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00058 epoch 3 (K=160.0), pass 1, starting sse = 136.69 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.20/18 = 0.01103 epoch 4 (K=640.0), pass 1, starting sse = 4.42 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/26 = 0.00530 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0308 hours FSRUNTIME@ mris_sphere 0.0308 hours 4 threads #VMPC# mris_sphere VmPeak 769740 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 0.338... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.59 (0.00-->6.13) (max @ vno 39414 --> 39415) face area 0.03 +- 0.03 (-0.02-->0.58) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.827, avgs=0 005/300: dt: 0.9000, rms radial error=176.568, avgs=0 010/300: dt: 0.9000, rms radial error=176.012, avgs=0 015/300: dt: 0.9000, rms radial error=175.281, avgs=0 020/300: dt: 0.9000, rms radial error=174.451, avgs=0 025/300: dt: 0.9000, rms radial error=173.564, avgs=0 030/300: dt: 0.9000, rms radial error=172.645, avgs=0 035/300: dt: 0.9000, rms radial error=171.710, avgs=0 040/300: dt: 0.9000, rms radial error=170.767, avgs=0 045/300: dt: 0.9000, rms radial error=169.821, avgs=0 050/300: dt: 0.9000, rms radial error=168.876, avgs=0 055/300: dt: 0.9000, rms radial error=167.933, avgs=0 060/300: dt: 0.9000, rms radial error=166.994, avgs=0 065/300: dt: 0.9000, rms radial error=166.059, avgs=0 070/300: dt: 0.9000, rms radial error=165.128, avgs=0 075/300: dt: 0.9000, rms radial error=164.202, avgs=0 080/300: dt: 0.9000, rms radial error=163.281, avgs=0 085/300: dt: 0.9000, rms radial error=162.364, avgs=0 090/300: dt: 0.9000, rms radial error=161.453, avgs=0 095/300: dt: 0.9000, rms radial error=160.546, avgs=0 100/300: dt: 0.9000, rms radial error=159.644, avgs=0 105/300: dt: 0.9000, rms radial error=158.747, avgs=0 110/300: dt: 0.9000, rms radial error=157.855, avgs=0 115/300: dt: 0.9000, rms radial error=156.968, avgs=0 120/300: dt: 0.9000, rms radial error=156.085, avgs=0 125/300: dt: 0.9000, rms radial error=155.208, avgs=0 130/300: dt: 0.9000, rms radial error=154.335, avgs=0 135/300: dt: 0.9000, rms radial error=153.466, avgs=0 140/300: dt: 0.9000, rms radial error=152.603, avgs=0 145/300: dt: 0.9000, rms radial error=151.744, avgs=0 150/300: dt: 0.9000, rms radial error=150.889, avgs=0 155/300: dt: 0.9000, rms radial error=150.040, avgs=0 160/300: dt: 0.9000, rms radial error=149.195, avgs=0 165/300: dt: 0.9000, rms radial error=148.355, avgs=0 170/300: dt: 0.9000, rms radial error=147.519, avgs=0 175/300: dt: 0.9000, rms radial error=146.688, avgs=0 180/300: dt: 0.9000, rms radial error=145.861, avgs=0 185/300: dt: 0.9000, rms radial error=145.039, avgs=0 190/300: dt: 0.9000, rms radial error=144.222, avgs=0 195/300: dt: 0.9000, rms radial error=143.409, avgs=0 200/300: dt: 0.9000, rms radial error=142.600, avgs=0 205/300: dt: 0.9000, rms radial error=141.796, avgs=0 210/300: dt: 0.9000, rms radial error=140.996, avgs=0 215/300: dt: 0.9000, rms radial error=140.201, avgs=0 220/300: dt: 0.9000, rms radial error=139.410, avgs=0 225/300: dt: 0.9000, rms radial error=138.624, avgs=0 230/300: dt: 0.9000, rms radial error=137.842, avgs=0 235/300: dt: 0.9000, rms radial error=137.064, avgs=0 240/300: dt: 0.9000, rms radial error=136.290, avgs=0 245/300: dt: 0.9000, rms radial error=135.521, avgs=0 250/300: dt: 0.9000, rms radial error=134.757, avgs=0 255/300: dt: 0.9000, rms radial error=133.996, avgs=0 260/300: dt: 0.9000, rms radial error=133.240, avgs=0 265/300: dt: 0.9000, rms radial error=132.488, avgs=0 270/300: dt: 0.9000, rms radial error=131.740, avgs=0 275/300: dt: 0.9000, rms radial error=130.997, avgs=0 280/300: dt: 0.9000, rms radial error=130.257, avgs=0 285/300: dt: 0.9000, rms radial error=129.522, avgs=0 290/300: dt: 0.9000, rms radial error=128.791, avgs=0 295/300: dt: 0.9000, rms radial error=128.064, avgs=0 300/300: dt: 0.9000, rms radial error=127.341, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12372.49 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00043 epoch 2 (K=40.0), pass 1, starting sse = 1838.65 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 = 140.53 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.24/20 = 0.01206 epoch 4 (K=640.0), pass 1, starting sse = 2.95 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.27/30 = 0.00915 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0318 hours FSRUNTIME@ mris_sphere 0.0318 hours 4 threads #VMPC# mris_sphere VmPeak 770092 mris_sphere done PIDs (3801326 3801329) completed and logs appended. #@# Fix Topology lh Fri Nov 22 12:08:22 CST 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_Bay3prisma lh #@# Fix Topology rh Fri Nov 22 12:08:22 CST 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_Bay3prisma rh Waiting for PID 3801885 of (3801885 3801888) to complete... Waiting for PID 3801888 of (3801885 3801888) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_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=-6 (nv=109270, nf=218552, ne=327828, g=4) 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 8 iterations marking ambiguous vertices... 1680 ambiguous faces found in tessellation segmenting defects... 13 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 10 12 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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: -9.0597 (-4.5299) -vertex loglikelihood: -6.3609 (-3.1804) -normal dot loglikelihood: -3.6246 (-3.6246) -quad curv loglikelihood: -6.0519 (-3.0260) Total Loglikelihood : -25.0972 CORRECTING DEFECT 0 (vertices=12, convex hull=28, v0=19794) After retessellation of defect 0 (v0=19794), euler #=-10 (108289,324612,216313) : difference with theory (-9) = 1 CORRECTING DEFECT 1 (vertices=6, convex hull=24, v0=60356) After retessellation of defect 1 (v0=60356), euler #=-9 (108292,324627,216326) : difference with theory (-8) = 1 CORRECTING DEFECT 2 (vertices=97, convex hull=44, v0=62271) After retessellation of defect 2 (v0=62271), euler #=-8 (108307,324689,216374) : difference with theory (-7) = 1 CORRECTING DEFECT 3 (vertices=10, convex hull=22, v0=67504) After retessellation of defect 3 (v0=67504), euler #=-7 (108309,324702,216386) : difference with theory (-6) = 1 CORRECTING DEFECT 4 (vertices=132, convex hull=54, v0=70642) After retessellation of defect 4 (v0=70642), euler #=-6 (108337,324808,216465) : difference with theory (-5) = 1 CORRECTING DEFECT 5 (vertices=8, convex hull=26, v0=72152) After retessellation of defect 5 (v0=72152), euler #=-5 (108339,324825,216481) : difference with theory (-4) = 1 CORRECTING DEFECT 6 (vertices=40, convex hull=64, v0=74328) After retessellation of defect 6 (v0=74328), euler #=-4 (108356,324900,216540) : difference with theory (-3) = 1 CORRECTING DEFECT 7 (vertices=9, convex hull=23, v0=75751) After retessellation of defect 7 (v0=75751), euler #=-3 (108357,324911,216551) : difference with theory (-2) = 1 CORRECTING DEFECT 8 (vertices=327, convex hull=70, v0=80272) After retessellation of defect 8 (v0=80272), euler #=-2 (108367,324973,216604) : difference with theory (-1) = 1 CORRECTING DEFECT 9 (vertices=40, convex hull=31, v0=88320) After retessellation of defect 9 (v0=88320), euler #=-1 (108374,325003,216628) : difference with theory (0) = 1 CORRECTING DEFECT 10 (vertices=282, convex hull=186, v0=89823) After retessellation of defect 10 (v0=89823), euler #=1 (108436,325283,216848) : difference with theory (1) = 0 CORRECTING DEFECT 11 (vertices=19, convex hull=55, v0=105751) After retessellation of defect 11 (v0=105751), euler #=2 (108447,325335,216890) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.14-->15.51) (max @ vno 79948 --> 86043) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.14-->15.51) (max @ vno 79948 --> 86043) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 38 mutations (34.9%), 71 crossovers (65.1%), 43 vertices were eliminated building final representation... 823 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=108447, nf=216890, ne=325335, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 68 intersecting 001: 2 intersecting terminating search with 0 intersecting topology fixing took 0.7 minutes FSRUNTIME@ mris_fix_topology lh 0.0114 hours 4 threads #VMPC# mris_fix_topology VmPeak 946196 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_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=-16 (nv=109766, nf=219564, ne=329346, g=9) 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 9 iterations marking ambiguous vertices... 497 ambiguous faces found in tessellation segmenting defects... 11 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 11 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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: -9.0132 (-4.5066) -vertex loglikelihood: -6.3506 (-3.1753) -normal dot loglikelihood: -3.6761 (-3.6761) -quad curv loglikelihood: -6.3175 (-3.1588) Total Loglikelihood : -25.3574 CORRECTING DEFECT 0 (vertices=12, convex hull=15, v0=31326) After retessellation of defect 0 (v0=31326), euler #=-8 (109419,328023,218596) : difference with theory (-8) = 0 CORRECTING DEFECT 1 (vertices=28, convex hull=24, v0=74044) After retessellation of defect 1 (v0=74044), euler #=-7 (109422,328038,218609) : difference with theory (-7) = 0 CORRECTING DEFECT 2 (vertices=45, convex hull=40, v0=83602) After retessellation of defect 2 (v0=83602), euler #=-6 (109431,328080,218643) : difference with theory (-6) = 0 CORRECTING DEFECT 3 (vertices=51, convex hull=86, v0=89225) After retessellation of defect 3 (v0=89225), euler #=-5 (109461,328209,218743) : difference with theory (-5) = 0 CORRECTING DEFECT 4 (vertices=22, convex hull=57, v0=92351) After retessellation of defect 4 (v0=92351), euler #=-4 (109472,328265,218789) : difference with theory (-4) = 0 CORRECTING DEFECT 5 (vertices=22, convex hull=60, v0=96704) After retessellation of defect 5 (v0=96704), euler #=-3 (109483,328319,218833) : difference with theory (-3) = 0 CORRECTING DEFECT 6 (vertices=30, convex hull=65, v0=98504) After retessellation of defect 6 (v0=98504), euler #=-2 (109496,328384,218886) : difference with theory (-2) = 0 CORRECTING DEFECT 7 (vertices=32, convex hull=55, v0=102037) After retessellation of defect 7 (v0=102037), euler #=-1 (109509,328444,218934) : difference with theory (-1) = 0 CORRECTING DEFECT 8 (vertices=35, convex hull=75, v0=104975) After retessellation of defect 8 (v0=104975), euler #=0 (109530,328536,219006) : difference with theory (0) = 0 CORRECTING DEFECT 9 (vertices=31, convex hull=59, v0=106673) After retessellation of defect 9 (v0=106673), euler #=1 (109539,328585,219047) : difference with theory (1) = 0 CORRECTING DEFECT 10 (vertices=40, convex hull=65, v0=108780) After retessellation of defect 10 (v0=108780), euler #=2 (109556,328662,219108) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.11-->4.91) (max @ vno 107239 --> 107884) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.11-->4.91) (max @ vno 107239 --> 107884) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 33 mutations (30.6%), 75 crossovers (69.4%), 26 vertices were eliminated building final representation... 210 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=109556, nf=219108, ne=328662, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 41 intersecting terminating search with 0 intersecting topology fixing took 0.5 minutes FSRUNTIME@ mris_fix_topology rh 0.0081 hours 4 threads #VMPC# mris_fix_topology VmPeak 946732 PIDs (3801885 3801888) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 108447 - 325335 + 216890 = 2 --> 0 holes F =2V-4: 216890 = 216894-4 (0) 2E=3F: 650670 = 650670 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 109556 - 328662 + 219108 = 2 --> 0 holes F =2V-4: 219108 = 219112-4 (0) 2E=3F: 657324 = 657324 (0) total defect index = 0 Fri Nov 22 12:09:05 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/defect2seg --s PIB15-273_VYr9_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 3802163 mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 14 non-cortical segments detected only using segment with 7229 vertices erasing segment 1 (vno[0] = 61867) erasing segment 2 (vno[0] = 66626) erasing segment 3 (vno[0] = 68450) erasing segment 4 (vno[0] = 71164) erasing segment 5 (vno[0] = 79455) erasing segment 6 (vno[0] = 79475) erasing segment 7 (vno[0] = 79627) erasing segment 8 (vno[0] = 80294) erasing segment 9 (vno[0] = 80319) erasing segment 10 (vno[0] = 81111) erasing segment 11 (vno[0] = 81132) erasing segment 12 (vno[0] = 82013) erasing segment 13 (vno[0] = 82728) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz 1000 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 525124 mris_defects_pointset done mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 9 non-cortical segments detected only using segment with 7009 vertices erasing segment 1 (vno[0] = 36746) erasing segment 2 (vno[0] = 40218) erasing segment 3 (vno[0] = 45092) erasing segment 4 (vno[0] = 48345) erasing segment 5 (vno[0] = 49443) erasing segment 6 (vno[0] = 54277) erasing segment 7 (vno[0] = 79141) erasing segment 8 (vno[0] = 83576) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz 2000 1 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 525476 mris_defects_pointset done Started at Fri Nov 22 12:09:04 CST 2024 Ended at Fri Nov 22 12:09:42 CST 2024 Defect2seg-Run-Time-Sec 38 Defect2seg-Run-Time-Min 0.76 Defect2seg-Run-Time-Hours 0.01 tkmeditfv PIB15-273_VYr9_Bay3prisma brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2024:11:22:12:09:04 defect2seg N 3 e 37.64 S 1.20 U 41.12 P 112% M 322596 F 11 R 485039 W 0 c 3924 w 1438 I 0 O 18088 L 29.30 27.73 26.99 @#@FSLOADPOST 2024:11:22:12:09:42 defect2seg N 3 28.59 27.76 27.04 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.70875 remeshing to edge length 0.70875 with 3 iterations avg qual before : 0.893833 after: 0.971024 Removing intersections Remeshed surface quality stats nv0 = 108447 nv = 113479 1.0464 Area 226954 0.30121 0.03355 0.054959 0.4901 Corner 680862 60.00000 8.81766 16.951352 145.8101 Edge 340431 0.84203 0.08245 0.273092 1.2641 Hinge 340431 9.71357 9.83697 0.000039 149.5433 mris_remesh done @#@FSTIME 2024:11:22:12:09:42 mris_remesh N 7 e 34.22 S 1.09 U 35.16 P 105% M 637100 F 3 R 859609 W 0 c 3358 w 541 I 0 O 7984 L 28.59 27.76 27.04 @#@FSLOADPOST 2024:11:22:12:10:16 mris_remesh N 7 28.22 27.73 27.05 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.708569 remeshing to edge length 0.708569 with 3 iterations avg qual before : 0.892194 after: 0.971259 Removing intersections Remeshed surface quality stats nv0 = 109556 nv = 114494 1.04507 Area 228984 0.30105 0.03346 0.075270 0.4798 Corner 686952 60.00000 8.78579 20.001051 139.7747 Edge 343476 0.84174 0.08207 0.480251 1.2800 Hinge 343476 9.55105 9.85296 0.000004 132.7115 mris_remesh done @#@FSTIME 2024:11:22:12:10:16 mris_remesh N 7 e 33.71 S 0.98 U 34.62 P 105% M 642448 F 1 R 855241 W 0 c 3294 w 921 I 0 O 8056 L 28.22 27.73 27.05 @#@FSLOADPOST 2024:11:22:12:10:50 mris_remesh N 7 28.11 27.73 27.07 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:12:10:50 mris_remove_intersection N 2 e 2.62 S 0.18 U 2.72 P 110% M 287628 F 1 R 134984 W 0 c 278 w 294 I 0 O 7984 L 28.11 27.73 27.07 @#@FSLOADPOST 2024:11:22:12:10:53 mris_remove_intersection N 2 28.34 27.79 27.09 rm -f ../surf/lh.inflated /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:12:10:53 mris_remove_intersection N 2 e 2.89 S 0.21 U 2.94 P 109% M 290168 F 2 R 139630 W 0 c 299 w 379 I 0 O 8056 L 28.34 27.79 27.09 @#@FSLOADPOST 2024:11:22:12:10:56 mris_remove_intersection N 2 28.34 27.79 27.09 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Fri Nov 22 12:10:56 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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: 207055 voxels (1.23%) border gray 222973 voxels (1.33%) 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=23022, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 99.3 +- 7.5 [70.0 --> 110.0] CCS GM (77.0) : 75.9 +- 11.3 [30.0 --> 110.0] white_mean = 99.3335 +/- 7.47871, gray_mean = 75.9196 +/- 11.3271 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=158 nbins=159 intensity peaks found at WM=102+-4.3, GM=72+-9.6 white_mode = 102, gray_mode = 72 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 60.7 (was 70.000000) setting MAX_BORDER_WHITE to 109.5 (was 105.000000) setting MIN_BORDER_WHITE to 72.0 (was 85.000000) setting MAX_CSF to 49.3 (was 40.000000) setting MAX_GRAY to 94.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 60.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 38.0 (was 40.000000) When placing the white surface white_border_hi = 109.479; white_border_low = 72; white_outside_low = 60.6729; white_inside_hi = 120; white_outside_hi = 109.479; When placing the pial surface pial_border_hi = 60.6729; pial_border_low = 38.0186; pial_outside_low = 10; pial_inside_hi = 94.5213; pial_outside_hi = 55.0093; #VMPC# mris_autodet_gwstats VmPeak 563484 mris_autodet_gwstats done @#@FSTIME 2024:11:22:12:10:56 mris_autodet_gwstats N 8 e 4.57 S 0.23 U 6.36 P 144% M 204864 F 1 R 104624 W 0 c 626 w 115 I 0 O 8 L 28.34 27.79 27.09 @#@FSLOADPOST 2024:11:22:12:11:00 mris_autodet_gwstats N 8 29.44 28.02 27.17 #-------------------------------------------- #@# AutoDetGWStats rh Fri Nov 22 12:11:00 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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: 207055 voxels (1.23%) border gray 222973 voxels (1.33%) 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=23022, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 99.3 +- 7.5 [70.0 --> 110.0] CCS GM (77.0) : 75.9 +- 11.3 [30.0 --> 110.0] white_mean = 99.3335 +/- 7.47871, gray_mean = 75.9196 +/- 11.3271 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=158 nbins=159 intensity peaks found at WM=102+-5.2, GM=74+-7.8 white_mode = 102, gray_mode = 74 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70.000000) setting MAX_BORDER_WHITE to 109.5 (was 105.000000) setting MIN_BORDER_WHITE to 74.0 (was 85.000000) setting MAX_CSF to 51.3 (was 40.000000) setting MAX_GRAY to 94.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 40.0 (was 40.000000) When placing the white surface white_border_hi = 109.479; white_border_low = 74; white_outside_low = 62.6729; white_inside_hi = 120; white_outside_hi = 109.479; When placing the pial surface pial_border_hi = 62.6729; pial_border_low = 40.0186; pial_outside_low = 10; pial_inside_hi = 94.5213; pial_outside_hi = 57.0093; #VMPC# mris_autodet_gwstats VmPeak 466456 mris_autodet_gwstats done @#@FSTIME 2024:11:22:12:11:00 mris_autodet_gwstats N 8 e 4.66 S 0.16 U 6.28 P 138% M 206348 F 2 R 103840 W 0 c 601 w 110 I 0 O 8 L 29.44 28.02 27.17 @#@FSLOADPOST 2024:11:22:12:11:05 mris_autodet_gwstats N 8 29.72 28.11 27.21 #-------------------------------------------- #@# WhitePreAparc lh Fri Nov 22 12:11:05 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 removing intersecting faces 000: 16 intersecting step 1 with no progress (num=16, old_num=16) 001: 16 intersecting 002: 13 intersecting step 1 with no progress (num=15, old_num=13) 003: 15 intersecting 004: 14 intersecting step 1 with no progress (num=16, old_num=14) 005: 16 intersecting step 2 with no progress (num=19, old_num=16) 006: 19 intersecting 007: 12 intersecting step 1 with no progress (num=18, old_num=12) 008: 18 intersecting step 2 with no progress (num=20, old_num=18) 009: 20 intersecting 010: 19 intersecting 011: 12 intersecting step 1 with no progress (num=21, old_num=12) 012: 21 intersecting 013: 18 intersecting step 1 with no progress (num=18, old_num=18) 014: 18 intersecting step 2 with no progress (num=27, old_num=18) 015: 27 intersecting 016: 25 intersecting step 1 with no progress (num=26, old_num=25) 017: 26 intersecting 018: 19 intersecting 019: 16 intersecting step 1 with no progress (num=23, old_num=16) 020: 23 intersecting 021: 18 intersecting step 1 with no progress (num=21, old_num=18) 022: 21 intersecting step 2 with no progress (num=25, old_num=21) 023: 25 intersecting step 3 with no progress (num=35, old_num=25) 024: 35 intersecting 025: 15 intersecting step 1 with no progress (num=17, old_num=15) 026: 17 intersecting step 2 with no progress (num=22, old_num=17) 027: 22 intersecting 028: 19 intersecting step 1 with no progress (num=34, old_num=19) 029: 34 intersecting 030: 25 intersecting 031: 19 intersecting step 1 with no progress (num=19, old_num=19) 032: 19 intersecting step 2 with no progress (num=28, old_num=19) 033: 28 intersecting 034: 22 intersecting step 1 with no progress (num=25, old_num=22) 035: 25 intersecting 036: 24 intersecting step 1 with no progress (num=27, old_num=24) 037: 27 intersecting step 2 with no progress (num=38, old_num=27) 038: 38 intersecting step 3 with no progress (num=44, old_num=38) 039: 44 intersecting 040: 43 intersecting 041: 42 intersecting step 1 with no progress (num=42, old_num=42) 042: 42 intersecting step 2 with no progress (num=43, old_num=42) 043: 43 intersecting step 3 with no progress (num=43, old_num=43) 044: 43 intersecting step 4 with no progress (num=43, old_num=43) 045: 43 intersecting step 5 with no progress (num=43, old_num=43) 046: 43 intersecting step 6 with no progress (num=43, old_num=43) 047: 43 intersecting step 7 with no progress (num=43, old_num=43) 048: 43 intersecting step 8 with no progress (num=43, old_num=43) 049: 43 intersecting step 9 with no progress (num=43, old_num=43) 050: 43 intersecting step 10 with no progress (num=43, old_num=43) 051: 43 intersecting step 11 with no progress (num=43, old_num=43) 052: 43 intersecting step 12 with no progress (num=43, old_num=43) 053: 43 intersecting step 13 with no progress (num=43, old_num=43) 054: 43 intersecting step 14 with no progress (num=43, old_num=43) 055: 43 intersecting step 15 with no progress (num=43, old_num=43) 056: 43 intersecting step 16 with no progress (num=43, old_num=43) terminating search with 12 intersecting Area 226954 0.26622 0.06165 0.000000 0.6847 Corner 680862 60.00000 9.41764 0.000121 179.9997 Edge 340431 0.78787 0.11245 0.000433 1.2831 Hinge 340431 6.45860 6.35164 0.000000 175.7159 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23022, wmmin=5, clip=110 MRIfindBrightNonWM(): 468 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 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6314, nmarked2=6, nripped=6314 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56740: xyz = (-53.6035,1.60395,14.9644) oxyz = (-53.6035,1.60395,14.9644) wxzy = (-53.6035,1.60395,14.9644) pxyz = (0,0,0) CBVO Creating mask 113479 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=6314 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6314, nmarked2=6, nripped=6314 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 = 109.4787140; border_low = 72.0000000; outside_low = 60.6728590; outside_hi = 109.4787140; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=2 had to be increased for 53 vertices, nripped=6314 mean border=82.7, 112 (112) missing vertices, mean dist 0.3 [0.8 (%34.7)->0.9 (%65.3))] %51 local maxima, %44 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0413 min Finding expansion regions mean absolute distance = 0.89 +- 1.08 3633 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=2537172.0, rms=10.621 001: dt: 0.5000, sse=1454056.1, rms=7.895 (25.663%) 002: dt: 0.5000, sse=892019.6, rms=6.009 (23.889%) 003: dt: 0.5000, sse=588591.2, rms=4.681 (22.101%) 004: dt: 0.5000, sse=423688.2, rms=3.764 (19.588%) 005: dt: 0.5000, sse=338648.2, rms=3.186 (15.370%) 006: dt: 0.5000, sse=298748.1, rms=2.870 (9.919%) 007: dt: 0.5000, sse=280934.4, rms=2.711 (5.528%) 008: dt: 0.5000, sse=273109.2, rms=2.637 (2.723%) rms = 2.6052/2.6372, sse=270136.8/273109.2, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=270136.8, rms=2.605 (1.213%) 010: dt: 0.2500, sse=176578.8, rms=1.515 (41.852%) 011: dt: 0.2500, sse=163121.1, rms=1.288 (14.974%) rms = 1.2416/1.2880, sse=160991.9/163121.1, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=160991.9, rms=1.242 (3.604%) rms = 1.2006/1.2416, sse=158742.1/160991.9, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=158742.1, rms=1.201 (3.304%) 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=6314 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 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 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6436, nmarked2=10, nripped=6436 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 = 109.4787140; border_low = 72.0000000; outside_low = 60.6728590; outside_hi = 109.4787140; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=1 had to be increased for 64 vertices, nripped=6436 mean border=85.5, 115 (52) missing vertices, mean dist -0.3 [0.5 (%68.3)->0.3 (%31.7))] %60 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0306 min Finding expansion regions mean absolute distance = 0.45 +- 0.78 3465 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=609836.4, rms=4.525 014: dt: 0.5000, sse=351544.7, rms=2.913 (35.631%) 015: dt: 0.5000, sse=300123.7, rms=2.473 (15.107%) 016: dt: 0.5000, sse=283237.0, rms=2.313 (6.478%) rms = 2.3969/2.3126, sse=291719.4/283237.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=228596.4, rms=1.653 (28.523%) 018: dt: 0.2500, sse=205171.8, rms=1.266 (23.399%) 019: dt: 0.2500, sse=198737.8, rms=1.137 (10.239%) rms = 1.0931/1.1366, sse=196958.4/198737.8, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=196958.4, rms=1.093 (3.821%) rms = 1.0548/1.0931, sse=195327.2/196958.4, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=195327.2, rms=1.055 (3.503%) 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=6436 removing 4 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 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 #FML# MRISripMidline(): nmarked=6486, nmarked2=10, nripped=6486 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 = 109.4787140; border_low = 72.0000000; outside_low = 60.6728590; outside_hi = 109.4787140; 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=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 89 vertices, nripped=6486 mean border=88.3, 107 (43) missing vertices, mean dist -0.2 [0.4 (%71.2)->0.2 (%28.8))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0175 min Finding expansion regions mean absolute distance = 0.35 +- 0.49 3872 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=459142.6, rms=3.703 022: dt: 0.5000, sse=276432.3, rms=2.261 (38.941%) 023: dt: 0.5000, sse=262392.2, rms=2.128 (5.849%) rms = 2.1967/2.1285, sse=268563.9/262392.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=211660.5, rms=1.463 (31.280%) 025: dt: 0.2500, sse=191389.6, rms=1.080 (26.135%) 026: dt: 0.2500, sse=187967.1, rms=1.002 (7.246%) rms = 0.9843/1.0021, sse=187910.5/187967.1, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=187910.5, rms=0.984 (1.781%) rms = 0.9506/0.9843, sse=186193.4/187910.5, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=186193.4, rms=0.951 (3.421%) 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=6486 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 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6509, nmarked2=10, nripped=6509 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 = 109.4787140; border_low = 72.0000000; outside_low = 60.6728590; outside_hi = 109.4787140; 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=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 106 vertices, nripped=6509 mean border=89.5, 97 (39) missing vertices, mean dist -0.1 [0.3 (%60.0)->0.2 (%40.0))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0155 min Finding expansion regions mean absolute distance = 0.28 +- 0.38 3358 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=235788.2, rms=1.854 029: dt: 0.5000, sse=204342.0, rms=1.361 (26.619%) rms = 1.6955/1.3605, sse=223787.2/204342.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=181960.1, rms=0.923 (32.136%) 031: dt: 0.2500, sse=176172.8, rms=0.785 (14.991%) rms = 0.7433/0.7849, sse=174168.5/176172.8, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=174168.5, rms=0.743 (5.298%) rms = 0.7216/0.7433, sse=173647.8/174168.5, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=173647.8, rms=0.722 (2.917%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes removing intersecting faces 000: 12 intersecting step 1 with no progress (num=12, old_num=12) 001: 12 intersecting step 2 with no progress (num=12, old_num=12) 002: 12 intersecting step 3 with no progress (num=12, old_num=12) 003: 12 intersecting step 4 with no progress (num=12, old_num=12) 004: 12 intersecting step 5 with no progress (num=12, old_num=12) 005: 12 intersecting step 6 with no progress (num=12, old_num=12) 006: 12 intersecting step 7 with no progress (num=12, old_num=12) 007: 12 intersecting step 8 with no progress (num=12, old_num=12) 008: 12 intersecting step 9 with no progress (num=12, old_num=12) 009: 12 intersecting step 10 with no progress (num=12, old_num=12) 010: 12 intersecting step 11 with no progress (num=12, old_num=12) 011: 12 intersecting step 12 with no progress (num=12, old_num=12) 012: 12 intersecting step 13 with no progress (num=12, old_num=12) 013: 12 intersecting step 14 with no progress (num=12, old_num=12) 014: 12 intersecting step 15 with no progress (num=12, old_num=12) 015: 12 intersecting step 16 with no progress (num=12, old_num=12) terminating search with 12 intersecting Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 3.14 minutes #VMPC# mris_place_surfaces VmPeak 2226088 mris_place_surface done @#@FSTIME 2024:11:22:12:11:05 mris_place_surface N 18 e 295.83 S 3.28 U 427.17 P 145% M 1789176 F 1 R 3382864 W 0 c 40023 w 1883 I 0 O 7984 L 29.72 28.11 27.21 @#@FSLOADPOST 2024:11:22:12:16:01 mris_place_surface N 18 24.61 26.82 26.98 #-------------------------------------------- #@# WhitePreAparc rh Fri Nov 22 12:16:01 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 228984 0.26654 0.06207 0.000077 0.5773 Corner 686952 60.00000 9.40318 0.552834 178.5433 Edge 343476 0.78836 0.11269 0.044426 1.3141 Hinge 343476 6.35353 6.32143 0.000011 170.8202 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23022, wmmin=5, clip=110 MRIfindBrightNonWM(): 468 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=6208, nmarked2=0, nripped=6208 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57247: xyz = (-1.18523,7.59169,18.5486) oxyz = (-1.18523,7.59169,18.5486) wxzy = (-1.18523,7.59169,18.5486) pxyz = (0,0,0) CBVO Creating mask 114494 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=6208 #FML# MRISripMidline(): nmarked=6208, nmarked2=0, nripped=6208 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 = 109.4787140; border_low = 74.0000000; outside_low = 62.6728590; outside_hi = 109.4787140; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=2 had to be increased for 36 vertices, nripped=6208 mean border=83.3, 83 (83) missing vertices, mean dist 0.3 [0.8 (%35.8)->0.9 (%64.2))] %44 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0393 min Finding expansion regions mean absolute distance = 0.87 +- 1.07 3697 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=2399873.0, rms=10.255 001: dt: 0.5000, sse=1324829.6, rms=7.459 (27.267%) 002: dt: 0.5000, sse=798241.9, rms=5.597 (24.964%) 003: dt: 0.5000, sse=535852.4, rms=4.378 (21.788%) 004: dt: 0.5000, sse=398089.2, rms=3.571 (18.428%) 005: dt: 0.5000, sse=331571.8, rms=3.085 (13.604%) 006: dt: 0.5000, sse=293971.7, rms=2.800 (9.251%) 007: dt: 0.5000, sse=280695.0, rms=2.672 (4.545%) 008: dt: 0.5000, sse=271518.9, rms=2.589 (3.132%) rms = 2.5604/2.5887, sse=268336.6/271518.9, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=268336.6, rms=2.560 (1.093%) 010: dt: 0.2500, sse=180271.8, rms=1.527 (40.367%) 011: dt: 0.2500, sse=168326.8, rms=1.327 (13.059%) rms = 1.2782/1.3275, sse=168238.4/168326.8, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=168238.4, rms=1.278 (3.714%) rms = 1.2454/1.2782, sse=169497.3/168238.4, time step reduction 3 of 3 to 0.062 0 1 1 013: dt: 0.1250, sse=169497.3, rms=1.245 (2.561%) maximum number of reductions reached, breaking from loop positioning took 1.0 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=6208 removing 2 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=6347, nmarked2=0, nripped=6347 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 = 109.4787140; border_low = 74.0000000; outside_low = 62.6728590; outside_hi = 109.4787140; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=1 had to be increased for 76 vertices, nripped=6347 mean border=85.9, 109 (50) missing vertices, mean dist -0.3 [0.5 (%67.6)->0.2 (%32.4))] %56 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0291 min Finding expansion regions mean absolute distance = 0.42 +- 0.75 3354 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=555239.2, rms=4.180 014: dt: 0.5000, sse=322156.5, rms=2.650 (36.595%) 015: dt: 0.5000, sse=282475.6, rms=2.293 (13.483%) 016: dt: 0.5000, sse=270694.5, rms=2.168 (5.449%) rms = 2.2769/2.1681, sse=280806.8/270694.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=221709.1, rms=1.544 (28.799%) 018: dt: 0.2500, sse=202157.4, rms=1.206 (21.854%) 019: dt: 0.2500, sse=197382.0, rms=1.109 (8.088%) rms = 1.0828/1.1088, sse=196584.9/197382.0, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=196584.9, rms=1.083 (2.342%) rms = 1.0530/1.0828, sse=195200.0/196584.9, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=195200.0, rms=1.053 (2.749%) 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=6347 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6394, nmarked2=0, nripped=6394 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 = 109.4787140; border_low = 74.0000000; outside_low = 62.6728590; outside_hi = 109.4787140; 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=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 82 vertices, nripped=6394 mean border=88.8, 101 (48) missing vertices, mean dist -0.2 [0.4 (%73.4)->0.2 (%26.6))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0169 min Finding expansion regions mean absolute distance = 0.33 +- 0.45 3219 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=481279.2, rms=3.813 022: dt: 0.5000, sse=273187.5, rms=2.183 (42.744%) 023: dt: 0.5000, sse=263779.7, rms=2.067 (5.316%) rms = 2.1501/2.0674, sse=269884.9/263779.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=214665.9, rms=1.411 (31.760%) 025: dt: 0.2500, sse=194398.4, rms=1.052 (25.441%) 026: dt: 0.2500, sse=191512.0, rms=0.987 (6.131%) rms = 0.9752/0.9874, sse=191669.0/191512.0, time step reduction 2 of 3 to 0.125 0 1 1 027: dt: 0.2500, sse=191669.0, rms=0.975 (1.237%) rms = 0.9491/0.9752, sse=190239.5/191669.0, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=190239.5, rms=0.949 (2.671%) 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=6394 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=6442, nmarked2=0, nripped=6442 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 = 109.4787140; border_low = 74.0000000; outside_low = 62.6728590; outside_hi = 109.4787140; 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=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 78 vertices, nripped=6442 mean border=89.9, 111 (39) missing vertices, mean dist -0.1 [0.3 (%60.2)->0.2 (%39.8))] %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0133 min Finding expansion regions mean absolute distance = 0.24 +- 0.34 2863 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=229792.3, rms=1.707 029: dt: 0.5000, sse=208918.3, rms=1.365 (20.055%) rms = 1.6960/1.3647, sse=228509.2/208918.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=186170.5, rms=0.914 (32.999%) 031: dt: 0.2500, sse=180496.0, rms=0.788 (13.821%) 032: dt: 0.2500, sse=177957.5, rms=0.729 (7.431%) rms = 0.7555/0.7295, sse=178021.6/177957.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.7233/0.7295, sse=177546.8/177957.5, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=177546.8, rms=0.723 (0.848%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.67 minutes #VMPC# mris_place_surfaces VmPeak 2069320 mris_place_surface done @#@FSTIME 2024:11:22:12:16:01 mris_place_surface N 18 e 167.43 S 2.23 U 297.94 P 179% M 1632668 F 3 R 2463511 W 0 c 27878 w 1779 I 0 O 8056 L 24.61 26.82 26.98 @#@FSLOADPOST 2024:11:22:12:18:49 mris_place_surface N 18 27.75 27.68 27.30 #-------------------------------------------- #@# CortexLabel lh Fri Nov 22 12:18:49 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 8 non-cortical segments detected only using segment with 7841 vertices erasing segment 1 (vno[0] = 53311) erasing segment 2 (vno[0] = 57420) erasing segment 3 (vno[0] = 66854) erasing segment 4 (vno[0] = 67741) erasing segment 5 (vno[0] = 69734) erasing segment 6 (vno[0] = 70462) erasing segment 7 (vno[0] = 106496) @#@FSTIME 2024:11:22:12:18:49 mri_label2label N 5 e 15.92 S 0.24 U 16.87 P 107% M 301852 F 1 R 145024 W 0 c 1578 w 334 I 0 O 9144 L 27.75 27.68 27.30 @#@FSLOADPOST 2024:11:22:12:19:05 mri_label2label N 5 28.04 27.74 27.33 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Fri Nov 22 12:19:05 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 5666 vertices erasing segment 1 (vno[0] = 37617) erasing segment 2 (vno[0] = 42124) erasing segment 3 (vno[0] = 53311) erasing segment 4 (vno[0] = 57420) erasing segment 5 (vno[0] = 60166) erasing segment 6 (vno[0] = 63740) erasing segment 7 (vno[0] = 69734) erasing segment 8 (vno[0] = 70462) erasing segment 9 (vno[0] = 98575) erasing segment 10 (vno[0] = 106496) @#@FSTIME 2024:11:22:12:19:05 mri_label2label N 5 e 16.34 S 0.25 U 17.16 P 106% M 314008 F 2 R 154101 W 0 c 1608 w 231 I 0 O 9336 L 28.04 27.74 27.33 @#@FSLOADPOST 2024:11:22:12:19:21 mri_label2label N 5 27.26 27.56 27.27 #-------------------------------------------- #@# CortexLabel rh Fri Nov 22 12:19:21 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2 non-cortical segments detected only using segment with 7708 vertices erasing segment 1 (vno[0] = 68279) @#@FSTIME 2024:11:22:12:19:21 mri_label2label N 5 e 17.32 S 0.23 U 18.15 P 106% M 279012 F 2 R 160099 W 0 c 1701 w 196 I 0 O 9032 L 27.26 27.56 27.27 @#@FSLOADPOST 2024:11:22:12:19:38 mri_label2label N 5 28.74 27.88 27.39 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Fri Nov 22 12:19:38 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 4 non-cortical segments detected only using segment with 5759 vertices erasing segment 1 (vno[0] = 45286) erasing segment 2 (vno[0] = 68279) erasing segment 3 (vno[0] = 95258) @#@FSTIME 2024:11:22:12:19:39 mri_label2label N 5 e 18.20 S 0.33 U 19.08 P 106% M 287300 F 2 R 146599 W 0 c 1815 w 369 I 0 O 9192 L 28.74 27.88 27.39 @#@FSLOADPOST 2024:11:22:12:19:57 mri_label2label N 5 29.53 28.12 27.47 #-------------------------------------------- #@# Smooth2 lh Fri Nov 22 12:19:57 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Fri Nov 22 12:19:57 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 3805950 of (3805950 3805953) to complete... Waiting for PID 3805953 of (3805950 3805953) 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 (3805950 3805953) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Fri Nov 22 12:20:00 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Fri Nov 22 12:20:00 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 3806044 of (3806044 3806048) to complete... Waiting for PID 3806048 of (3806044 3806048) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 43.8 mm, total surface area = 68688 mm^2 step 000: RMS=0.169 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.020 (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 35.932245 mris_inflate stimesec 1.122383 mris_inflate ru_maxrss 176244 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 558487 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8880 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3087 mris_inflate ru_nivcsw 3274 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 43.8 mm, total surface area = 69554 mm^2 step 000: RMS=0.168 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.2 minutes mris_inflate utimesec 31.252095 mris_inflate stimesec 1.126993 mris_inflate ru_maxrss 177780 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 642728 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8960 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3253 mris_inflate ru_nivcsw 2847 PIDs (3806044 3806048) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Fri Nov 22 12:20:18 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Fri Nov 22 12:20:18 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf reconbatchjobs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 3806270 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806274 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806277 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806280 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806285 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806288 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806291 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806295 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806298 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806302 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806306 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... Waiting for PID 3806309 of (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 15.828*4pi (198.903) --> -15 handles ICI = 133.7, FI = 1204.7, variation=19416.188 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 127 vertices thresholded to be in k1 ~ [-0.23 0.57], k2 ~ [-0.09 1.38] total integrated curvature = 0.709*4pi (8.907) --> 0 handles ICI = 1.5, FI = 7.7, variation=137.772 97 vertices thresholded to be in [-0.08 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 92 vertices thresholded to be in [-0.13 0.30] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.023 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 16.710*4pi (209.987) --> -16 handles ICI = 130.0, FI = 1222.2, variation=19479.069 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 130 vertices thresholded to be in k1 ~ [-0.19 1.30], k2 ~ [-0.12 0.06] total integrated curvature = 0.690*4pi (8.672) --> 0 handles ICI = 1.5, FI = 7.1, variation=130.736 85 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 77 vertices thresholded to be in [-0.13 0.27] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.022 done. PIDs (3806270 3806274 3806277 3806280 3806285 3806288 3806291 3806295 3806298 3806302 3806306 3806309) completed and logs appended. #-------------------------------------------- #@# Sphere lh Fri Nov 22 12:21:01 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Fri Nov 22 12:21:01 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 3806654 of (3806654 3806657) to complete... Waiting for PID 3806657 of (3806654 3806657) 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 0.313... 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 %18.92 pass 1: epoch 2 of 3 starting distance error %18.93 unfolding complete - removing small folds... starting distance error %18.90 removing remaining folds... final distance error %18.90 MRISunfold() return, current seed 1234 -01: dt=0.0000, 112 negative triangles VmPeak 772836 090: dt=0.9900, 112 negative triangles 091: dt=0.9900, 52 negative triangles 092: dt=0.9900, 34 negative triangles 093: dt=0.9900, 36 negative triangles 094: dt=0.9900, 44 negative triangles 095: dt=0.9900, 38 negative triangles 096: dt=0.9900, 43 negative triangles 097: dt=0.9900, 38 negative triangles 098: dt=0.9900, 47 negative triangles 099: dt=0.9900, 36 negative triangles 100: dt=0.9900, 40 negative triangles 101: dt=0.9900, 35 negative triangles 102: dt=0.9405, 37 negative triangles 103: dt=0.9405, 34 negative triangles 104: dt=0.9405, 37 negative triangles 105: dt=0.9405, 33 negative triangles 106: dt=0.9405, 37 negative triangles 107: dt=0.9405, 33 negative triangles 108: dt=0.9405, 38 negative triangles 109: dt=0.9405, 33 negative triangles 110: dt=0.9405, 38 negative triangles 111: dt=0.9405, 33 negative triangles 112: dt=0.9405, 37 negative triangles 113: dt=0.9405, 33 negative triangles 114: dt=0.9405, 37 negative triangles 115: dt=0.8935, 33 negative triangles 116: dt=0.8935, 37 negative triangles 117: dt=0.8935, 33 negative triangles 118: dt=0.8935, 37 negative triangles 119: dt=0.8935, 33 negative triangles 120: dt=0.8935, 37 negative triangles 121: dt=0.8935, 33 negative triangles 122: dt=0.8935, 36 negative triangles 123: dt=0.8935, 34 negative triangles 124: dt=0.8935, 35 negative triangles 125: dt=0.8935, 32 negative triangles 126: dt=0.8935, 36 negative triangles 127: dt=0.8935, 32 negative triangles 128: dt=0.8935, 35 negative triangles 129: dt=0.8935, 33 negative triangles 130: dt=0.8935, 35 negative triangles 131: dt=0.8935, 32 negative triangles 132: dt=0.8935, 35 negative triangles 133: dt=0.8935, 33 negative triangles 134: dt=0.8935, 35 negative triangles 135: dt=0.8488, 32 negative triangles 136: dt=0.8488, 35 negative triangles 137: dt=0.8488, 32 negative triangles 138: dt=0.8488, 37 negative triangles 139: dt=0.8488, 31 negative triangles 140: dt=0.8488, 35 negative triangles 141: dt=0.8488, 32 negative triangles 142: dt=0.8488, 35 negative triangles 143: dt=0.8488, 33 negative triangles 144: dt=0.8488, 34 negative triangles 145: dt=0.8488, 32 negative triangles 146: dt=0.8488, 35 negative triangles 147: dt=0.8488, 32 negative triangles 148: dt=0.8488, 35 negative triangles 149: dt=0.8064, 32 negative triangles 150: dt=0.8064, 33 negative triangles 151: dt=0.8064, 32 negative triangles 152: dt=0.8064, 35 negative triangles 153: dt=0.8064, 32 negative triangles 154: dt=0.8064, 34 negative triangles 155: dt=0.8064, 31 negative triangles 156: dt=0.8064, 33 negative triangles 157: dt=0.8064, 31 negative triangles 158: dt=0.8064, 33 negative triangles 159: dt=0.7660, 32 negative triangles 160: dt=0.7660, 36 negative triangles 161: dt=0.7660, 32 negative triangles 162: dt=0.7660, 34 negative triangles 163: dt=0.7660, 33 negative triangles 164: dt=0.7660, 33 negative triangles 165: dt=0.7660, 32 negative triangles 166: dt=0.7660, 35 negative triangles 167: dt=0.7660, 34 negative triangles 168: dt=0.7660, 33 negative triangles 169: dt=0.7277, 32 negative triangles 170: dt=0.7277, 35 negative triangles 171: dt=0.7277, 32 negative triangles 172: dt=0.7277, 34 negative triangles 173: dt=0.7277, 31 negative triangles 174: dt=0.7277, 33 negative triangles 175: dt=0.7277, 32 negative triangles 176: dt=0.7277, 35 negative triangles 177: dt=0.7277, 32 negative triangles 178: dt=0.7277, 34 negative triangles 179: dt=0.6914, 31 negative triangles 180: dt=0.6914, 33 negative triangles 181: dt=0.6914, 31 negative triangles 182: dt=0.6914, 34 negative triangles 183: dt=0.6914, 32 negative triangles 184: dt=0.6914, 35 negative triangles 185: dt=0.6914, 32 negative triangles 186: dt=0.6914, 34 negative triangles 187: dt=0.6914, 32 negative triangles 188: dt=0.6914, 33 negative triangles 189: dt=0.6914, 30 negative triangles 190: dt=0.6914, 33 negative triangles 191: dt=0.6914, 31 negative triangles 192: dt=0.6914, 33 negative triangles 193: dt=0.6914, 32 negative triangles 194: dt=0.6914, 33 negative triangles 195: dt=0.6914, 31 negative triangles 196: dt=0.6914, 34 negative triangles 197: dt=0.6914, 32 negative triangles 198: dt=0.6914, 34 negative triangles 199: dt=0.6568, 30 negative triangles 200: dt=0.6568, 34 negative triangles 201: dt=0.6568, 31 negative triangles 202: dt=0.6568, 33 negative triangles 203: dt=0.6568, 30 negative triangles 204: dt=0.6568, 34 negative triangles 205: dt=0.6568, 30 negative triangles 206: dt=0.6568, 33 negative triangles 207: dt=0.6568, 30 negative triangles 208: dt=0.6568, 34 negative triangles 209: dt=0.6239, 30 negative triangles 210: dt=0.6239, 33 negative triangles 211: dt=0.6239, 32 negative triangles 212: dt=0.6239, 33 negative triangles 213: dt=0.6239, 29 negative triangles 214: dt=0.6239, 32 negative triangles 215: dt=0.6239, 30 negative triangles 216: dt=0.6239, 32 negative triangles 217: dt=0.6239, 29 negative triangles 218: dt=0.6239, 32 negative triangles 219: dt=0.6239, 30 negative triangles 220: dt=0.6239, 33 negative triangles 221: dt=0.6239, 31 negative triangles 222: dt=0.6239, 34 negative triangles 223: dt=0.5927, 32 negative triangles 224: dt=0.5927, 35 negative triangles 225: dt=0.5927, 33 negative triangles 226: dt=0.5927, 34 negative triangles 227: dt=0.5927, 31 negative triangles 228: dt=0.5927, 34 negative triangles 229: dt=0.5927, 32 negative triangles 230: dt=0.5927, 35 negative triangles 231: dt=0.5927, 32 negative triangles 232: dt=0.5927, 34 negative triangles 233: dt=0.5631, 32 negative triangles 234: dt=0.5631, 33 negative triangles 235: dt=0.5631, 30 negative triangles 236: dt=0.5631, 33 negative triangles 237: dt=0.5631, 31 negative triangles 238: dt=0.5631, 35 negative triangles 239: dt=0.5631, 31 negative triangles 240: dt=0.5631, 33 negative triangles 241: dt=0.5631, 30 negative triangles 242: dt=0.5631, 31 negative triangles 243: dt=0.5350, 31 negative triangles 244: dt=0.5350, 32 negative triangles 245: dt=0.5350, 32 negative triangles 246: dt=0.5350, 33 negative triangles 247: dt=0.5350, 29 negative triangles 248: dt=0.5350, 32 negative triangles 249: dt=0.5350, 32 negative triangles 250: dt=0.5350, 33 negative triangles 251: dt=0.5350, 31 negative triangles 252: dt=0.5350, 33 negative triangles 253: dt=0.5082, 30 negative triangles 254: dt=0.5082, 31 negative triangles 255: dt=0.5082, 33 negative triangles 256: dt=0.5082, 33 negative triangles 257: dt=0.5082, 33 negative triangles 258: dt=0.5082, 34 negative triangles 259: dt=0.5082, 29 negative triangles 260: dt=0.5082, 33 negative triangles 261: dt=0.5082, 34 negative triangles 262: dt=0.5082, 30 negative triangles 263: dt=0.4828, 31 negative triangles expanding nbhd size to 1 264: dt=0.9900, 33 negative triangles 265: dt=0.9900, 31 negative triangles 266: dt=0.9900, 35 negative triangles 267: dt=0.9900, 34 negative triangles 268: dt=0.9900, 35 negative triangles 269: dt=0.9900, 35 negative triangles 270: dt=0.9900, 34 negative triangles 271: dt=0.9900, 35 negative triangles 272: dt=0.9900, 36 negative triangles 273: dt=0.9405, 35 negative triangles 274: dt=0.9405, 36 negative triangles 275: dt=0.9405, 34 negative triangles 276: dt=0.9405, 35 negative triangles 277: dt=0.9405, 34 negative triangles 278: dt=0.9405, 34 negative triangles 279: dt=0.9405, 35 negative triangles 280: dt=0.9405, 34 negative triangles 281: dt=0.9405, 34 negative triangles 282: dt=0.9405, 34 negative triangles 283: dt=0.8935, 34 negative triangles 284: dt=0.8935, 34 negative triangles 285: dt=0.8935, 34 negative triangles 286: dt=0.8935, 34 negative triangles 287: dt=0.8935, 34 negative triangles 288: dt=0.8935, 34 negative triangles 289: dt=0.8935, 34 negative triangles 290: dt=0.8935, 34 negative triangles 291: dt=0.8935, 34 negative triangles 292: dt=0.8935, 34 negative triangles 293: dt=0.8488, 34 negative triangles 294: dt=0.8488, 34 negative triangles 295: dt=0.8488, 34 negative triangles 296: dt=0.8488, 34 negative triangles 297: dt=0.8488, 34 negative triangles 298: dt=0.8488, 34 negative triangles 299: dt=0.8488, 34 negative triangles 300: dt=0.8488, 34 negative triangles 301: dt=0.8488, 34 negative triangles 302: dt=0.8488, 34 negative triangles 303: dt=0.8064, 34 negative triangles 304: dt=0.8064, 34 negative triangles 305: dt=0.8064, 34 negative triangles 306: dt=0.8064, 34 negative triangles 307: dt=0.8064, 34 negative triangles 308: dt=0.8064, 34 negative triangles 309: dt=0.8064, 34 negative triangles 310: dt=0.8064, 34 negative triangles 311: dt=0.8064, 34 negative triangles 312: dt=0.8064, 34 negative triangles 313: dt=0.7660, 34 negative triangles 314: dt=0.7660, 34 negative triangles 315: dt=0.7660, 34 negative triangles 316: dt=0.7660, 34 negative triangles 317: dt=0.7660, 34 negative triangles 318: dt=0.7660, 34 negative triangles 319: dt=0.7660, 34 negative triangles 320: dt=0.7660, 34 negative triangles 321: dt=0.7660, 34 negative triangles 322: dt=0.7660, 34 negative triangles 323: dt=0.7277, 34 negative triangles 324: dt=0.7277, 34 negative triangles 325: dt=0.7277, 34 negative triangles 326: dt=0.7277, 34 negative triangles 327: dt=0.7277, 34 negative triangles 328: dt=0.7277, 34 negative triangles 329: dt=0.7277, 34 negative triangles 330: dt=0.7277, 34 negative triangles 331: dt=0.7277, 35 negative triangles 332: dt=0.7277, 35 negative triangles 333: dt=0.6914, 34 negative triangles 334: dt=0.6914, 34 negative triangles 335: dt=0.6914, 34 negative triangles 336: dt=0.6914, 34 negative triangles 337: dt=0.6914, 34 negative triangles 338: dt=0.6914, 34 negative triangles 339: dt=0.6914, 35 negative triangles 340: dt=0.6914, 34 negative triangles 341: dt=0.6914, 34 negative triangles 342: dt=0.6914, 35 negative triangles 343: dt=0.6568, 35 negative triangles 344: dt=0.6568, 34 negative triangles 345: dt=0.6568, 34 negative triangles 346: dt=0.6568, 35 negative triangles 347: dt=0.6568, 35 negative triangles 348: dt=0.6568, 35 negative triangles 349: dt=0.6568, 35 negative triangles 350: dt=0.6568, 35 negative triangles 351: dt=0.6568, 34 negative triangles 352: dt=0.6568, 35 negative triangles 353: dt=0.6239, 35 negative triangles 354: dt=0.6239, 34 negative triangles 355: dt=0.6239, 35 negative triangles 356: dt=0.6239, 36 negative triangles 357: dt=0.6239, 36 negative triangles 358: dt=0.6239, 35 negative triangles 359: dt=0.6239, 36 negative triangles 360: dt=0.6239, 35 negative triangles 361: dt=0.6239, 36 negative triangles 362: dt=0.6239, 35 negative triangles 363: dt=0.5927, 35 negative triangles 364: dt=0.5927, 34 negative triangles 365: dt=0.5927, 35 negative triangles 366: dt=0.5927, 35 negative triangles 367: dt=0.5927, 35 negative triangles 368: dt=0.5927, 35 negative triangles 369: dt=0.5927, 35 negative triangles 370: dt=0.5927, 36 negative triangles 371: dt=0.5927, 35 negative triangles 372: dt=0.5927, 36 negative triangles 373: dt=0.5631, 35 negative triangles 374: dt=0.5631, 35 negative triangles 375: dt=0.5631, 35 negative triangles 376: dt=0.5631, 35 negative triangles 377: dt=0.5631, 36 negative triangles 378: dt=0.5631, 34 negative triangles 379: dt=0.5631, 34 negative triangles 380: dt=0.5631, 35 negative triangles 381: dt=0.5631, 35 negative triangles 382: dt=0.5631, 34 negative triangles 383: dt=0.5350, 36 negative triangles 384: dt=0.5350, 35 negative triangles 385: dt=0.5350, 35 negative triangles 386: dt=0.5350, 35 negative triangles 387: dt=0.5350, 36 negative triangles 388: dt=0.5350, 33 negative triangles 389: dt=0.5350, 35 negative triangles 390: dt=0.5350, 34 negative triangles 391: dt=0.5350, 35 negative triangles 392: dt=0.5350, 35 negative triangles 393: dt=0.5082, 34 negative triangles 394: dt=0.5082, 34 negative triangles 395: dt=0.5082, 34 negative triangles 396: dt=0.5082, 35 negative triangles 397: dt=0.5082, 35 negative triangles 398: dt=0.5082, 34 negative triangles 399: dt=0.5082, 35 negative triangles 400: dt=0.5082, 35 negative triangles 401: dt=0.5082, 34 negative triangles 402: dt=0.5082, 35 negative triangles 403: dt=0.4828, 34 negative triangles 404: dt=0.4828, 35 negative triangles 405: dt=0.4828, 34 negative triangles 406: dt=0.4828, 35 negative triangles 407: dt=0.4828, 33 negative triangles 408: dt=0.4828, 35 negative triangles 409: dt=0.4828, 34 negative triangles 410: dt=0.4828, 34 negative triangles 411: dt=0.4828, 33 negative triangles 412: dt=0.4828, 34 negative triangles 413: dt=0.4587, 34 negative triangles 414: dt=0.4587, 34 negative triangles 415: dt=0.4587, 33 negative triangles 416: dt=0.4587, 33 negative triangles 417: dt=0.4587, 31 negative triangles 418: dt=0.4587, 31 negative triangles 419: dt=0.4587, 32 negative triangles 420: dt=0.4587, 32 negative triangles 421: dt=0.4587, 32 negative triangles 422: dt=0.4587, 33 negative triangles 423: dt=0.4357, 32 negative triangles 424: dt=0.4357, 31 negative triangles 425: dt=0.4357, 30 negative triangles 426: dt=0.4357, 31 negative triangles 427: dt=0.4357, 31 negative triangles 428: dt=0.4357, 32 negative triangles 429: dt=0.4357, 30 negative triangles 430: dt=0.4357, 31 negative triangles 431: dt=0.4357, 32 negative triangles 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957: dt=0.0303, 31 negative triangles 958: dt=0.0303, 31 negative triangles 959: dt=0.0303, 31 negative triangles 960: dt=0.0303, 31 negative triangles 961: dt=0.0287, 31 negative triangles 962: dt=0.0287, 32 negative triangles 963: dt=0.0287, 32 negative triangles 964: dt=0.0287, 33 negative triangles 965: dt=0.0287, 33 negative triangles 966: dt=0.0287, 33 negative triangles 967: dt=0.0287, 33 negative triangles 968: dt=0.0287, 33 negative triangles 969: dt=0.0287, 34 negative triangles 970: dt=0.0287, 34 negative triangles 971: dt=0.0273, 32 negative triangles 972: dt=0.0273, 33 negative triangles 973: dt=0.0273, 34 negative triangles 974: dt=0.0273, 33 negative triangles 975: dt=0.0273, 33 negative triangles 976: dt=0.0273, 33 negative triangles 977: dt=0.0273, 32 negative triangles 978: dt=0.0273, 33 negative triangles 979: dt=0.0273, 33 negative triangles 980: dt=0.0273, 33 negative triangles 981: dt=0.0259, 33 negative triangles 982: dt=0.0259, 33 negative triangles 983: dt=0.0259, 35 negative triangles 984: dt=0.0259, 34 negative triangles 985: dt=0.0259, 34 negative triangles 986: dt=0.0259, 34 negative triangles 987: dt=0.0259, 33 negative triangles 988: dt=0.0259, 34 negative triangles 989: dt=0.0259, 33 negative triangles 990: dt=0.0259, 33 negative triangles 991: dt=0.0246, 33 negative triangles 992: dt=0.0246, 33 negative triangles 993: dt=0.0246, 33 negative triangles 994: dt=0.0246, 33 negative triangles 995: dt=0.0246, 34 negative triangles 996: dt=0.0246, 33 negative triangles 997: dt=0.0246, 32 negative triangles 998: dt=0.0246, 32 negative triangles 999: dt=0.0246, 34 negative triangles 1000: dt=0.0246, 34 negative triangles 1001: dt=0.0234, 35 negative triangles 1002: dt=0.0234, 35 negative triangles 1003: dt=0.0234, 34 negative triangles 1004: dt=0.0234, 34 negative triangles 1005: dt=0.0234, 34 negative triangles 1006: dt=0.0234, 34 negative triangles 1007: dt=0.0234, 34 negative triangles 1008: dt=0.0234, 32 negative triangles 1009: dt=0.0234, 33 negative triangles 1010: dt=0.0234, 33 negative triangles 1011: dt=0.0222, 33 negative triangles 1012: dt=0.0222, 33 negative triangles 1013: dt=0.0222, 33 negative triangles 1014: dt=0.0222, 33 negative triangles 1015: dt=0.0222, 33 negative triangles 1016: dt=0.0222, 34 negative triangles 1017: dt=0.0222, 33 negative triangles 1018: dt=0.0222, 33 negative triangles 1019: dt=0.0222, 33 negative triangles 1020: dt=0.0222, 33 negative triangles 1021: dt=0.0211, 32 negative triangles 1022: dt=0.0211, 34 negative triangles 1023: dt=0.0211, 33 negative triangles 1024: dt=0.0211, 32 negative triangles 1025: dt=0.0211, 30 negative triangles 1026: dt=0.0211, 31 negative triangles 1027: dt=0.0211, 32 negative triangles 1028: dt=0.0211, 30 negative triangles 1029: dt=0.0211, 30 negative triangles 1030: dt=0.0211, 29 negative triangles 1031: dt=0.0201, 30 negative triangles 1032: dt=0.0201, 30 negative triangles 1033: dt=0.0201, 30 negative triangles 1034: dt=0.0201, 30 negative triangles 1035: dt=0.0201, 31 negative triangles 1036: dt=0.0201, 29 negative triangles 1037: dt=0.0201, 29 negative triangles 1038: dt=0.0201, 33 negative triangles 1039: dt=0.0201, 33 negative triangles 1040: dt=0.0201, 32 negative triangles 1041: dt=0.0191, 32 negative triangles 1042: dt=0.0191, 31 negative triangles 1043: dt=0.0191, 33 negative triangles 1044: dt=0.0191, 34 negative triangles 1045: dt=0.0191, 31 negative triangles 1046: dt=0.0191, 32 negative triangles 1047: dt=0.0191, 32 negative triangles 1048: dt=0.0191, 31 negative triangles 1049: dt=0.0191, 31 negative triangles 1050: dt=0.0191, 31 negative triangles 1051: dt=0.0181, 32 negative triangles 1052: dt=0.0181, 32 negative triangles 1053: dt=0.0181, 30 negative triangles 1054: dt=0.0181, 30 negative triangles 1055: dt=0.0181, 31 negative triangles 1056: dt=0.0181, 32 negative triangles 1057: dt=0.0181, 32 negative triangles 1058: dt=0.0181, 32 negative triangles 1059: dt=0.0181, 32 negative triangles 1060: dt=0.0181, 35 negative triangles 1061: dt=0.0172, 32 negative triangles 1062: dt=0.0172, 32 negative triangles 1063: dt=0.0172, 34 negative triangles 1064: dt=0.0172, 32 negative triangles 1065: dt=0.0172, 32 negative triangles 1066: dt=0.0172, 32 negative triangles 1067: dt=0.0172, 32 negative triangles 1068: dt=0.0172, 32 negative triangles 1069: dt=0.0172, 32 negative triangles 1070: dt=0.0172, 31 negative triangles 1071: dt=0.0164, 31 negative triangles 1072: dt=0.0164, 30 negative triangles 1073: dt=0.0164, 28 negative triangles 1074: dt=0.0164, 31 negative triangles 1075: dt=0.0164, 30 negative triangles 1076: dt=0.0164, 29 negative triangles 1077: dt=0.0164, 29 negative triangles 1078: dt=0.0164, 29 negative triangles 1079: dt=0.0164, 28 negative triangles 1080: dt=0.0164, 29 negative triangles 1081: dt=0.0155, 32 negative triangles 1082: dt=0.0155, 31 negative triangles 1083: dt=0.0155, 33 negative triangles 1084: dt=0.0155, 32 negative triangles 1085: dt=0.0155, 34 negative triangles 1086: dt=0.0155, 34 negative triangles 1087: dt=0.0155, 32 negative triangles 1088: dt=0.0155, 33 negative triangles 1089: dt=0.0155, 33 negative triangles 1090: dt=0.0155, 32 negative triangles 1091: 31 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1421 hours FSRUNTIME@ mris_sphere 0.1421 hours 4 threads #VMPC# mris_sphere VmPeak 772836 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 0.310... 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 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 %19.38 pass 1: epoch 2 of 3 starting distance error %19.32 unfolding complete - removing small folds... starting distance error %19.29 removing remaining folds... final distance error %19.29 MRISunfold() return, current seed 1234 -01: dt=0.0000, 113 negative triangles VmPeak 773684 104: dt=0.9900, 113 negative triangles 105: dt=0.9900, 54 negative triangles 106: dt=0.9900, 32 negative triangles 107: dt=0.9900, 24 negative triangles 108: dt=0.9900, 20 negative triangles 109: dt=0.9900, 14 negative triangles 110: dt=0.9900, 13 negative triangles 111: dt=0.9900, 11 negative triangles 112: dt=0.9900, 11 negative triangles 113: dt=0.9900, 11 negative triangles 114: dt=0.9900, 11 negative triangles 115: dt=0.9900, 11 negative triangles 116: dt=0.9900, 11 negative triangles 117: dt=0.9900, 11 negative triangles 118: dt=0.9900, 11 negative triangles 119: dt=0.9900, 11 negative triangles 120: dt=0.9900, 11 negative triangles 121: dt=0.9900, 10 negative triangles 122: dt=0.9900, 9 negative triangles 123: dt=0.9900, 9 negative triangles 124: dt=0.9900, 9 negative triangles 125: dt=0.9900, 9 negative triangles 126: dt=0.9900, 9 negative triangles 127: dt=0.9900, 9 negative triangles 128: dt=0.9900, 9 negative triangles 129: dt=0.9900, 9 negative triangles 130: dt=0.9900, 9 negative triangles 131: dt=0.9900, 9 negative triangles 132: dt=0.9900, 8 negative triangles 133: dt=0.9900, 8 negative triangles 134: dt=0.9900, 8 negative triangles 135: dt=0.9900, 8 negative triangles 136: dt=0.9900, 8 negative triangles 137: dt=0.9900, 7 negative triangles 138: dt=0.9900, 7 negative triangles 139: dt=0.9900, 7 negative triangles 140: dt=0.9900, 7 negative triangles 141: dt=0.9900, 6 negative triangles 142: dt=0.9900, 8 negative triangles 143: dt=0.9900, 6 negative triangles 144: dt=0.9900, 7 negative triangles 145: dt=0.9900, 5 negative triangles 146: dt=0.9900, 6 negative triangles 147: dt=0.9900, 4 negative triangles 148: dt=0.9900, 6 negative triangles 149: dt=0.9900, 4 negative triangles 150: dt=0.9900, 6 negative triangles 151: dt=0.9900, 4 negative triangles 152: dt=0.9900, 5 negative triangles 153: dt=0.9900, 4 negative triangles 154: dt=0.9900, 5 negative triangles 155: dt=0.9900, 4 negative triangles 156: dt=0.9900, 5 negative triangles 157: dt=0.9405, 4 negative triangles 158: dt=0.9405, 5 negative triangles 159: dt=0.9405, 4 negative triangles 160: dt=0.9405, 5 negative triangles 161: dt=0.9405, 4 negative triangles 162: dt=0.9405, 3 negative triangles 163: dt=0.9405, 6 negative triangles 164: dt=0.9405, 3 negative triangles 165: dt=0.9405, 2 negative triangles 166: dt=0.9405, 4 negative triangles 167: dt=0.9405, 2 negative triangles 168: dt=0.9405, 2 negative triangles 169: dt=0.9405, 2 negative triangles 170: dt=0.9405, 5 negative triangles 171: dt=0.9405, 2 negative triangles 172: dt=0.9405, 2 negative triangles 173: dt=0.9405, 2 negative triangles 174: dt=0.9405, 2 negative triangles 175: dt=0.8935, 2 negative triangles 176: dt=0.8935, 3 negative triangles 177: dt=0.8935, 2 negative triangles 178: dt=0.8935, 1 negative triangles 179: dt=0.8935, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.0755 hours FSRUNTIME@ mris_sphere 0.0755 hours 4 threads #VMPC# mris_sphere VmPeak 773684 mris_sphere done PIDs (3806654 3806657) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Fri Nov 22 12:29:33 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Fri Nov 22 12:29:33 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 3812525 of (3812525 3812528) to complete... Waiting for PID 3812528 of (3812525 3812528) 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/PIB15-273_VYr9_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 = 5.433 curvature mean = 0.020, std = 0.823 curvature mean = 0.014, std = 0.883 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (4.50, -12.50, -1.50) sse = 187119.0, elapsed since starting=0.1396 min MRISrigidBodyAlignGlobal() done 0.14 min curvature mean = -0.004, std = 0.856 curvature mean = 0.006, std = 0.957 curvature mean = -0.005, std = 0.869 curvature mean = 0.002, std = 0.984 curvature mean = -0.006, std = 0.873 curvature mean = 0.001, std = 0.994 2 Reading smoothwm curvature mean = -0.020, std = 0.255 curvature mean = 0.038, std = 0.252 curvature mean = 0.056, std = 0.413 curvature mean = 0.037, std = 0.310 curvature mean = 0.021, std = 0.635 curvature mean = 0.036, std = 0.337 curvature mean = 0.009, std = 0.774 curvature mean = 0.036, std = 0.349 curvature mean = 0.002, std = 0.866 MRISregister() return, current seed 0 -01: dt=0.0000, 34 negative triangles VmPeak 772872 099: dt=0.9900, 34 negative triangles 100: dt=0.9900, 31 negative triangles 101: dt=0.9900, 31 negative triangles 102: dt=0.9900, 30 negative triangles 103: dt=0.9900, 30 negative triangles 104: dt=0.9900, 32 negative triangles 105: dt=0.9900, 33 negative triangles 106: dt=0.9900, 30 negative triangles 107: dt=0.9900, 33 negative triangles 108: dt=0.9900, 29 negative triangles 109: dt=0.9900, 32 negative triangles 110: dt=0.9900, 30 negative triangles 111: dt=0.9900, 32 negative triangles 112: dt=0.9900, 29 negative triangles 113: dt=0.9900, 32 negative triangles 114: dt=0.9900, 31 negative triangles 115: dt=0.9900, 31 negative triangles 116: dt=0.9900, 29 negative triangles 117: dt=0.9900, 32 negative triangles 118: dt=0.9405, 31 negative triangles 119: dt=0.9405, 31 negative triangles 120: dt=0.9405, 29 negative triangles 121: dt=0.9405, 32 negative triangles 122: dt=0.9405, 29 negative triangles 123: dt=0.9405, 30 negative triangles 124: dt=0.9405, 29 negative triangles 125: dt=0.9405, 31 negative triangles 126: dt=0.9405, 29 negative triangles 127: dt=0.9405, 30 negative triangles 128: dt=0.8935, 29 negative triangles 129: dt=0.8935, 31 negative triangles 130: dt=0.8935, 28 negative triangles 131: dt=0.8935, 30 negative triangles 132: dt=0.8935, 27 negative triangles 133: dt=0.8935, 30 negative triangles 134: dt=0.8935, 28 negative triangles 135: dt=0.8935, 30 negative triangles 136: dt=0.8935, 27 negative triangles 137: dt=0.8935, 32 negative triangles 138: dt=0.8935, 28 negative triangles 139: dt=0.8935, 30 negative triangles 140: dt=0.8935, 29 negative triangles 141: dt=0.8935, 32 negative triangles 142: dt=0.8488, 28 negative triangles 143: dt=0.8488, 32 negative triangles 144: dt=0.8488, 28 negative triangles 145: dt=0.8488, 33 negative triangles 146: dt=0.8488, 29 negative triangles 147: dt=0.8488, 31 negative triangles 148: dt=0.8488, 27 negative triangles 149: dt=0.8488, 31 negative triangles 150: dt=0.8488, 27 negative triangles 151: dt=0.8488, 33 negative triangles 152: dt=0.8064, 29 negative triangles 153: dt=0.8064, 31 negative triangles 154: dt=0.8064, 29 negative triangles 155: dt=0.8064, 30 negative triangles 156: dt=0.8064, 27 negative triangles 157: dt=0.8064, 30 negative triangles 158: dt=0.8064, 29 negative triangles 159: dt=0.8064, 30 negative triangles 160: dt=0.8064, 28 negative triangles 161: dt=0.8064, 30 negative triangles 162: dt=0.7660, 29 negative triangles 163: dt=0.7660, 33 negative triangles 164: dt=0.7660, 28 negative triangles 165: dt=0.7660, 32 negative triangles 166: dt=0.7660, 27 negative triangles 167: dt=0.7660, 29 negative triangles 168: dt=0.7660, 26 negative triangles 169: dt=0.7660, 32 negative triangles 170: dt=0.7660, 27 negative triangles 171: dt=0.7660, 30 negative triangles 172: dt=0.7660, 27 negative triangles 173: dt=0.7660, 31 negative triangles 174: dt=0.7660, 26 negative triangles 175: dt=0.7660, 33 negative triangles 176: dt=0.7660, 26 negative triangles 177: dt=0.7660, 30 negative triangles 178: dt=0.7277, 26 negative triangles 179: dt=0.7277, 32 negative triangles 180: dt=0.7277, 28 negative triangles 181: dt=0.7277, 31 negative triangles 182: dt=0.7277, 30 negative triangles 183: dt=0.7277, 29 negative triangles 184: dt=0.7277, 29 negative triangles 185: dt=0.7277, 31 negative triangles 186: dt=0.7277, 29 negative triangles 187: dt=0.7277, 32 negative triangles 188: dt=0.6914, 29 negative triangles 189: dt=0.6914, 32 negative triangles 190: dt=0.6914, 28 negative triangles 191: dt=0.6914, 32 negative triangles 192: dt=0.6914, 29 negative triangles 193: dt=0.6914, 31 negative triangles 194: dt=0.6914, 30 negative triangles 195: dt=0.6914, 31 negative triangles 196: dt=0.6914, 27 negative triangles 197: dt=0.6914, 29 negative triangles 198: dt=0.6568, 28 negative triangles 199: dt=0.6568, 28 negative triangles 200: dt=0.6568, 28 negative triangles 201: dt=0.6568, 32 negative triangles 202: dt=0.6568, 30 negative triangles 203: dt=0.6568, 30 negative triangles 204: dt=0.6568, 29 negative triangles 205: dt=0.6568, 31 negative triangles 206: dt=0.6568, 26 negative triangles 207: dt=0.6568, 30 negative triangles 208: dt=0.6239, 31 negative triangles 209: dt=0.6239, 32 negative triangles 210: dt=0.6239, 28 negative triangles 211: dt=0.6239, 28 negative triangles 212: dt=0.6239, 29 negative triangles 213: dt=0.6239, 31 negative triangles 214: dt=0.6239, 29 negative triangles 215: dt=0.6239, 30 negative triangles 216: dt=0.6239, 29 negative triangles 217: dt=0.6239, 30 negative triangles 218: dt=0.5927, 29 negative triangles expanding nbhd size to 1 219: dt=0.9900, 33 negative triangles 220: dt=0.9900, 29 negative triangles 221: dt=0.9900, 32 negative triangles 222: dt=0.9900, 32 negative triangles 223: dt=0.9900, 33 negative triangles 224: dt=0.9900, 34 negative triangles 225: dt=0.9900, 33 negative triangles 226: dt=0.9900, 31 negative triangles 227: dt=0.9900, 32 negative triangles 228: dt=0.9405, 30 negative triangles 229: dt=0.9405, 30 negative triangles 230: dt=0.9405, 31 negative triangles 231: dt=0.9405, 31 negative triangles 232: dt=0.9405, 31 negative triangles 233: dt=0.9405, 30 negative triangles 234: dt=0.9405, 31 negative triangles 235: dt=0.9405, 30 negative triangles 236: dt=0.9405, 31 negative triangles 237: dt=0.9405, 30 negative triangles 238: dt=0.8935, 30 negative triangles 239: dt=0.8935, 30 negative triangles 240: dt=0.8935, 30 negative triangles 241: dt=0.8935, 30 negative triangles 242: dt=0.8935, 30 negative triangles 243: dt=0.8935, 30 negative triangles 244: dt=0.8935, 30 negative triangles 245: dt=0.8935, 30 negative triangles 246: dt=0.8935, 30 negative triangles 247: dt=0.8935, 30 negative triangles 248: dt=0.8488, 30 negative triangles 249: dt=0.8488, 30 negative triangles 250: dt=0.8488, 30 negative triangles 251: dt=0.8488, 30 negative triangles 252: dt=0.8488, 29 negative triangles 253: dt=0.8488, 30 negative triangles 254: dt=0.8488, 29 negative triangles 255: dt=0.8488, 30 negative triangles 256: dt=0.8488, 29 negative triangles 257: dt=0.8488, 29 negative triangles 258: dt=0.8064, 29 negative triangles 259: dt=0.8064, 29 negative triangles 260: dt=0.8064, 29 negative triangles 261: dt=0.8064, 29 negative triangles 262: dt=0.8064, 30 negative triangles 263: dt=0.8064, 29 negative triangles 264: dt=0.8064, 29 negative triangles 265: dt=0.8064, 29 negative triangles 266: dt=0.8064, 29 negative triangles 267: dt=0.8064, 29 negative triangles 268: dt=0.7660, 29 negative triangles 269: dt=0.7660, 29 negative triangles 270: dt=0.7660, 30 negative triangles 271: dt=0.7660, 30 negative triangles 272: dt=0.7660, 30 negative triangles 273: dt=0.7660, 29 negative triangles 274: dt=0.7660, 29 negative triangles 275: dt=0.7660, 29 negative triangles 276: dt=0.7660, 29 negative triangles 277: dt=0.7660, 29 negative triangles 278: dt=0.7277, 30 negative triangles 279: dt=0.7277, 29 negative triangles 280: dt=0.7277, 29 negative triangles 281: dt=0.7277, 29 negative triangles 282: dt=0.7277, 29 negative triangles 283: dt=0.7277, 30 negative triangles 284: dt=0.7277, 31 negative triangles 285: dt=0.7277, 29 negative triangles 286: dt=0.7277, 30 negative triangles 287: dt=0.7277, 30 negative triangles 288: dt=0.6914, 30 negative triangles 289: dt=0.6914, 30 negative triangles 290: dt=0.6914, 30 negative triangles 291: dt=0.6914, 30 negative triangles 292: dt=0.6914, 30 negative triangles 293: dt=0.6914, 31 negative triangles 294: dt=0.6914, 30 negative triangles 295: dt=0.6914, 29 negative triangles 296: dt=0.6914, 30 negative triangles 297: dt=0.6914, 30 negative triangles 298: dt=0.6568, 31 negative triangles 299: dt=0.6568, 30 negative triangles 300: dt=0.6568, 30 negative triangles 301: dt=0.6568, 31 negative triangles 302: dt=0.6568, 32 negative triangles 303: dt=0.6568, 29 negative triangles 304: dt=0.6568, 30 negative triangles 305: dt=0.6568, 31 negative triangles 306: dt=0.6568, 31 negative triangles 307: dt=0.6568, 32 negative triangles 308: dt=0.6239, 29 negative triangles 309: dt=0.6239, 29 negative triangles 310: dt=0.6239, 31 negative triangles 311: dt=0.6239, 30 negative triangles 312: dt=0.6239, 31 negative triangles 313: dt=0.6239, 30 negative triangles 314: dt=0.6239, 31 negative triangles 315: dt=0.6239, 30 negative triangles 316: dt=0.6239, 29 negative triangles 317: dt=0.6239, 31 negative triangles 318: dt=0.5927, 30 negative triangles 319: dt=0.5927, 30 negative triangles 320: dt=0.5927, 29 negative triangles 321: dt=0.5927, 30 negative triangles 322: dt=0.5927, 30 negative triangles 323: dt=0.5927, 30 negative triangles 324: dt=0.5927, 31 negative triangles 325: dt=0.5927, 32 negative triangles 326: dt=0.5927, 30 negative triangles 327: dt=0.5927, 29 negative triangles 328: dt=0.5631, 30 negative triangles 329: dt=0.5631, 31 negative triangles 330: dt=0.5631, 30 negative triangles 331: dt=0.5631, 30 negative triangles 332: dt=0.5631, 29 negative triangles 333: dt=0.5631, 30 negative triangles 334: dt=0.5631, 30 negative triangles 335: dt=0.5631, 29 negative triangles 336: dt=0.5631, 29 negative triangles 337: dt=0.5631, 27 negative triangles 338: dt=0.5350, 27 negative triangles 339: dt=0.5350, 27 negative triangles 340: dt=0.5350, 30 negative triangles 341: dt=0.5350, 28 negative triangles 342: dt=0.5350, 29 negative triangles 343: dt=0.5350, 31 negative triangles 344: dt=0.5350, 31 negative triangles 345: dt=0.5350, 30 negative triangles 346: dt=0.5350, 28 negative triangles 347: dt=0.5350, 29 negative triangles 348: dt=0.5082, 30 negative triangles 349: dt=0.5082, 30 negative triangles 350: dt=0.5082, 31 negative triangles 351: dt=0.5082, 29 negative triangles 352: dt=0.5082, 28 negative triangles 353: dt=0.5082, 28 negative triangles 354: dt=0.5082, 31 negative triangles 355: dt=0.5082, 28 negative triangles 356: dt=0.5082, 29 negative triangles 357: dt=0.5082, 29 negative triangles 358: dt=0.4828, 28 negative triangles 359: dt=0.4828, 28 negative triangles 360: dt=0.4828, 29 negative triangles 361: dt=0.4828, 28 negative triangles 362: dt=0.4828, 29 negative triangles 363: dt=0.4828, 31 negative triangles 364: dt=0.4828, 31 negative triangles 365: dt=0.4828, 27 negative triangles 366: dt=0.4828, 29 negative triangles 367: dt=0.4828, 29 negative triangles 368: dt=0.4587, 31 negative triangles 369: dt=0.4587, 29 negative triangles 370: dt=0.4587, 31 negative triangles 371: dt=0.4587, 33 negative triangles 372: dt=0.4587, 30 negative triangles 373: dt=0.4587, 30 negative triangles 374: dt=0.4587, 28 negative triangles 375: dt=0.4587, 28 negative triangles 376: dt=0.4587, 28 negative triangles 377: dt=0.4587, 32 negative triangles 378: dt=0.4357, 29 negative triangles 379: dt=0.4357, 30 negative triangles 380: dt=0.4357, 31 negative triangles 381: dt=0.4357, 32 negative triangles 382: dt=0.4357, 29 negative triangles 383: dt=0.4357, 32 negative triangles 384: dt=0.4357, 30 negative triangles 385: dt=0.4357, 32 negative triangles 386: 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dt=0.0319, 25 negative triangles 912: dt=0.0319, 23 negative triangles 913: dt=0.0319, 25 negative triangles 914: dt=0.0319, 25 negative triangles 915: dt=0.0319, 24 negative triangles 916: dt=0.0319, 24 negative triangles 917: dt=0.0319, 24 negative triangles 918: dt=0.0319, 25 negative triangles 919: dt=0.0319, 26 negative triangles 920: dt=0.0303, 26 negative triangles 921: dt=0.0303, 27 negative triangles 922: dt=0.0303, 27 negative triangles 923: dt=0.0303, 26 negative triangles 924: dt=0.0303, 25 negative triangles 925: dt=0.0303, 26 negative triangles 926: dt=0.0303, 24 negative triangles 927: dt=0.0303, 24 negative triangles 928: dt=0.0303, 24 negative triangles 929: dt=0.0303, 26 negative triangles 930: dt=0.0287, 26 negative triangles 931: dt=0.0287, 24 negative triangles 932: dt=0.0287, 24 negative triangles 933: dt=0.0287, 25 negative triangles 934: dt=0.0287, 25 negative triangles 935: dt=0.0287, 26 negative triangles 936: dt=0.0287, 26 negative triangles 937: dt=0.0287, 26 negative triangles 938: dt=0.0287, 24 negative triangles 939: dt=0.0287, 24 negative triangles 940: dt=0.0273, 24 negative triangles 941: dt=0.0273, 25 negative triangles 942: dt=0.0273, 24 negative triangles 943: dt=0.0273, 27 negative triangles 944: dt=0.0273, 30 negative triangles 945: dt=0.0273, 30 negative triangles 946: dt=0.0273, 31 negative triangles 947: dt=0.0273, 29 negative triangles 948: dt=0.0273, 30 negative triangles 949: dt=0.0273, 29 negative triangles 950: dt=0.0259, 29 negative triangles 951: dt=0.0259, 29 negative triangles 952: dt=0.0259, 29 negative triangles 953: dt=0.0259, 29 negative triangles 954: dt=0.0259, 30 negative triangles 955: dt=0.0259, 29 negative triangles 956: dt=0.0259, 29 negative triangles 957: dt=0.0259, 29 negative triangles 958: dt=0.0259, 30 negative triangles 959: dt=0.0259, 28 negative triangles 960: dt=0.0246, 29 negative triangles 961: dt=0.0246, 26 negative triangles 962: dt=0.0246, 25 negative triangles 963: dt=0.0246, 24 negative triangles 964: dt=0.0246, 24 negative triangles 965: dt=0.0246, 23 negative triangles 966: dt=0.0246, 24 negative triangles 967: dt=0.0246, 25 negative triangles 968: dt=0.0246, 24 negative triangles 969: dt=0.0246, 25 negative triangles 970: dt=0.0234, 27 negative triangles 971: dt=0.0234, 27 negative triangles 972: dt=0.0234, 27 negative triangles 973: dt=0.0234, 27 negative triangles 974: dt=0.0234, 28 negative triangles 975: dt=0.0234, 29 negative triangles 976: dt=0.0234, 29 negative triangles 977: dt=0.0234, 29 negative triangles 978: dt=0.0234, 28 negative triangles 979: dt=0.0234, 26 negative triangles 980: dt=0.0222, 26 negative triangles 981: dt=0.0222, 28 negative triangles 982: dt=0.0222, 27 negative triangles 983: dt=0.0222, 26 negative triangles 984: dt=0.0222, 28 negative triangles 985: dt=0.0222, 27 negative triangles 986: dt=0.0222, 27 negative triangles 987: dt=0.0222, 25 negative triangles 988: dt=0.0222, 25 negative triangles 989: dt=0.0222, 25 negative triangles 990: dt=0.0211, 25 negative triangles 991: dt=0.0211, 25 negative triangles 992: dt=0.0211, 26 negative triangles 993: dt=0.0211, 25 negative triangles 994: dt=0.0211, 24 negative triangles 995: dt=0.0211, 25 negative triangles 996: dt=0.0211, 25 negative triangles 997: dt=0.0211, 24 negative triangles 998: dt=0.0211, 23 negative triangles 999: dt=0.0211, 23 negative triangles 1000: dt=0.0201, 24 negative triangles 1001: dt=0.0201, 24 negative triangles 1002: dt=0.0201, 22 negative triangles 1003: dt=0.0201, 22 negative triangles 1004: dt=0.0201, 22 negative triangles 1005: dt=0.0201, 22 negative triangles 1006: dt=0.0201, 22 negative triangles 1007: dt=0.0201, 23 negative triangles 1008: dt=0.0201, 23 negative triangles 1009: dt=0.0201, 24 negative triangles 1010: dt=0.0191, 23 negative triangles 1011: dt=0.0191, 24 negative triangles 1012: dt=0.0191, 23 negative triangles 1013: dt=0.0191, 23 negative triangles 1014: dt=0.0191, 22 negative triangles 1015: dt=0.0191, 22 negative triangles 1016: dt=0.0191, 25 negative triangles 1017: dt=0.0191, 24 negative triangles 1018: dt=0.0191, 25 negative triangles 1019: dt=0.0191, 24 negative triangles 1020: dt=0.0181, 25 negative triangles 1021: dt=0.0181, 25 negative triangles 1022: dt=0.0181, 25 negative triangles 1023: dt=0.0181, 25 negative triangles 1024: dt=0.0181, 25 negative triangles 1025: dt=0.0181, 25 negative triangles 1026: dt=0.0181, 24 negative triangles 1027: dt=0.0181, 25 negative triangles 1028: dt=0.0181, 25 negative triangles 1029: dt=0.0181, 26 negative triangles 1030: dt=0.0172, 25 negative triangles 1031: dt=0.0172, 25 negative triangles 1032: dt=0.0172, 25 negative triangles 1033: dt=0.0172, 26 negative triangles 1034: dt=0.0172, 27 negative triangles 1035: dt=0.0172, 26 negative triangles 1036: dt=0.0172, 27 negative triangles 1037: dt=0.0172, 26 negative triangles 1038: dt=0.0172, 27 negative triangles 1039: dt=0.0172, 28 negative triangles 1040: dt=0.0164, 28 negative triangles 1041: dt=0.0164, 28 negative triangles 1042: dt=0.0164, 28 negative triangles 1043: dt=0.0164, 28 negative triangles 1044: dt=0.0164, 28 negative triangles 1045: dt=0.0164, 28 negative triangles 1046: dt=0.0164, 28 negative triangles 1047: dt=0.0164, 28 negative triangles 1048: dt=0.0164, 28 negative triangles 1049: dt=0.0164, 29 negative triangles 1050: dt=0.0155, 28 negative triangles 1051: dt=0.0155, 29 negative triangles 1052: dt=0.0155, 30 negative triangles 1053: dt=0.0155, 28 negative triangles 1054: dt=0.0155, 28 negative triangles 1055: dt=0.0155, 28 negative triangles 1056: dt=0.0155, 27 negative triangles 1057: dt=0.0155, 27 negative triangles 1058: dt=0.0155, 29 negative triangles 1059: dt=0.0155, 29 negative triangles 1060: dt=0.0148, 29 negative triangles 1061: dt=0.0148, 29 negative triangles 1062: dt=0.0148, 28 negative triangles 1063: dt=0.0148, 28 negative triangles 1064: dt=0.0148, 27 negative triangles 1065: dt=0.0148, 28 negative triangles 1066: dt=0.0148, 27 negative triangles 1067: dt=0.0148, 27 negative triangles 1068: dt=0.0148, 26 negative triangles 1069: dt=0.0148, 26 negative triangles 1070: dt=0.0140, 26 negative triangles 1071: dt=0.0140, 25 negative triangles 1072: dt=0.0140, 23 negative triangles 1073: dt=0.0140, 23 negative triangles 1074: dt=0.0140, 24 negative triangles 1075: dt=0.0140, 24 negative triangles 1076: dt=0.0140, 24 negative triangles 1077: dt=0.0140, 24 negative triangles 1078: dt=0.0140, 24 negative triangles 1079: dt=0.0140, 24 negative triangles 1080: dt=0.0133, 23 negative triangles 1081: dt=0.0133, 23 negative triangles 1082: dt=0.0133, 21 negative triangles 1083: dt=0.0133, 23 negative triangles 1084: dt=0.0133, 23 negative triangles 1085: dt=0.0133, 21 negative triangles 1086: dt=0.0133, 23 negative triangles 1087: dt=0.0133, 21 negative triangles 1088: dt=0.0133, 23 negative triangles 1089: dt=0.0133, 21 negative triangles 1090: dt=0.0133, 23 negative triangles 1091: dt=0.0133, 23 negative triangles 1092: dt=0.0127, 23 negative triangles 1093: dt=0.0127, 21 negative triangles 1094: dt=0.0127, 21 negative triangles 1095: dt=0.0127, 20 negative triangles 1096: dt=0.0127, 22 negative triangles 1097: dt=0.0127, 20 negative triangles 1098: dt=0.0127, 21 negative triangles writing registered surface to ../surf/lh.sphere.reg... 1099: dt=0.0127, 23 negative triangles 1100: 23 negative triangles registration took 0.13 hours #VMPC# mris_register VmPeak 772872 FSRUNTIME@ mris_register 0.1271 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/PIB15-273_VYr9_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 = 5.456 curvature mean = 0.022, std = 0.810 curvature mean = 0.016, std = 0.878 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (16.50, -9.50, 0.50) sse = 231676.4, elapsed since starting=0.1353 min MRISrigidBodyAlignGlobal() done 0.14 min curvature mean = 0.016, std = 0.846 curvature mean = 0.006, std = 0.955 curvature mean = 0.016, std = 0.858 curvature mean = 0.002, std = 0.983 curvature mean = 0.016, std = 0.861 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.022, std = 0.260 curvature mean = 0.038, std = 0.244 curvature mean = 0.061, std = 0.406 curvature mean = 0.035, std = 0.302 curvature mean = 0.025, std = 0.618 curvature mean = 0.035, std = 0.329 curvature mean = 0.010, std = 0.757 curvature mean = 0.034, std = 0.340 curvature mean = 0.002, std = 0.853 MRISregister() return, current seed 0 -01: dt=0.0000, 5 negative triangles VmPeak 773720 096: dt=0.9900, 5 negative triangles expanding nbhd size to 1 097: dt=0.9900, 7 negative triangles 098: dt=0.9900, 4 negative triangles 099: dt=0.9900, 4 negative triangles 100: dt=0.9900, 4 negative triangles 101: dt=0.9900, 4 negative triangles 102: dt=0.9900, 4 negative triangles 103: dt=0.9900, 4 negative triangles 104: dt=0.9900, 4 negative triangles 105: dt=0.9900, 4 negative triangles 106: dt=0.9900, 4 negative triangles 107: dt=0.9900, 4 negative triangles 108: dt=0.9405, 4 negative triangles 109: dt=0.9405, 4 negative triangles 110: dt=0.9405, 4 negative triangles 111: dt=0.9405, 4 negative triangles 112: dt=0.9405, 4 negative triangles 113: dt=0.9405, 4 negative triangles 114: dt=0.9405, 4 negative triangles 115: dt=0.9405, 4 negative triangles 116: dt=0.9405, 4 negative triangles 117: dt=0.9405, 4 negative triangles 118: dt=0.8935, 4 negative triangles 119: dt=0.8935, 3 negative triangles 120: dt=0.8935, 3 negative triangles 121: dt=0.8935, 2 negative triangles 122: dt=0.8935, 2 negative triangles 123: dt=0.8935, 2 negative triangles 124: dt=0.8935, 2 negative triangles 125: dt=0.8935, 2 negative triangles 126: dt=0.8935, 2 negative triangles 127: dt=0.8935, 2 negative triangles 128: dt=0.8935, 2 negative triangles 129: dt=0.8935, 2 negative triangles 130: dt=0.8935, 2 negative triangles 131: dt=0.8488, 2 negative triangles 132: dt=0.8488, 2 negative triangles 133: dt=0.8488, 2 negative triangles 134: dt=0.8488, 2 negative triangles 135: dt=0.8488, 2 negative triangles 136: dt=0.8488, 2 negative triangles 137: dt=0.8488, 2 negative triangles 138: dt=0.8488, 1 negative triangles 139: dt=0.8488, 1 negative triangles 140: dt=0.8488, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.08 hours #VMPC# mris_register VmPeak 773720 FSRUNTIME@ mris_register 0.0757 hours 4 threads PIDs (3812525 3812528) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Fri Nov 22 12:37:11 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri Nov 22 12:37:11 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 3815661 of (3815661 3815664) to complete... Waiting for PID 3815664 of (3815661 3815664) 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 (3815661 3815664) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Fri Nov 22 12:37:12 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Fri Nov 22 12:37:12 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 3815737 of (3815737 3815741) to complete... Waiting for PID 3815741 of (3815737 3815741) 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 (3815737 3815741) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Fri Nov 22 12:37:13 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Fri Nov 22 12:37:13 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 3815851 of (3815851 3815860) to complete... Waiting for PID 3815860 of (3815851 3815860) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 939 labels changed using aseg relabeling using gibbs priors... 000: 2757 changed, 113479 examined... 001: 619 changed, 11690 examined... 002: 141 changed, 3530 examined... 003: 39 changed, 866 examined... 004: 21 changed, 243 examined... 005: 8 changed, 116 examined... 006: 2 changed, 40 examined... 007: 0 changed, 14 examined... 212 labels changed using aseg 000: 95 total segments, 47 labels (127 vertices) changed 001: 50 total segments, 2 labels (2 vertices) changed 002: 48 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... 1584 vertices marked for relabeling... 1558 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 PIB15-273_VYr9_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... 1022 labels changed using aseg relabeling using gibbs priors... 000: 2477 changed, 114494 examined... 001: 590 changed, 10781 examined... 002: 131 changed, 3432 examined... 003: 45 changed, 824 examined... 004: 17 changed, 276 examined... 005: 8 changed, 110 examined... 006: 3 changed, 49 examined... 007: 1 changed, 15 examined... 008: 0 changed, 8 examined... 192 labels changed using aseg 000: 88 total segments, 48 labels (129 vertices) changed 001: 41 total segments, 1 labels (1 vertices) changed 002: 40 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... 1438 vertices marked for relabeling... 1438 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 13 seconds. PIDs (3815851 3815860) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Fri Nov 22 12:37:25 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 removing intersecting faces 000: 12 intersecting step 1 with no progress (num=18, old_num=12) 001: 18 intersecting step 2 with no progress (num=20, old_num=18) 002: 20 intersecting 003: 19 intersecting 004: 12 intersecting step 1 with no progress (num=21, old_num=12) 005: 21 intersecting 006: 18 intersecting step 1 with no progress (num=18, old_num=18) 007: 18 intersecting step 2 with no progress (num=27, old_num=18) 008: 27 intersecting 009: 25 intersecting step 1 with no progress (num=26, old_num=25) 010: 26 intersecting 011: 19 intersecting 012: 16 intersecting step 1 with no progress (num=23, old_num=16) 013: 23 intersecting 014: 18 intersecting step 1 with no progress (num=21, old_num=18) 015: 21 intersecting step 2 with no progress (num=25, old_num=21) 016: 25 intersecting step 3 with no progress (num=35, old_num=25) 017: 35 intersecting 018: 15 intersecting step 1 with no progress (num=17, old_num=15) 019: 17 intersecting step 2 with no progress (num=22, old_num=17) 020: 22 intersecting 021: 19 intersecting step 1 with no progress (num=34, old_num=19) 022: 34 intersecting 023: 25 intersecting 024: 19 intersecting step 1 with no progress (num=19, old_num=19) 025: 19 intersecting step 2 with no progress (num=28, old_num=19) 026: 28 intersecting 027: 22 intersecting step 1 with no progress (num=25, old_num=22) 028: 25 intersecting 029: 24 intersecting step 1 with no progress (num=27, old_num=24) 030: 27 intersecting step 2 with no progress (num=38, old_num=27) 031: 38 intersecting step 3 with no progress (num=44, old_num=38) 032: 44 intersecting 033: 43 intersecting 034: 42 intersecting step 1 with no progress (num=42, old_num=42) 035: 42 intersecting step 2 with no progress (num=43, old_num=42) 036: 43 intersecting step 3 with no progress (num=43, old_num=43) 037: 43 intersecting step 4 with no progress (num=43, old_num=43) 038: 43 intersecting step 5 with no progress (num=43, old_num=43) 039: 43 intersecting step 6 with no progress (num=43, old_num=43) 040: 43 intersecting step 7 with no progress (num=43, old_num=43) 041: 43 intersecting step 8 with no progress (num=43, old_num=43) 042: 43 intersecting step 9 with no progress (num=43, old_num=43) 043: 43 intersecting step 10 with no progress (num=43, old_num=43) 044: 43 intersecting step 11 with no progress (num=43, old_num=43) 045: 43 intersecting step 12 with no progress (num=43, old_num=43) 046: 43 intersecting step 13 with no progress (num=43, old_num=43) 047: 43 intersecting step 14 with no progress (num=43, old_num=43) 048: 43 intersecting step 15 with no progress (num=43, old_num=43) 049: 43 intersecting step 16 with no progress (num=43, old_num=43) terminating search with 12 intersecting Area 226954 0.33351 0.11571 0.000000 1.6763 Corner 680862 60.00000 13.87374 0.000121 179.9997 Edge 340431 0.88800 0.19300 0.000433 3.1100 Hinge 340431 10.86680 10.84951 0.000019 179.9596 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23022, wmmin=5, clip=110 MRIfindBrightNonWM(): 468 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 8094/113479 vertices (105385 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 428 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56740: xyz = (-53.8613,2.03512,15.1657) oxyz = (-53.8613,2.03512,15.1657) wxzy = (-53.8613,2.03512,15.1657) pxyz = (0,0,0) CBVO Creating mask 113479 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4787140; border_low = 72.0000000; outside_low = 60.6728590; outside_hi = 109.4787140; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=2 had to be increased for 113 vertices, nripped=8522 mean border=82.8, 83 (83) missing vertices, mean dist 0.4 [1.6 (%12.9)->0.7 (%87.1))] %48 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0465 min Finding expansion regions mean absolute distance = 0.81 +- 1.04 2660 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=1541784.5, rms=8.121 001: dt: 0.5000, sse=693726.3, rms=5.067 (37.609%) 002: dt: 0.5000, sse=407276.5, rms=3.466 (31.592%) 003: dt: 0.5000, sse=324824.2, rms=2.827 (18.435%) 004: dt: 0.5000, sse=293427.3, rms=2.542 (10.088%) rms = 2.5147/2.5419, sse=289155.4/293427.3, time step reduction 1 of 3 to 0.250 0 0 1 005: dt: 0.5000, sse=289155.4, rms=2.515 (1.068%) 006: dt: 0.2500, sse=214096.1, rms=1.617 (35.713%) 007: dt: 0.2500, sse=203667.1, rms=1.454 (10.080%) rms = 1.4141/1.4537, sse=200515.3/203667.1, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=200515.3, rms=1.414 (2.725%) rms = 1.3871/1.4141, sse=199230.4/200515.3, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=199230.4, rms=1.387 (1.905%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4787140; border_low = 72.0000000; outside_low = 60.6728590; outside_hi = 109.4787140; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=1 had to be increased for 54 vertices, nripped=8522 mean border=85.4, 49 (18) missing vertices, mean dist -0.3 [0.6 (%64.8)->0.2 (%35.2))] %58 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0474 min Finding expansion regions mean absolute distance = 0.44 +- 0.79 3257 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=539430.9, rms=4.182 010: dt: 0.5000, sse=334459.6, rms=2.762 (33.962%) 011: dt: 0.5000, sse=290276.5, rms=2.364 (14.404%) 012: dt: 0.5000, sse=280767.6, rms=2.269 (4.027%) rms = 2.3595/2.2688, sse=289610.7/280767.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=234206.0, rms=1.678 (26.020%) 014: dt: 0.2500, sse=211666.4, rms=1.361 (18.942%) 015: dt: 0.2500, sse=207115.9, rms=1.276 (6.194%) rms = 1.2559/1.2763, sse=206139.5/207115.9, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=206139.5, rms=1.256 (1.595%) rms = 1.2355/1.2559, sse=205135.1/206139.5, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=205135.1, rms=1.235 (1.630%) 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 = 109.4787140; border_low = 72.0000000; outside_low = 60.6728590; outside_hi = 109.4787140; 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=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 59 vertices, nripped=8522 mean border=88.2, 57 (13) missing vertices, mean dist -0.2 [0.4 (%71.4)->0.2 (%28.6))] %74 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0233 min Finding expansion regions mean absolute distance = 0.37 +- 0.51 3520 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=471541.9, rms=3.810 018: dt: 0.5000, sse=288623.3, rms=2.373 (37.714%) 019: dt: 0.5000, sse=271088.8, rms=2.209 (6.917%) rms = 2.2595/2.2087, sse=276524.3/271088.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=224797.9, rms=1.615 (26.858%) 021: dt: 0.2500, sse=204859.4, rms=1.292 (20.051%) 022: dt: 0.2500, sse=201742.8, rms=1.224 (5.219%) rms = 1.2119/1.2242, sse=201388.6/201742.8, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=201388.6, rms=1.212 (0.999%) rms = 1.1893/1.2119, sse=199338.9/201388.6, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=199338.9, rms=1.189 (1.872%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4787140; border_low = 72.0000000; outside_low = 60.6728590; outside_hi = 109.4787140; 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=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 100 vertices, nripped=8522 mean border=89.4, 72 (12) missing vertices, mean dist -0.1 [0.3 (%60.1)->0.2 (%39.9))] %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0252 min Finding expansion regions mean absolute distance = 0.28 +- 0.38 3419 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=247751.7, rms=1.986 025: dt: 0.5000, sse=224408.7, rms=1.528 (23.035%) rms = 1.7979/1.5282, sse=235621.7/224408.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=199258.4, rms=1.178 (22.917%) 027: dt: 0.2500, sse=193186.5, rms=1.068 (9.354%) rms = 1.0377/1.0678, sse=193733.4/193186.5, time step reduction 2 of 3 to 0.125 0 1 1 028: dt: 0.2500, sse=193733.4, rms=1.038 (2.820%) rms = 1.0287/1.0377, sse=192863.6/193733.4, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=192863.6, rms=1.029 (0.867%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes removing intersecting faces 000: 8 intersecting step 1 with no progress (num=9, old_num=8) 001: 9 intersecting 002: 6 intersecting step 1 with no progress (num=10, old_num=6) 003: 10 intersecting step 2 with no progress (num=11, old_num=10) 004: 11 intersecting step 3 with no progress (num=29, old_num=11) 005: 29 intersecting 006: 17 intersecting step 1 with no progress (num=28, old_num=17) 007: 28 intersecting 008: 22 intersecting step 1 with no progress (num=31, old_num=22) 009: 31 intersecting step 2 with no progress (num=31, old_num=31) 010: 31 intersecting step 3 with no progress (num=31, old_num=31) 011: 31 intersecting step 4 with no progress (num=31, old_num=31) 012: 31 intersecting step 5 with no progress (num=31, old_num=31) 013: 31 intersecting step 6 with no progress (num=31, old_num=31) 014: 31 intersecting step 7 with no progress (num=31, old_num=31) 015: 31 intersecting step 8 with no progress (num=31, old_num=31) 016: 31 intersecting step 9 with no progress (num=31, old_num=31) 017: 31 intersecting step 10 with no progress (num=31, old_num=31) 018: 31 intersecting step 11 with no progress (num=31, old_num=31) 019: 31 intersecting step 12 with no progress (num=31, old_num=31) 020: 31 intersecting step 13 with no progress (num=31, old_num=31) 021: 31 intersecting step 14 with no progress (num=31, old_num=31) 022: 31 intersecting step 15 with no progress (num=31, old_num=31) 023: 31 intersecting step 16 with no progress (num=31, old_num=31) terminating search with 6 intersecting Writing output to ../surf/lh.white #ET# mris_place_surface 2.99 minutes #VMPC# mris_place_surfaces VmPeak 2153136 mris_place_surface done @#@FSTIME 2024:11:22:12:37:25 mris_place_surface N 25 e 270.97 S 2.51 U 404.53 P 150% M 1728096 F 1 R 2754986 W 0 c 37374 w 1695 I 0 O 7984 L 31.22 31.43 30.02 @#@FSLOADPOST 2024:11:22:12:41:56 mris_place_surface N 25 32.18 31.77 30.51 #-------------------------------------------- #@# WhiteSurfs rh Fri Nov 22 12:41:56 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 228984 0.33388 0.11636 0.001948 1.9077 Corner 686952 60.00000 13.91355 0.550732 178.5898 Edge 343476 0.88854 0.19277 0.037296 2.8170 Hinge 343476 10.57752 10.83392 0.000011 179.9341 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=23022, wmmin=5, clip=110 MRIfindBrightNonWM(): 468 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 7908/114494 vertices (106586 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 384 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57247: xyz = (-1.18523,7.59169,18.5486) oxyz = (-1.18523,7.59169,18.5486) wxzy = (-1.18523,7.59169,18.5486) pxyz = (0,0,0) CBVO Creating mask 114494 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4787140; border_low = 74.0000000; outside_low = 62.6728590; outside_hi = 109.4787140; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=2 had to be increased for 109 vertices, nripped=8292 mean border=83.4, 76 (76) missing vertices, mean dist 0.4 [1.8 (%11.4)->0.7 (%88.6))] %41 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0531 min Finding expansion regions mean absolute distance = 0.78 +- 1.01 2778 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=1459143.0, rms=7.816 001: dt: 0.5000, sse=605671.8, rms=4.593 (41.241%) 002: dt: 0.5000, sse=346918.9, rms=2.992 (34.851%) 003: dt: 0.5000, sse=288094.1, rms=2.485 (16.939%) 004: dt: 0.5000, sse=267532.0, rms=2.279 (8.287%) rms = 2.3435/2.2793, sse=274336.6/267532.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=221512.0, rms=1.724 (24.351%) 006: dt: 0.2500, sse=203943.5, rms=1.451 (15.831%) 007: dt: 0.2500, sse=200353.9, rms=1.391 (4.154%) rms = 1.3740/1.3910, sse=199680.0/200353.9, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=199680.0, rms=1.374 (1.222%) rms = 1.3553/1.3740, sse=198828.4/199680.0, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=198828.4, rms=1.355 (1.363%) 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 = 109.4787140; border_low = 74.0000000; outside_low = 62.6728590; outside_hi = 109.4787140; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=1 had to be increased for 54 vertices, nripped=8292 mean border=85.8, 71 (21) missing vertices, mean dist -0.3 [0.5 (%63.7)->0.2 (%36.3))] %54 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0287 min Finding expansion regions mean absolute distance = 0.41 +- 0.75 3056 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=480987.5, rms=3.822 010: dt: 0.5000, sse=297816.9, rms=2.448 (35.954%) 011: dt: 0.5000, sse=265286.5, rms=2.115 (13.610%) 012: dt: 0.5000, sse=258061.0, rms=2.032 (3.887%) rms = 2.1606/2.0324, sse=268660.5/258060.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=216398.3, rms=1.460 (28.175%) 014: dt: 0.2500, sse=199868.9, rms=1.163 (20.315%) 015: dt: 0.2500, sse=196953.2, rms=1.099 (5.533%) rms = 1.0812/1.0989, sse=196631.4/196953.2, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=196631.4, rms=1.081 (1.611%) rms = 1.0599/1.0812, sse=195570.4/196631.4, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=195570.4, rms=1.060 (1.967%) 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 = 109.4787140; border_low = 74.0000000; outside_low = 62.6728590; outside_hi = 109.4787140; 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=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 67 vertices, nripped=8292 mean border=88.7, 65 (9) missing vertices, mean dist -0.2 [0.4 (%73.6)->0.2 (%26.4))] %74 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0172 min Finding expansion regions mean absolute distance = 0.33 +- 0.46 3211 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=479754.6, rms=3.837 018: dt: 0.5000, sse=273335.2, rms=2.201 (42.636%) 019: dt: 0.5000, sse=257211.0, rms=2.041 (7.243%) rms = 2.1109/2.0414, sse=263942.9/257211.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=211357.5, rms=1.409 (30.997%) 021: dt: 0.2500, sse=193379.8, rms=1.057 (24.929%) 022: dt: 0.2500, sse=190340.8, rms=0.989 (6.501%) rms = 0.9770/0.9887, sse=190041.1/190340.8, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=190041.1, rms=0.977 (1.183%) rms = 0.9546/0.9770, sse=189187.9/190041.1, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=189187.9, rms=0.955 (2.296%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4787140; border_low = 74.0000000; outside_low = 62.6728590; outside_hi = 109.4787140; 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=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 91 vertices, nripped=8292 mean border=89.8, 94 (8) missing vertices, mean dist -0.1 [0.3 (%60.3)->0.2 (%39.7))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0238 min Finding expansion regions mean absolute distance = 0.24 +- 0.35 2944 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=228782.6, rms=1.721 025: dt: 0.5000, sse=211729.2, rms=1.369 (20.489%) rms = 1.6701/1.3685, sse=229259.2/211729.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=190686.3, rms=0.928 (32.166%) 027: dt: 0.2500, sse=185399.5, rms=0.791 (14.769%) 028: dt: 0.2500, sse=182431.0, rms=0.731 (7.590%) rms = 0.7412/0.7312, sse=181751.8/182431.0, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.7268/0.7312, sse=182002.8/182431.0, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=182002.8, rms=0.727 (0.601%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 2.42 minutes #VMPC# mris_place_surfaces VmPeak 2047076 mris_place_surface done @#@FSTIME 2024:11:22:12:41:56 mris_place_surface N 25 e 152.83 S 3.84 U 284.38 P 188% M 1622212 F 3 R 4839967 W 0 c 26242 w 1894 I 0 O 8056 L 32.18 31.77 30.51 @#@FSLOADPOST 2024:11:22:12:44:29 mris_place_surface N 25 32.07 31.68 30.65 #-------------------------------------------- #@# T1PialSurf lh Fri Nov 22 12:44:29 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 removing intersecting faces 000: 6 intersecting step 1 with no progress (num=10, old_num=6) 001: 10 intersecting step 2 with no progress (num=11, old_num=10) 002: 11 intersecting step 3 with no progress (num=16, old_num=11) 003: 16 intersecting 004: 10 intersecting 005: 2 intersecting terminating search with 0 intersecting Area 226954 0.33530 0.12982 0.000000 1.9633 Corner 680862 60.00000 15.40055 0.154141 176.8936 Edge 340431 0.89210 0.21371 0.000006 3.9047 Hinge 340431 11.00915 11.25270 0.000019 179.9819 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=23022, wmmin=5, clip=110 MRIfindBrightNonWM(): 468 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 66.2699 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 5906/113479 vertices (107573 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 56740: xyz = (-54.034,2.15581,15.2381) oxyz = (-54.034,2.15581,15.2381) wxzy = (-54.034,2.15581,15.2381) pxyz = (-54.034,2.15581,15.2381) CBVO Creating mask 113479 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.5212860; border_hi = 60.6728590; border_low = 38.0185810; outside_low = 10.0000000; outside_hi = 55.0092890; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=2 had to be increased for 124 vertices, nripped=5906 mean border=58.2, 154 (154) missing vertices, mean dist 1.9 [2.6 (%0.0)->2.6 (%100.0))] %22 local maxima, %47 large gradients and %26 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0391 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=21996630.0, rms=31.881 001: dt: 0.5000, sse=16461192.0, rms=27.545 (13.600%) 002: dt: 0.5000, sse=12210887.0, rms=23.683 (14.023%) 003: dt: 0.5000, sse=9127696.0, rms=20.427 (13.745%) 004: dt: 0.5000, sse=6954520.0, rms=17.777 (12.973%) 005: dt: 0.5000, sse=5336732.5, rms=15.512 (12.741%) 006: dt: 0.5000, sse=4009203.2, rms=13.369 (13.816%) 007: dt: 0.5000, sse=2937125.0, rms=11.346 (15.134%) 008: dt: 0.5000, sse=2092370.5, rms=9.450 (16.707%) 009: dt: 0.5000, sse=1492473.8, rms=7.829 (17.155%) 010: dt: 0.5000, sse=1093715.1, rms=6.532 (16.572%) 011: dt: 0.5000, sse=870764.8, rms=5.677 (13.086%) 012: dt: 0.5000, sse=738238.8, rms=5.100 (10.163%) 013: dt: 0.5000, sse=683815.1, rms=4.841 (5.073%) 014: dt: 0.5000, sse=639768.8, rms=4.621 (4.552%) 015: dt: 0.5000, sse=628431.4, rms=4.560 (1.319%) 016: dt: 0.5000, sse=606117.2, rms=4.441 (2.615%) rms = 4.4373/4.4408, sse=606024.3/606117.3, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=606024.3, rms=4.437 (0.079%) 018: dt: 0.2500, sse=415211.4, rms=3.257 (26.591%) 019: dt: 0.2500, sse=373300.2, rms=2.939 (9.777%) 020: dt: 0.2500, sse=363937.4, rms=2.861 (2.664%) 021: dt: 0.2500, sse=356990.2, rms=2.802 (2.046%) rms = 2.7777/2.8021, sse=354231.6/356990.2, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=354231.6, rms=2.778 (0.870%) 023: dt: 0.1250, sse=337216.5, rms=2.628 (5.403%) rms = 2.5970/2.6276, sse=333882.0/337216.5, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=333882.0, rms=2.597 (1.167%) 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 = 94.5212860; border_hi = 60.6728590; border_low = 38.0185810; outside_low = 10.0000000; outside_hi = 55.0092890; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=1 had to be increased for 5118 vertices, nripped=5906 mean border=56.1, 797 (12) missing vertices, mean dist 0.2 [0.1 (%43.4)->0.5 (%56.6))] %38 local maxima, %36 large gradients and %21 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0129 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=584682.4, rms=4.117 025: dt: 0.5000, sse=552913.9, rms=3.928 (4.597%) rms = 4.1036/3.9279, sse=579761.5/552913.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=431900.3, rms=3.129 (20.348%) 027: dt: 0.2500, sse=387674.2, rms=2.784 (11.024%) 028: dt: 0.2500, sse=376198.5, rms=2.685 (3.556%) rms = 2.6532/2.6847, sse=372583.7/376198.5, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=372583.8, rms=2.653 (1.175%) 030: dt: 0.1250, sse=356508.9, rms=2.504 (5.608%) rms = 2.4721/2.5044, sse=353120.2/356508.9, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=353120.2, rms=2.472 (1.290%) 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 = 94.5212860; border_hi = 60.6728590; border_low = 38.0185810; outside_low = 10.0000000; outside_hi = 55.0092890; 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=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 5895 vertices, nripped=5906 mean border=55.0, 1073 (8) missing vertices, mean dist 0.1 [0.1 (%46.4)->0.4 (%53.6))] %49 local maxima, %24 large gradients and %20 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0076 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=421709.0, rms=3.024 rms = 3.6998/3.0237, sse=519786.4/421709.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=374689.6, rms=2.634 (12.895%) 033: dt: 0.2500, sse=363460.6, rms=2.531 (3.883%) rms = 2.5235/2.5315, sse=362352.3/363460.6, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=362352.3, rms=2.524 (0.314%) 035: dt: 0.1250, sse=351203.0, rms=2.416 (4.257%) rms = 2.3937/2.4161, sse=348865.1/351203.0, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=348865.1, rms=2.394 (0.928%) 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 = 94.5212860; border_hi = 60.6728590; border_low = 38.0185810; outside_low = 10.0000000; outside_hi = 55.0092890; 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=113479 Gdiag_no=-1 vno start=0, stop=113479 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 5079 vertices, nripped=5906 mean border=54.2, 2167 (8) missing vertices, mean dist 0.1 [0.1 (%49.3)->0.3 (%50.7))] %53 local maxima, %20 large gradients and %20 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0056 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=373658.3, rms=2.622 rms = 3.2172/2.6217, sse=447883.2/373658.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=354100.2, rms=2.440 (6.931%) rms = 2.4060/2.4400, sse=350275.6/354100.2, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=350275.7, rms=2.406 (1.395%) 039: dt: 0.1250, sse=343896.2, rms=2.343 (2.636%) rms = 2.3192/2.3426, sse=341424.7/343896.2, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=341424.7, rms=2.319 (0.998%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 16 intersecting 001: 4 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 2.72 minutes #VMPC# mris_place_surfaces VmPeak 1432080 mris_place_surface done @#@FSTIME 2024:11:22:12:44:29 mris_place_surface N 28 e 184.44 S 2.92 U 343.68 P 187% M 995056 F 4 R 2501230 W 0 c 32337 w 2235 I 0 O 7984 L 32.07 31.68 30.65 @#@FSLOADPOST 2024:11:22:12:47:34 mris_place_surface N 28 29.59 29.77 30.04 #-------------------------------------------- #@# T1PialSurf rh Fri Nov 22 12:47:34 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 228984 0.33607 0.12958 0.001583 2.3329 Corner 686952 60.00000 15.23137 0.312178 178.5898 Edge 343476 0.89282 0.21138 0.018614 3.2325 Hinge 343476 10.69925 11.10230 0.000011 179.9341 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=23022, wmmin=5, clip=110 MRIfindBrightNonWM(): 468 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 67.2699 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 6007/114494 vertices (108487 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 57247: xyz = (-1.18523,7.59169,18.5486) oxyz = (-1.18523,7.59169,18.5486) wxzy = (-1.18523,7.59169,18.5486) pxyz = (-1.18523,7.59169,18.5486) CBVO Creating mask 114494 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.5212860; border_hi = 62.6728590; border_low = 40.0185810; outside_low = 10.0000000; outside_hi = 57.0092890; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=2 had to be increased for 130 vertices, nripped=6007 mean border=59.5, 149 (149) missing vertices, mean dist 2.0 [1.0 (%0.0)->2.5 (%100.0))] %24 local maxima, %51 large gradients and %20 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0426 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=20812336.0, rms=30.871 001: dt: 0.5000, sse=15332818.0, rms=26.460 (14.288%) 002: dt: 0.5000, sse=11205606.0, rms=22.575 (14.683%) 003: dt: 0.5000, sse=8270872.0, rms=19.342 (14.320%) 004: dt: 0.5000, sse=6239116.5, rms=16.741 (13.448%) 005: dt: 0.5000, sse=4757198.0, rms=14.553 (13.073%) 006: dt: 0.5000, sse=3551107.2, rms=12.491 (14.168%) 007: dt: 0.5000, sse=2593554.0, rms=10.570 (15.377%) 008: dt: 0.5000, sse=1873669.4, rms=8.855 (16.230%) 009: dt: 0.5000, sse=1362010.1, rms=7.396 (16.477%) 010: dt: 0.5000, sse=1034619.5, rms=6.285 (15.013%) 011: dt: 0.5000, sse=850975.4, rms=5.565 (11.465%) 012: dt: 0.5000, sse=747539.9, rms=5.113 (8.121%) 013: dt: 0.5000, sse=688144.9, rms=4.832 (5.481%) 014: dt: 0.5000, sse=651601.1, rms=4.651 (3.765%) 015: dt: 0.5000, sse=633525.1, rms=4.556 (2.030%) 016: dt: 0.5000, sse=615736.4, rms=4.462 (2.069%) rms = 4.4221/4.4619, sse=608718.6/615736.4, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=608718.6, rms=4.422 (0.893%) 018: dt: 0.2500, sse=401652.1, rms=3.133 (29.149%) 019: dt: 0.2500, sse=357797.5, rms=2.788 (11.009%) 020: dt: 0.2500, sse=347685.8, rms=2.700 (3.152%) 021: dt: 0.2500, sse=341700.8, rms=2.648 (1.948%) rms = 2.6297/2.6477, sse=339761.7/341700.8, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=339761.7, rms=2.630 (0.677%) 023: dt: 0.1250, sse=319578.9, rms=2.443 (7.119%) rms = 2.4142/2.4425, sse=316673.6/319578.9, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=316673.6, rms=2.414 (1.160%) 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 = 94.5212860; border_hi = 62.6728590; border_low = 40.0185810; outside_low = 10.0000000; outside_hi = 57.0092890; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=1 had to be increased for 3533 vertices, nripped=6007 mean border=57.0, 630 (15) missing vertices, mean dist 0.2 [0.1 (%41.6)->0.4 (%58.4))] %43 local maxima, %36 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0143 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=657233.4, rms=4.467 025: dt: 0.5000, sse=572491.6, rms=3.999 (10.475%) rms = 4.1199/3.9988, sse=590425.4/572491.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=428952.8, rms=3.060 (23.484%) 027: dt: 0.2500, sse=380441.3, rms=2.672 (12.660%) 028: dt: 0.2500, sse=367848.9, rms=2.560 (4.217%) rms = 2.5212/2.5597, sse=363573.5/367848.9, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=363573.5, rms=2.521 (1.502%) 030: dt: 0.1250, sse=346030.8, rms=2.352 (6.731%) rms = 2.3183/2.3516, sse=342729.5/346030.8, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=342729.5, rms=2.318 (1.414%) 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 = 94.5212860; border_hi = 62.6728590; border_low = 40.0185810; outside_low = 10.0000000; outside_hi = 57.0092890; 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=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 4004 vertices, nripped=6007 mean border=55.3, 789 (9) missing vertices, mean dist 0.1 [0.1 (%38.9)->0.3 (%61.1))] %58 local maxima, %21 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0103 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=468240.9, rms=3.314 rms = 4.1046/3.3135, sse=596668.0/468240.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=383987.7, rms=2.659 (19.759%) 033: dt: 0.2500, sse=362307.8, rms=2.461 (7.453%) 034: dt: 0.2500, sse=356330.3, rms=2.408 (2.151%) rms = 2.3980/2.4077, sse=355177.2/356330.3, time step reduction 2 of 3 to 0.125 0 0 1 035: dt: 0.2500, sse=355177.2, rms=2.398 (0.403%) 036: dt: 0.1250, sse=342937.4, rms=2.275 (5.147%) rms = 2.2483/2.2746, sse=340308.3/342937.4, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=340308.3, rms=2.248 (1.158%) 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 = 94.5212860; border_hi = 62.6728590; border_low = 40.0185810; outside_low = 10.0000000; outside_hi = 57.0092890; 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=114494 Gdiag_no=-1 vno start=0, stop=114494 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 3580 vertices, nripped=6007 mean border=54.5, 1565 (7) missing vertices, mean dist 0.1 [0.2 (%45.5)->0.2 (%54.5))] %63 local maxima, %16 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0055 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=367916.6, rms=2.514 rms = 3.3307/2.5136, sse=471357.4/367916.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 038: dt: 0.2500, sse=343754.1, rms=2.278 (9.361%) rms = 2.2376/2.2783, sse=339531.9/343754.1, time step reduction 2 of 3 to 0.125 0 0 1 039: dt: 0.2500, sse=339531.9, rms=2.238 (1.784%) 040: dt: 0.1250, sse=333740.6, rms=2.176 (2.740%) rms = 2.1510/2.1763, sse=331255.2/333740.6, time step reduction 3 of 3 to 0.062 0 0 1 041: dt: 0.1250, sse=331255.2, rms=2.151 (1.162%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 19 intersecting 001: 6 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.71 minutes #VMPC# mris_place_surfaces VmPeak 1425716 mris_place_surface done @#@FSTIME 2024:11:22:12:47:34 mris_place_surface N 28 e 171.08 S 1.59 U 326.34 P 191% M 988708 F 1 R 1250709 W 0 c 30712 w 2341 I 0 O 8056 L 29.59 29.77 30.04 @#@FSLOADPOST 2024:11:22:12:50:25 mris_place_surface N 28 25.52 27.89 29.27 #@# white curv lh Fri Nov 22 12:50:25 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:12:50:25 mris_place_surface N 5 e 1.75 S 0.10 U 2.20 P 131% M 156656 F 1 R 42241 W 0 c 208 w 113 I 0 O 888 L 25.52 27.89 29.27 @#@FSLOADPOST 2024:11:22:12:50:27 mris_place_surface N 5 25.52 27.89 29.27 #@# white area lh Fri Nov 22 12:50:27 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2024:11:22:12:50:27 mris_place_surface N 3 e 0.77 S 0.10 U 1.16 P 163% M 156676 F 2 R 42191 W 0 c 119 w 134 I 0 O 888 L 25.52 27.89 29.27 @#@FSLOADPOST 2024:11:22:12:50:28 mris_place_surface N 3 25.52 27.89 29.27 #@# pial curv lh Fri Nov 22 12:50:28 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:12:50:28 mris_place_surface N 5 e 1.70 S 0.08 U 2.04 P 124% M 156580 F 2 R 42161 W 0 c 201 w 115 I 0 O 888 L 25.52 27.89 29.27 @#@FSLOADPOST 2024:11:22:12:50:29 mris_place_surface N 5 25.64 27.87 29.26 #@# pial area lh Fri Nov 22 12:50:29 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2024:11:22:12:50:29 mris_place_surface N 3 e 0.79 S 0.10 U 1.18 P 161% M 156700 F 2 R 42234 W 0 c 122 w 114 I 0 O 888 L 25.64 27.87 29.26 @#@FSLOADPOST 2024:11:22:12:50:30 mris_place_surface N 3 25.64 27.87 29.26 #@# thickness lh Fri Nov 22 12:50:30 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 113479 vertices processed 25000 of 113479 vertices processed 50000 of 113479 vertices processed 75000 of 113479 vertices processed 100000 of 113479 vertices processed 0 of 113479 vertices processed 25000 of 113479 vertices processed 50000 of 113479 vertices processed 75000 of 113479 vertices processed 100000 of 113479 vertices processed thickness calculation complete, 77:412 truncations. 54211 vertices at 0 distance 99086 vertices at 1 distance 48427 vertices at 2 distance 16425 vertices at 3 distance 5487 vertices at 4 distance 2038 vertices at 5 distance 764 vertices at 6 distance 303 vertices at 7 distance 82 vertices at 8 distance 47 vertices at 9 distance 24 vertices at 10 distance 12 vertices at 11 distance 11 vertices at 12 distance 9 vertices at 13 distance 6 vertices at 14 distance 9 vertices at 15 distance 7 vertices at 16 distance 6 vertices at 17 distance 2 vertices at 18 distance 1 vertices at 19 distance 1 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2024:11:22:12:50:30 mris_place_surface N 6 e 29.51 S 0.19 U 29.84 P 101% M 156932 F 1 R 159413 W 0 c 2816 w 120 I 0 O 888 L 25.64 27.87 29.26 @#@FSLOADPOST 2024:11:22:12:51:00 mris_place_surface N 6 25.78 27.73 29.17 #@# area and vertex vol lh Fri Nov 22 12:51:00 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Total face volume 189232 Total vertex volume 189020 (mask=0) #@# PIB15-273_VYr9_Bay3prisma lh 189020 vertexvol Done @#@FSTIME 2024:11:22:12:51:00 vertexvol N 4 e 2.23 S 0.22 U 2.76 P 133% M 260892 F 2 R 102230 W 0 c 286 w 300 I 0 O 2664 L 25.78 27.73 29.17 @#@FSLOADPOST 2024:11:22:12:51:02 vertexvol N 4 25.78 27.73 29.17 #@# white curv rh Fri Nov 22 12:51:02 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:12:51:02 mris_place_surface N 5 e 1.91 S 0.09 U 2.46 P 134% M 158264 F 1 R 42568 W 0 c 243 w 126 I 0 O 896 L 25.78 27.73 29.17 @#@FSLOADPOST 2024:11:22:12:51:04 mris_place_surface N 5 25.88 27.72 29.16 #@# white area rh Fri Nov 22 12:51:04 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2024:11:22:12:51:04 mris_place_surface N 3 e 0.81 S 0.08 U 1.24 P 162% M 158184 F 4 R 42623 W 0 c 124 w 135 I 0 O 896 L 25.88 27.72 29.16 @#@FSLOADPOST 2024:11:22:12:51:05 mris_place_surface N 3 25.88 27.72 29.16 #@# pial curv rh Fri Nov 22 12:51:05 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:12:51:05 mris_place_surface N 5 e 1.79 S 0.09 U 2.22 P 129% M 158132 F 2 R 42608 W 0 c 229 w 92 I 0 O 896 L 25.88 27.72 29.16 @#@FSLOADPOST 2024:11:22:12:51:07 mris_place_surface N 5 25.88 27.72 29.16 #@# pial area rh Fri Nov 22 12:51:07 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2024:11:22:12:51:07 mris_place_surface N 3 e 0.84 S 0.08 U 1.27 P 162% M 158316 F 2 R 42633 W 0 c 122 w 129 I 0 O 896 L 25.88 27.72 29.16 @#@FSLOADPOST 2024:11:22:12:51:08 mris_place_surface N 3 25.88 27.72 29.16 #@# thickness rh Fri Nov 22 12:51:08 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 114494 vertices processed 25000 of 114494 vertices processed 50000 of 114494 vertices processed 75000 of 114494 vertices processed 100000 of 114494 vertices processed 0 of 114494 vertices processed 25000 of 114494 vertices processed 50000 of 114494 vertices processed 75000 of 114494 vertices processed 100000 of 114494 vertices processed thickness calculation complete, 38:337 truncations. 60972 vertices at 0 distance 101499 vertices at 1 distance 46237 vertices at 2 distance 13998 vertices at 3 distance 4179 vertices at 4 distance 1282 vertices at 5 distance 425 vertices at 6 distance 152 vertices at 7 distance 64 vertices at 8 distance 59 vertices at 9 distance 31 vertices at 10 distance 19 vertices at 11 distance 8 vertices at 12 distance 6 vertices at 13 distance 9 vertices at 14 distance 13 vertices at 15 distance 8 vertices at 16 distance 5 vertices at 17 distance 6 vertices at 18 distance 5 vertices at 19 distance 11 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2024:11:22:12:51:08 mris_place_surface N 6 e 33.39 S 0.25 U 33.88 P 102% M 158428 F 2 R 207035 W 0 c 3198 w 109 I 0 O 896 L 25.88 27.72 29.16 @#@FSLOADPOST 2024:11:22:12:51:41 mris_place_surface N 6 26.52 27.74 29.12 #@# area and vertex vol rh Fri Nov 22 12:51:41 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Total face volume 189737 Total vertex volume 189533 (mask=0) #@# PIB15-273_VYr9_Bay3prisma rh 189533 vertexvol Done @#@FSTIME 2024:11:22:12:51:41 vertexvol N 4 e 1.83 S 0.20 U 2.22 P 132% M 262724 F 3 R 74862 W 0 c 230 w 347 I 0 O 2688 L 26.52 27.74 29.12 @#@FSLOADPOST 2024:11:22:12:51:43 vertexvol N 4 27.28 27.87 29.15 #----------------------------------------- #@# Curvature Stats lh Fri Nov 22 12:51:43 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PIB15-273_VYr9_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 [ PIB15-273_VYr9_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 [ 181 ] Gb_filter = 0 WARN: S lookup min: -0.067747 WARN: S explicit min: 0.000000 vertex = 438 @#@FSTIME 2024:11:22:12:51:43 mris_curvature_stats N 11 e 2.90 S 0.14 U 3.15 P 113% M 156976 F 2 R 73607 W 0 c 323 w 411 I 0 O 7144 L 27.28 27.87 29.15 @#@FSLOADPOST 2024:11:22:12:51:46 mris_curvature_stats N 11 27.28 27.87 29.15 #----------------------------------------- #@# Curvature Stats rh Fri Nov 22 12:51:46 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PIB15-273_VYr9_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 [ PIB15-273_VYr9_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 [ 208 ] Gb_filter = 0 WARN: S lookup min: -0.084568 WARN: S explicit min: 0.000000 vertex = 500 @#@FSTIME 2024:11:22:12:51:46 mris_curvature_stats N 11 e 3.07 S 0.12 U 3.31 P 111% M 158332 F 1 R 74260 W 0 c 333 w 398 I 0 O 7208 L 27.28 27.87 29.15 @#@FSLOADPOST 2024:11:22:12:51:49 mris_curvature_stats N 11 27.74 27.96 29.18 #-------------------------------------------- #@# Cortical ribbon mask Fri Nov 22 12:51:49 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 = 32 writing volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz mris_volmask took 5.13 minutes writing ribbon files @#@FSTIME 2024:11:22:12:51:49 mris_volmask N 12 e 308.11 S 1.49 U 308.70 P 100% M 897148 F 2 R 1202856 W 0 c 28823 w 262 I 0 O 752 L 27.74 27.96 29.18 @#@FSLOADPOST 2024:11:22:12:56:57 mris_volmask N 12 25.36 26.36 28.10 #----------------------------------------- #@# Cortical Parc 2 lh Fri Nov 22 12:56:57 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Fri Nov 22 12:56:57 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 3849204 of (3849204 3849209) to complete... Waiting for PID 3849209 of (3849204 3849209) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 112 labels changed using aseg relabeling using gibbs priors... 000: 7529 changed, 113479 examined... 001: 1723 changed, 29408 examined... 002: 474 changed, 9241 examined... 003: 191 changed, 2749 examined... 004: 92 changed, 1133 examined... 005: 43 changed, 528 examined... 006: 18 changed, 232 examined... 007: 10 changed, 110 examined... 008: 7 changed, 53 examined... 009: 5 changed, 37 examined... 010: 1 changed, 25 examined... 011: 2 changed, 6 examined... 012: 1 changed, 12 examined... 013: 1 changed, 7 examined... 014: 0 changed, 7 examined... 88 labels changed using aseg 000: 202 total segments, 120 labels (1130 vertices) changed 001: 87 total segments, 5 labels (13 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 33 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1143 vertices marked for relabeling... 1117 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 14 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 43 labels changed using aseg relabeling using gibbs priors... 000: 7948 changed, 114494 examined... 001: 1783 changed, 30781 examined... 002: 521 changed, 9467 examined... 003: 206 changed, 2985 examined... 004: 87 changed, 1216 examined... 005: 43 changed, 522 examined... 006: 25 changed, 275 examined... 007: 21 changed, 157 examined... 008: 8 changed, 108 examined... 009: 5 changed, 49 examined... 010: 2 changed, 31 examined... 011: 1 changed, 13 examined... 012: 1 changed, 7 examined... 013: 0 changed, 7 examined... 39 labels changed using aseg 000: 222 total segments, 129 labels (1587 vertices) changed 001: 94 total segments, 3 labels (23 vertices) changed 002: 91 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... 1024 vertices marked for relabeling... 1024 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. PIDs (3849204 3849209) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Fri Nov 22 12:57:12 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Fri Nov 22 12:57:12 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 3849349 of (3849349 3849352) to complete... Waiting for PID 3849352 of (3849349 3849352) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 1233 labels changed using aseg relabeling using gibbs priors... 000: 1781 changed, 113479 examined... 001: 424 changed, 8296 examined... 002: 130 changed, 2391 examined... 003: 67 changed, 716 examined... 004: 46 changed, 369 examined... 005: 29 changed, 238 examined... 006: 19 changed, 151 examined... 007: 13 changed, 96 examined... 008: 8 changed, 66 examined... 009: 6 changed, 42 examined... 010: 7 changed, 39 examined... 011: 4 changed, 43 examined... 012: 4 changed, 26 examined... 013: 2 changed, 23 examined... 014: 2 changed, 14 examined... 015: 2 changed, 14 examined... 016: 2 changed, 16 examined... 017: 2 changed, 12 examined... 018: 2 changed, 10 examined... 019: 3 changed, 14 examined... 020: 1 changed, 13 examined... 021: 0 changed, 8 examined... 343 labels changed using aseg 000: 50 total segments, 17 labels (140 vertices) changed 001: 34 total segments, 1 labels (17 vertices) changed 002: 33 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... 743 vertices marked for relabeling... 743 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 1268 labels changed using aseg relabeling using gibbs priors... 000: 1737 changed, 114494 examined... 001: 410 changed, 8165 examined... 002: 96 changed, 2348 examined... 003: 52 changed, 566 examined... 004: 30 changed, 285 examined... 005: 17 changed, 177 examined... 006: 14 changed, 103 examined... 007: 7 changed, 70 examined... 008: 7 changed, 43 examined... 009: 5 changed, 28 examined... 010: 3 changed, 25 examined... 011: 1 changed, 20 examined... 012: 2 changed, 7 examined... 013: 3 changed, 14 examined... 014: 3 changed, 12 examined... 015: 2 changed, 12 examined... 016: 1 changed, 10 examined... 017: 1 changed, 7 examined... 018: 1 changed, 7 examined... 019: 1 changed, 7 examined... 020: 1 changed, 8 examined... 021: 1 changed, 7 examined... 022: 1 changed, 7 examined... 023: 1 changed, 8 examined... 024: 1 changed, 7 examined... 025: 2 changed, 8 examined... 026: 0 changed, 9 examined... 328 labels changed using aseg 000: 47 total segments, 14 labels (33 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 805 vertices marked for relabeling... 805 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. PIDs (3849349 3849352) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Fri Nov 22 12:57:23 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts pctsurfcon --s PIB15-273_VYr9_Bay3prisma --lh-only #----------------------------------------- #@# WM/GM Contrast rh Fri Nov 22 12:57:23 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts pctsurfcon --s PIB15-273_VYr9_Bay3prisma --rh-only Waiting for PID 3849526 of (3849526 3849546) to complete... Waiting for PID 3849546 of (3849526 3849546) to complete... pctsurfcon --s PIB15-273_VYr9_Bay3prisma --lh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts/pctsurfcon.log Fri Nov 22 12:57:23 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849526/lh.wm.mgh --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 73046 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849526/lh.wm.mgh Dim: 113479 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849526/lh.gm.mgh --projfrac 0.3 --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 86313 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849526/lh.gm.mgh Dim: 113479 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849526/lh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849526/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/stats/lh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Seg base 1000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh Vertex Area is 0.670618 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 PIB15-273_VYr9_Bay3prisma --rh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts/pctsurfcon.log Fri Nov 22 12:57:23 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849546/rh.wm.mgh --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 73702 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849546/rh.wm.mgh Dim: 114494 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849546/rh.gm.mgh --projfrac 0.3 --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 87785 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849546/rh.gm.mgh Dim: 114494 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849546/rh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.3849546/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/stats/rh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Seg base 2000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh Vertex Area is 0.672124 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 (3849526 3849546) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Fri Nov 22 12:57:28 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1240 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1805 voxels changed to hypointensity... 3034 hypointense voxels neighboring cortex changed @#@FSTIME 2024:11:22:12:57:28 mri_relabel_hypointensities N 3 e 17.88 S 0.93 U 18.82 P 110% M 444600 F 2 R 604391 W 0 c 1819 w 120 I 0 O 608 L 27.61 26.80 28.20 @#@FSLOADPOST 2024:11:22:12:57:46 mri_relabel_hypointensities N 3 27.62 26.84 28.18 #----------------------------------------- #@# APas-to-ASeg Fri Nov 22 12:57:46 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz --threads 4 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Done loading 0 64 192 128 65 193 1 2 194 66 3 195 67 4 196 68 5 197 69 6 198 129 7 199 70 8 200 71 9 201 72 10 202 11 203 73 12 204 13 205 74 14 206 130 15 207 75 16 208 17 209 76 18 210 19 211 131 77 20 212 21 213 22 78 214 23 215 24 216 132 25 217 79 26 218 27 219 80 28 220 29 221 133 30 222 81 31 223 32 224 33 225 82 226 34 134 227 35 36 228 229 37 230 38 83 231 39 135 232 40 233 41 234 42 235 84 43 136 236 44 237 45 85 238 46 239 47 86 48 137 240 49 241 50 242 87 51 243 52 244 138 88 53 245 54 246 55 247 56 248 89 139 57 249 58 250 59 251 90 60 252 61 253 140 62 254 91 63 255 92 141 93 142 94 95 143 96 144 97 145 98 146 99 147 148 100 149 101 150 102 151 103 152 104 153 154 105 155 106 156 107 157 158 108 159 109 160 110 161 162 111 163 112 164 113 165 166 167 114 168 169 170 171 115 172 173 174 175 176 116 177 178 179 180 181 117 182 183 184 118 185 186 187 188 119 189 190 191 120 121 122 123 124 125 126 127 nrelabeled = 91410 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 986660 mri_surf2volseg done @#@FSTIME 2024:11:22:12:57:46 mri_surf2volseg N 20 e 8.43 S 0.84 U 15.23 P 190% M 799180 F 2 R 545885 W 0 c 1518 w 324 I 0 O 632 L 27.62 26.84 28.18 @#@FSLOADPOST 2024:11:22:12:57:54 mri_surf2volseg N 20 27.73 26.89 28.18 mri_brainvol_stats PIB15-273_VYr9_Bay3prisma ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1434297.0 #CBVS2 BrainSegVol 947588.0 #CBVS2 BrainSegVolNotVent 921105.0 #CBVS2 SupraTentVol 829785.0 #CBVS2 SupraTentVolNotVent 803302.0 #CBVS2 lhCtxGM 189232.8 #CBVS2 rhCtxGM 189728.3 #CBVS2 lhCerebralWM 189441.0 #CBVS2 rhCerebralWM 186942.0 #CBVS2 SubCortGMVol 48999.0 #CBVS2 CerebellumVol 117803.0 #CBVS2 CerebellumGMVol 94623.0 #CBVS2 VentChorVol 23486.0 #CBVS2 3rd4th5thCSF 2997.0 #CBVS2 AllCSF 26483.0 #CBVS2 CCVol 2950.0 @#@FSTIME 2024:11:22:12:57:54 mri_brainvol_stats N 1 e 3.69 S 0.29 U 7.15 P 201% M 208340 F 5 R 183136 W 0 c 697 w 188 I 0 O 8 L 27.73 26.89 28.18 @#@FSLOADPOST 2024:11:22:12:57:58 mri_brainvol_stats N 1 27.73 26.89 28.18 #----------------------------------------- #@# AParc-to-ASeg aparc Fri Nov 22 12:57:58 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8094 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7908 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Done loading 0 64 128 192 1 193 65 2 66 194 3 195 4 196 5 67 197 6 7 198 8 199 9 200 68 10 201 11 202 12 203 13 204 14 205 15 206 16 69 207 17 208 18 209 19 210 20 211 21 212 22 213 23 214 24 215 25 216 26 217 27 218 28 219 29 220 30 31 221 32 222 70 33 223 34 224 35 225 36 226 227 37 38 228 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 52 242 53 243 54 244 71 55 245 56 246 57 247 58 248 59 249 60 250 61 251 62 252 63 253 254 255 72 129 73 130 74 75 131 76 132 77 133 78 134 79 80 135 81 136 82 83 137 84 138 85 139 86 140 87 88 141 142 89 143 90 144 91 145 146 92 147 93 148 94 149 150 95 151 96 152 97 153 98 154 99 155 100 156 101 157 102 158 103 104 159 105 160 106 107 161 108 162 109 110 163 111 164 112 113 165 114 166 115 116 167 117 118 168 119 169 120 170 121 171 122 172 123 173 124 174 125 175 126 176 127 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 377895 ndotcheck = 13494 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 970688 mri_surf2volseg done @#@FSTIME 2024:11:22:12:57:58 mri_surf2volseg N 25 e 63.68 S 0.99 U 119.68 P 189% M 784420 F 1 R 660924 W 0 c 11270 w 3909 I 0 O 728 L 27.73 26.89 28.18 @#@FSLOADPOST 2024:11:22:12:59:02 mri_surf2volseg N 25 27.54 27.11 28.18 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Fri Nov 22 12:59:02 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8094 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.a2009s.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7908 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.a2009s.annot Done loading 0 192 128 64 193 65 1 194 2 66 195 3 196 4 197 198 5 199 67 6 200 7 201 202 8 203 9 204 10 205 206 11 68 207 12 208 13 209 210 14 211 15 212 213 16 214 17 215 18 216 217 19 69 218 20 219 21 220 221 22 222 23 223 24 224 225 25 226 26 227 27 228 229 28 230 29 231 232 30 233 31 70 234 32 235 236 33 237 34 238 35 239 240 36 241 37 242 38 243 244 39 245 40 246 41 247 248 42 249 43 250 44 251 252 45 46 253 254 71 47 255 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 72 129 73 130 74 75 131 76 132 77 133 78 134 79 80 135 81 136 82 137 83 84 138 85 139 86 140 87 141 88 142 89 143 90 144 91 145 146 92 147 93 148 94 149 150 95 151 96 152 97 153 98 154 99 155 100 156 101 157 102 158 103 159 104 105 160 106 161 107 162 108 109 163 110 164 111 112 165 113 114 166 115 167 116 117 168 118 169 119 170 120 171 121 122 172 123 173 124 174 125 175 126 176 127 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 377895 ndotcheck = 13494 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 970772 mri_surf2volseg done @#@FSTIME 2024:11:22:12:59:02 mri_surf2volseg N 25 e 59.91 S 1.05 U 113.29 P 190% M 784604 F 1 R 655742 W 0 c 10730 w 2982 I 0 O 784 L 27.54 27.11 28.18 @#@FSLOADPOST 2024:11:22:13:00:02 mri_surf2volseg N 25 28.13 27.50 28.25 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Fri Nov 22 13:00:02 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8094 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.DKTatlas.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7908 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.DKTatlas.annot Done loading 0 128 64 192 193 65 1 2 194 66 3 195 196 4 197 5 67 198 6 199 200 7 201 8 202 9 203 68 10 204 205 11 206 12 207 13 208 69 209 14 210 15 211 16 212 213 17 214 18 215 19 216 20 217 21 218 22 219 23 220 24 221 25 70 26 222 27 223 28 224 29 225 30 226 31 227 32 228 33 229 34 230 35 231 36 232 37 233 38 234 39 235 40 236 41 237 42 238 43 239 44 240 45 241 71 46 242 47 243 48 244 49 245 50 246 51 247 52 248 53 249 54 250 55 251 56 252 57 253 58 254 59 255 60 61 62 72 63 129 73 130 74 131 75 132 76 77 133 78 134 79 135 80 81 136 82 137 83 84 138 85 139 86 140 87 141 88 142 89 143 144 90 145 91 146 92 147 148 93 149 94 150 95 151 96 152 153 97 154 98 155 99 156 100 157 101 158 102 103 159 104 160 105 106 161 107 162 108 163 109 110 164 111 112 165 113 166 114 115 167 116 168 117 169 118 119 170 120 171 121 172 122 123 173 124 174 125 175 126 176 127 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 377895 ndotcheck = 13494 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 970688 mri_surf2volseg done @#@FSTIME 2024:11:22:13:00:02 mri_surf2volseg N 25 e 60.55 S 1.53 U 114.12 P 191% M 784420 F 2 R 1581330 W 0 c 10848 w 437 I 0 O 720 L 28.13 27.50 28.25 @#@FSLOADPOST 2024:11:22:13:01:02 mri_surf2volseg N 25 29.13 27.71 28.27 #----------------------------------------- #@# WMParc Fri Nov 22 13:01:02 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot 3000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot 4000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8094 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7908 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Done loading 192 0 64 128 65 1 193 66 2 194 67 3 195 68 4 196 69 5 197 6 70 198 7 199 8 71 129 200 9 201 72 10 202 11 203 12 204 13 205 14 206 15 207 73 16 208 17 209 18 210 19 211 20 212 130 21 74 213 22 214 23 215 24 216 25 217 26 218 27 219 28 220 29 221 30 75 222 31 131 223 32 224 33 225 34 226 35 227 36 228 37 229 38 230 39 231 40 76 232 41 233 42 234 43 132 235 44 236 45 237 46 238 47 239 48 240 49 241 50 242 51 243 52 77 244 53 245 54 246 55 247 56 248 57 133 249 58 250 59 251 60 252 61 253 62 254 63 78 255 134 79 80 135 81 136 82 83 137 84 138 85 86 139 87 140 88 89 141 90 91 142 92 93 143 94 95 144 96 97 145 98 99 146 100 101 147 102 148 103 104 149 105 150 106 151 107 152 108 153 154 109 155 110 156 111 157 112 158 113 159 160 114 161 115 116 162 117 163 118 164 119 165 166 120 167 121 122 168 123 169 124 170 125 171 126 172 127 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 373433 ndotcheck = 3768 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 970688 mri_surf2volseg done @#@FSTIME 2024:11:22:13:01:02 mri_surf2volseg N 25 e 26.88 S 1.22 U 49.89 P 190% M 784256 F 0 R 553357 W 0 c 4735 w 8543 I 0 O 808 L 29.13 27.71 28.27 @#@FSLOADPOST 2024:11:22:13:01:29 mri_surf2volseg N 25 26.66 27.27 28.10 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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) = 1351565 mm^3 (det: 1.441370 ) 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 2024:11:22:13:01:29 mri_segstats N 24 e 257.65 S 1.18 U 530.72 P 206% M 240200 F 0 R 1580725 W 0 c 49679 w 1917 I 0 O 24 L 26.66 27.27 28.10 @#@FSLOADPOST 2024:11:22:13:05:47 mri_segstats N 24 25.71 26.92 27.79 #----------------------------------------- #@# Parcellation Stats lh Fri Nov 22 13:05:47 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh pial #----------------------------------------- #@# Parcellation Stats rh Fri Nov 22 13:05:47 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh pial Waiting for PID 3853973 of (3853973 3853977 3853980 3853984) to complete... Waiting for PID 3853977 of (3853973 3853977 3853980 3853984) to complete... Waiting for PID 3853980 of (3853973 3853977 3853980 3853984) to complete... Waiting for PID 3853984 of (3853973 3853977 3853980 3853984) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189232 Total vertex volume 189020 (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) = 1351565 mm^3 (det: 1.441370 ) 1184 779 1696 2.278 0.361 0.084 0.013 5 0.7 bankssts 816 514 1324 2.496 0.761 0.119 0.018 9 0.7 caudalanteriorcingulate 2227 1464 3757 2.503 0.505 0.110 0.022 15 2.1 caudalmiddlefrontal 2099 1310 2613 1.855 0.405 0.140 0.036 30 3.1 cuneus 642 443 2016 3.417 0.765 0.109 0.028 5 0.7 entorhinal 3061 2268 7276 2.746 0.581 0.140 0.034 42 4.1 fusiform 4761 3248 8212 2.302 0.502 0.124 0.025 50 4.9 inferiorparietal 3671 2597 7856 2.710 0.537 0.132 0.031 105 4.8 inferiortemporal 1237 838 1820 1.972 0.714 0.122 0.030 16 1.4 isthmuscingulate 6224 4072 9535 2.122 0.522 0.139 0.031 79 8.0 lateraloccipital 3158 2208 6263 2.724 0.609 0.132 0.034 36 4.2 lateralorbitofrontal 4057 2726 5639 1.920 0.564 0.137 0.033 54 5.6 lingual 2430 1800 4349 2.298 0.571 0.143 0.035 40 3.3 medialorbitofrontal 3763 2504 7879 2.684 0.548 0.121 0.025 43 3.9 middletemporal 862 555 1758 2.666 0.731 0.093 0.020 6 0.6 parahippocampal 1813 1051 2824 2.439 0.543 0.090 0.019 10 1.4 paracentral 2151 1443 4066 2.590 0.484 0.113 0.026 19 2.2 parsopercularis 930 693 2149 2.669 0.530 0.149 0.036 15 1.5 parsorbitalis 1888 1281 3432 2.387 0.541 0.121 0.025 17 2.0 parstriangularis 1990 1313 2144 1.813 0.494 0.130 0.031 20 2.7 pericalcarine 5564 3488 7216 1.897 0.603 0.107 0.024 50 5.3 postcentral 1393 934 2358 2.314 0.637 0.123 0.027 17 1.6 posteriorcingulate 6751 4215 11777 2.554 0.607 0.110 0.026 56 7.5 precentral 4329 3062 7312 2.247 0.537 0.129 0.028 50 4.9 precuneus 832 617 1993 2.820 0.645 0.151 0.038 14 1.3 rostralanteriorcingulate 5743 4247 11545 2.410 0.515 0.147 0.034 80 8.4 rostralmiddlefrontal 8555 5865 17603 2.687 0.547 0.121 0.026 76 9.2 superiorfrontal 7255 4752 10539 2.060 0.479 0.114 0.022 66 6.5 superiorparietal 5339 3597 11209 2.753 0.629 0.115 0.026 50 5.6 superiortemporal 5721 3872 9991 2.407 0.528 0.122 0.024 57 5.7 supramarginal 319 275 975 2.758 0.412 0.188 0.047 7 0.6 frontalpole 638 496 2557 3.478 0.742 0.130 0.030 7 0.8 temporalpole 706 408 1029 2.217 0.341 0.106 0.024 6 0.7 transversetemporal 3250 2238 6307 2.854 0.812 0.132 0.040 38 5.6 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 PIB15-273_VYr9_Bay3prisma lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189232 Total vertex volume 189020 (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) = 1351565 mm^3 (det: 1.441370 ) 1184 714 1696 2.278 0.361 0.090 0.018 18 0.9 bankssts 816 579 1324 2.496 0.761 0.142 0.052 29 1.5 caudalanteriorcingulate 2227 1525 3757 2.503 0.505 0.138 0.349 20188 2.2 caudalmiddlefrontal 2099 1594 2613 1.855 0.405 0.129 0.032 41 2.5 cuneus 642 782 2016 3.417 0.765 0.257 0.070 23 2.4 entorhinal 3061 2959 7276 2.746 0.581 0.166 0.048 81 5.6 fusiform 4761 3791 8212 2.302 0.502 0.133 0.027 63 5.3 inferiorparietal 3671 3204 7856 2.710 0.537 0.157 0.042 141 6.3 inferiortemporal 1237 1063 1820 1.972 0.714 0.186 0.067 232 3.5 isthmuscingulate 6224 4936 9535 2.122 0.522 0.137 0.034 128 8.0 lateraloccipital 3158 2412 6263 2.724 0.609 0.132 0.037 67 4.5 lateralorbitofrontal 4057 3393 5639 1.920 0.564 0.141 0.035 78 5.6 lingual 2430 2022 4349 2.298 0.571 0.144 0.036 65 3.2 medialorbitofrontal 3763 3250 7879 2.684 0.548 0.143 0.033 79 5.2 middletemporal 862 788 1758 2.666 0.731 0.166 0.044 12 1.8 parahippocampal 1813 1270 2824 2.439 0.543 0.091 0.017 11 1.2 paracentral 2151 1716 4066 2.590 0.484 0.127 0.028 33 2.2 parsopercularis 930 928 2149 2.669 0.530 0.167 0.036 12 1.4 parsorbitalis 1888 1533 3432 2.387 0.541 0.140 0.027 23 2.4 parstriangularis 1990 1116 2144 1.813 0.494 0.103 0.029 23 2.1 pericalcarine 5564 4227 7216 1.897 0.603 0.115 0.022 44 5.0 postcentral 1393 1088 2358 2.314 0.637 0.159 0.041 170 2.1 posteriorcingulate 6751 4887 11777 2.554 0.607 0.108 0.022 74 5.9 precentral 4329 3403 7312 2.247 0.537 0.140 0.031 67 5.6 precuneus 832 801 1993 2.820 0.645 0.199 0.070 72 2.0 rostralanteriorcingulate 5743 5249 11545 2.410 0.515 0.170 0.040 134 9.0 rostralmiddlefrontal 8555 7045 17603 2.687 0.547 0.137 0.031 134 10.1 superiorfrontal 7255 5445 10539 2.060 0.479 0.120 0.023 87 6.7 superiorparietal 5339 4377 11209 2.753 0.629 0.131 0.028 139 6.1 superiortemporal 5721 4402 9991 2.407 0.528 0.127 0.027 70 6.4 supramarginal 319 447 975 2.758 0.412 0.210 0.035 4 0.5 frontalpole 638 942 2557 3.478 0.742 0.221 0.045 22 1.3 temporalpole 706 545 1029 2.217 0.341 0.102 0.020 4 0.6 transversetemporal 3250 2096 6307 2.854 0.812 0.151 0.047 98 6.3 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189737 Total vertex volume 189533 (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) = 1351565 mm^3 (det: 1.441370 ) 1021 671 1527 2.342 0.309 0.083 0.016 4 0.7 bankssts 936 639 1661 2.363 0.787 0.141 0.027 17 1.1 caudalanteriorcingulate 2843 1903 4872 2.347 0.455 0.117 0.022 25 2.6 caudalmiddlefrontal 2259 1388 2701 1.776 0.410 0.128 0.031 29 3.0 cuneus 621 451 2336 3.611 0.726 0.118 0.024 6 0.6 entorhinal 3554 2418 7248 2.610 0.574 0.128 0.035 61 4.5 fusiform 6760 4617 11490 2.318 0.405 0.120 0.024 72 6.7 inferiorparietal 3572 2536 7776 2.685 0.667 0.133 0.031 50 4.4 inferiortemporal 1151 757 1629 1.889 0.716 0.123 0.030 16 1.3 isthmuscingulate 6729 4430 10341 2.125 0.502 0.136 0.030 92 8.0 lateraloccipital 3305 2330 6165 2.523 0.639 0.139 0.039 43 5.6 lateralorbitofrontal 4188 2784 6032 2.038 0.565 0.134 0.033 52 5.7 lingual 2587 1833 4689 2.315 0.676 0.126 0.031 33 3.3 medialorbitofrontal 3824 2660 8143 2.590 0.487 0.120 0.024 44 3.7 middletemporal 914 580 1836 2.656 0.762 0.098 0.020 7 0.8 parahippocampal 1913 1053 2925 2.582 0.585 0.087 0.018 11 1.4 paracentral 1428 979 2633 2.531 0.378 0.110 0.025 14 1.4 parsopercularis 1093 821 2460 2.394 0.514 0.142 0.035 18 1.8 parsorbitalis 1646 1195 3163 2.344 0.507 0.127 0.026 15 1.8 parstriangularis 2454 1570 2470 1.657 0.400 0.113 0.027 25 2.7 pericalcarine 5089 3175 6713 1.918 0.488 0.102 0.019 40 4.1 postcentral 1344 937 2502 2.359 0.690 0.122 0.025 16 1.4 posteriorcingulate 6571 4139 11321 2.512 0.523 0.102 0.020 46 5.8 precentral 4276 2927 7162 2.279 0.541 0.123 0.026 44 4.4 precuneus 601 411 1205 2.832 0.691 0.110 0.024 6 0.6 rostralanteriorcingulate 6504 5023 13483 2.321 0.556 0.150 0.035 103 9.9 rostralmiddlefrontal 7838 5400 15841 2.608 0.565 0.125 0.029 77 9.6 superiorfrontal 8030 5239 11980 2.084 0.434 0.101 0.019 64 6.3 superiorparietal 4689 3134 9575 2.655 0.568 0.107 0.022 42 4.3 superiortemporal 4324 2970 7752 2.374 0.467 0.116 0.025 43 4.4 supramarginal 354 324 1155 2.727 0.526 0.213 0.056 9 0.9 frontalpole 595 442 2051 3.531 0.574 0.137 0.035 7 0.9 temporalpole 447 254 703 2.536 0.291 0.106 0.022 5 0.4 transversetemporal 3126 2140 5993 2.785 0.743 0.123 0.036 34 4.4 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 PIB15-273_VYr9_Bay3prisma rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189737 Total vertex volume 189533 (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) = 1351565 mm^3 (det: 1.441370 ) 1021 628 1527 2.342 0.309 0.095 0.022 10 0.9 bankssts 936 757 1661 2.363 0.787 0.171 0.045 56 1.5 caudalanteriorcingulate 2843 2193 4872 2.347 0.455 0.121 0.026 36 2.6 caudalmiddlefrontal 2259 1775 2701 1.776 0.410 0.127 0.025 27 2.4 cuneus 621 862 2336 3.611 0.726 0.294 0.069 20 2.2 entorhinal 3554 3072 7248 2.610 0.574 0.149 0.036 69 5.3 fusiform 6760 5243 11490 2.318 0.405 0.130 0.027 98 7.5 inferiorparietal 3572 3087 7776 2.685 0.667 0.149 0.037 91 4.9 inferiortemporal 1151 980 1629 1.889 0.716 0.176 0.053 46 2.3 isthmuscingulate 6729 5309 10341 2.125 0.502 0.137 0.033 115 8.7 lateraloccipital 3305 2557 6165 2.523 0.639 0.143 0.043 84 5.2 lateralorbitofrontal 4188 3321 6032 2.038 0.565 0.134 0.036 60 5.6 lingual 2587 2230 4689 2.315 0.676 0.149 0.037 53 4.0 medialorbitofrontal 3824 3532 8143 2.590 0.487 0.146 0.028 72 4.5 middletemporal 914 801 1836 2.656 0.762 0.165 0.042 16 1.7 parahippocampal 1913 1223 2925 2.582 0.585 0.093 0.017 13 1.4 paracentral 1428 1114 2633 2.531 0.378 0.119 0.024 13 1.4 parsopercularis 1093 1234 2460 2.394 0.514 0.178 0.033 14 1.8 parsorbitalis 1646 1434 3163 2.344 0.507 0.147 0.033 23 2.2 parstriangularis 2454 1528 2470 1.657 0.400 0.104 0.024 33 2.1 pericalcarine 5089 3850 6713 1.918 0.488 0.110 0.019 39 3.9 postcentral 1344 1152 2502 2.359 0.690 0.157 0.038 44 2.3 posteriorcingulate 6571 4779 11321 2.512 0.523 0.102 0.018 61 4.7 precentral 4276 3321 7162 2.279 0.541 0.131 0.028 68 4.7 precuneus 601 475 1205 2.832 0.691 0.133 0.025 13 0.6 rostralanteriorcingulate 6504 6477 13483 2.321 0.556 0.175 0.037 107 10.3 rostralmiddlefrontal 7838 6600 15841 2.608 0.565 0.142 0.030 105 9.6 superiorfrontal 8030 6191 11980 2.084 0.434 0.114 0.019 68 6.3 superiorparietal 4689 3923 9575 2.655 0.568 0.124 0.023 43 4.5 superiortemporal 4324 3432 7752 2.374 0.467 0.125 0.025 47 4.4 supramarginal 354 529 1155 2.727 0.526 0.245 0.049 6 0.8 frontalpole 595 765 2051 3.531 0.574 0.193 0.031 13 0.9 temporalpole 447 305 703 2.536 0.291 0.095 0.019 4 0.3 transversetemporal 3126 2137 5993 2.785 0.743 0.149 0.044 75 5.2 insula PIDs (3853973 3853977 3853980 3853984) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Nov 22 13:06:00 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 2 rh Fri Nov 22 13:06:00 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh white Waiting for PID 3854175 of (3854175 3854178) to complete... Waiting for PID 3854178 of (3854175 3854178) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189232 Total vertex volume 189020 (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) = 1351565 mm^3 (det: 1.441370 ) 879 690 1731 2.416 0.425 0.167 0.038 16 1.4 G_and_S_frontomargin 1260 884 2557 2.498 0.476 0.147 0.030 17 1.7 G_and_S_occipital_inf 1600 909 2463 2.284 0.576 0.102 0.027 17 1.7 G_and_S_paracentral 1168 791 2430 2.678 0.439 0.122 0.027 12 1.1 G_and_S_subcentral 617 520 1720 2.663 0.516 0.199 0.056 15 1.6 G_and_S_transv_frontopol 1727 1257 3540 2.702 0.511 0.138 0.033 24 2.5 G_and_S_cingul-Ant 1090 722 1866 2.679 0.517 0.104 0.017 7 0.8 G_and_S_cingul-Mid-Ant 1124 752 1914 2.473 0.494 0.111 0.025 9 1.2 G_and_S_cingul-Mid-Post 428 294 1053 2.662 0.517 0.145 0.035 7 0.6 G_cingul-Post-dorsal 221 155 433 2.205 0.800 0.148 0.040 4 0.3 G_cingul-Post-ventral 2042 1245 2711 1.882 0.444 0.140 0.037 29 3.1 G_cuneus 1092 746 2534 2.630 0.357 0.132 0.032 15 1.3 G_front_inf-Opercular 426 306 1113 2.679 0.344 0.154 0.033 8 0.6 G_front_inf-Orbital 1043 710 2482 2.684 0.509 0.142 0.033 14 1.4 G_front_inf-Triangul 2889 2137 7009 2.583 0.513 0.149 0.034 44 4.1 G_front_middle 5792 3900 13495 2.824 0.541 0.124 0.027 58 6.6 G_front_sup 638 426 1418 3.081 0.776 0.128 0.047 11 1.1 G_Ins_lg_and_S_cent_ins 713 508 2145 3.298 0.858 0.148 0.048 12 1.4 G_insular_short 1453 948 2922 2.413 0.506 0.130 0.028 19 1.6 G_occipital_middle 1564 968 2462 2.145 0.544 0.131 0.030 20 1.8 G_occipital_sup 1239 904 3101 2.754 0.561 0.140 0.035 19 1.7 G_oc-temp_lat-fusifor 2830 1903 4161 1.913 0.587 0.151 0.039 44 4.6 G_oc-temp_med-Lingual 1041 673 2891 3.122 0.825 0.098 0.027 8 1.0 G_oc-temp_med-Parahip 1986 1482 5039 2.747 0.630 0.149 0.040 33 3.0 G_orbital 2170 1490 4851 2.588 0.527 0.143 0.032 32 2.9 G_pariet_inf-Angular 2593 1799 5337 2.502 0.529 0.130 0.027 32 3.0 G_pariet_inf-Supramar 2688 1775 4503 2.126 0.493 0.114 0.022 27 2.3 G_parietal_sup 2091 1208 2878 1.938 0.543 0.107 0.027 23 2.2 G_postcentral 2502 1416 5537 2.870 0.584 0.107 0.029 24 2.9 G_precentral 2062 1514 4317 2.340 0.511 0.143 0.035 34 2.8 G_precuneus 981 752 2113 2.333 0.491 0.172 0.041 25 1.6 G_rectus 558 366 784 2.219 0.786 0.107 0.041 6 0.7 G_subcallosal 613 363 986 2.247 0.336 0.102 0.024 6 0.6 G_temp_sup-G_T_transv 1797 1216 5416 3.193 0.542 0.135 0.036 25 2.5 G_temp_sup-Lateral 558 380 1336 3.372 0.501 0.090 0.020 3 0.5 G_temp_sup-Plan_polar 770 511 1481 2.370 0.609 0.096 0.024 6 0.7 G_temp_sup-Plan_tempo 1914 1358 5056 2.804 0.569 0.142 0.039 92 2.9 G_temporal_inf 1823 1158 4594 2.831 0.522 0.124 0.027 27 1.9 G_temporal_middle 407 272 470 1.981 0.411 0.098 0.016 2 0.3 Lat_Fis-ant-Horizont 406 278 571 2.455 0.598 0.098 0.024 2 0.4 Lat_Fis-ant-Vertical 996 649 1199 2.318 0.513 0.115 0.024 7 1.0 Lat_Fis-post 1937 1265 2588 1.867 0.437 0.149 0.038 29 2.9 Pole_occipital 1383 1077 5334 3.391 0.677 0.156 0.038 22 2.2 Pole_temporal 2426 1627 2726 1.906 0.542 0.127 0.029 24 3.1 S_calcarine 2946 2005 3327 1.900 0.661 0.109 0.023 17 3.1 S_central 991 652 1174 1.982 0.444 0.090 0.013 4 0.6 S_cingul-Marginalis 473 326 681 2.572 0.406 0.100 0.023 2 0.5 S_circular_insula_ant 1545 1035 2275 2.646 0.685 0.099 0.022 9 1.7 S_circular_insula_inf 1554 1053 2063 2.385 0.482 0.119 0.027 9 2.0 S_circular_insula_sup 734 488 1229 2.674 0.359 0.105 0.016 6 0.5 S_collat_transv_ant 459 309 461 1.906 0.377 0.140 0.030 4 0.7 S_collat_transv_post 1779 1177 2487 2.240 0.483 0.108 0.023 13 1.6 S_front_inf 993 696 1364 2.179 0.451 0.123 0.029 7 1.2 S_front_middle 1982 1360 3188 2.416 0.487 0.116 0.025 14 2.0 S_front_sup 670 444 798 2.261 0.281 0.098 0.018 4 0.5 S_interm_prim-Jensen 2762 1855 3264 1.984 0.411 0.110 0.019 18 2.4 S_intrapariet_and_P_trans 626 422 683 1.921 0.277 0.119 0.021 5 0.6 S_oc_middle_and_Lunatus 975 647 1269 2.170 0.351 0.118 0.022 7 1.0 S_oc_sup_and_transversal 568 364 891 2.281 0.372 0.123 0.024 6 0.5 S_occipital_ant 581 432 967 2.510 0.369 0.135 0.032 6 0.7 S_oc-temp_lat 1838 1277 2787 2.361 0.570 0.114 0.021 15 1.5 S_oc-temp_med_and_Lingual 327 230 453 2.311 0.490 0.125 0.024 2 0.3 S_orbital_lateral 528 392 759 2.316 0.612 0.136 0.031 6 0.6 S_orbital_med-olfact 1086 737 1970 2.926 0.525 0.125 0.031 9 1.5 S_orbital-H_Shaped 1849 1221 2528 2.124 0.576 0.112 0.021 14 1.7 S_parieto_occipital 1148 712 874 1.623 0.673 0.117 0.026 19 1.2 S_pericallosal 2801 1846 3264 1.928 0.464 0.114 0.022 20 2.7 S_postcentral 1248 823 1857 2.583 0.396 0.097 0.018 6 1.0 S_precentral-inf-part 1467 953 1954 2.257 0.438 0.101 0.018 8 1.2 S_precentral-sup-part 605 424 798 2.288 0.475 0.116 0.020 4 0.5 S_suborbital 680 471 888 2.173 0.438 0.130 0.023 6 0.6 S_subparietal 1144 836 1670 2.483 0.458 0.128 0.022 9 1.3 S_temporal_inf 5084 3430 7355 2.311 0.461 0.105 0.019 35 4.2 S_temporal_sup 379 258 475 2.226 0.395 0.127 0.021 3 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189737 Total vertex volume 189533 (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) = 1351565 mm^3 (det: 1.441370 ) 783 629 1721 2.345 0.512 0.168 0.046 18 1.4 G_and_S_frontomargin 1036 723 1743 2.313 0.428 0.141 0.028 15 1.1 G_and_S_occipital_inf 1141 593 1915 2.557 0.569 0.096 0.021 9 0.9 G_and_S_paracentral 1172 778 2278 2.459 0.440 0.123 0.020 12 1.0 G_and_S_subcentral 998 856 2805 2.638 0.584 0.185 0.053 21 2.3 G_and_S_transv_frontopol 2371 1669 4545 2.560 0.625 0.122 0.029 23 2.7 G_and_S_cingul-Ant 1204 834 2239 2.569 0.574 0.129 0.029 13 1.5 G_and_S_cingul-Mid-Ant 1053 716 1952 2.570 0.465 0.104 0.020 7 0.8 G_and_S_cingul-Mid-Post 385 271 1022 2.643 0.541 0.157 0.036 7 0.6 G_cingul-Post-dorsal 219 133 436 2.324 0.718 0.136 0.039 4 0.3 G_cingul-Post-ventral 2171 1311 2666 1.808 0.405 0.132 0.035 30 3.1 G_cuneus 958 670 2412 2.781 0.359 0.122 0.025 13 1.0 G_front_inf-Opercular 347 268 958 2.691 0.379 0.163 0.039 7 0.7 G_front_inf-Orbital 624 449 1448 2.531 0.491 0.141 0.030 8 0.8 G_front_inf-Triangul 3996 2986 9188 2.431 0.548 0.153 0.034 69 6.1 G_front_middle 5057 3387 11760 2.784 0.571 0.131 0.031 61 6.5 G_front_sup 516 351 1280 3.038 0.641 0.128 0.040 8 0.7 G_Ins_lg_and_S_cent_ins 562 417 1481 2.844 0.757 0.142 0.044 9 0.9 G_insular_short 1998 1374 4492 2.529 0.434 0.137 0.032 29 2.3 G_occipital_middle 1821 1158 2753 2.072 0.398 0.119 0.027 20 1.9 G_occipital_sup 1573 1008 3624 2.706 0.502 0.125 0.033 24 1.9 G_oc-temp_lat-fusifor 2662 1724 4345 2.183 0.614 0.144 0.035 41 3.9 G_oc-temp_med-Lingual 1240 839 3813 3.261 0.857 0.120 0.034 15 1.6 G_oc-temp_med-Parahip 2345 1711 5465 2.547 0.712 0.148 0.042 43 4.0 G_orbital 2479 1699 5403 2.506 0.397 0.139 0.031 42 3.2 G_pariet_inf-Angular 1837 1282 4029 2.600 0.463 0.128 0.027 22 1.9 G_pariet_inf-Supramar 2233 1453 4202 2.318 0.391 0.113 0.022 26 2.0 G_parietal_sup 1833 1065 2558 1.890 0.436 0.108 0.023 20 1.8 G_postcentral 2521 1425 5071 2.709 0.408 0.102 0.024 23 2.4 G_precentral 1835 1261 3965 2.454 0.490 0.124 0.029 23 2.0 G_precuneus 683 497 1330 2.152 0.583 0.129 0.038 13 1.0 G_rectus 435 287 732 2.598 0.705 0.107 0.029 3 0.4 G_subcallosal 377 197 644 2.577 0.291 0.106 0.026 5 0.4 G_temp_sup-G_T_transv 1627 1100 4567 3.007 0.499 0.136 0.031 24 2.2 G_temp_sup-Lateral 742 508 1568 3.146 0.711 0.084 0.026 4 0.8 G_temp_sup-Plan_polar 773 512 1444 2.460 0.496 0.103 0.022 7 0.6 G_temp_sup-Plan_tempo 1960 1420 5364 2.858 0.754 0.157 0.045 43 3.1 G_temporal_inf 2251 1560 5489 2.678 0.470 0.125 0.026 32 2.2 G_temporal_middle 372 255 417 1.914 0.310 0.094 0.014 2 0.2 Lat_Fis-ant-Horizont 205 149 356 2.529 0.417 0.112 0.019 1 0.1 Lat_Fis-ant-Vertical 1193 786 1505 2.261 0.417 0.102 0.019 6 1.0 Lat_Fis-post 3329 2100 4136 1.825 0.459 0.141 0.032 52 4.3 Pole_occipital 1522 1151 4793 3.122 0.576 0.142 0.034 22 2.2 Pole_temporal 2517 1692 2750 1.753 0.485 0.113 0.027 23 2.7 S_calcarine 2781 1885 3259 1.976 0.601 0.092 0.016 11 2.1 S_central 1093 738 1469 2.195 0.441 0.089 0.012 4 0.6 S_cingul-Marginalis 582 419 1007 2.528 0.618 0.130 0.036 5 0.9 S_circular_insula_ant 1221 773 1664 2.500 0.761 0.076 0.014 5 0.7 S_circular_insula_inf 1201 792 1607 2.502 0.360 0.103 0.025 7 1.3 S_circular_insula_sup 998 696 1551 2.439 0.438 0.100 0.017 4 0.8 S_collat_transv_ant 374 257 425 1.942 0.313 0.121 0.023 2 0.4 S_collat_transv_post 1284 918 1863 2.170 0.418 0.115 0.023 10 1.3 S_front_inf 1657 1199 2300 2.056 0.403 0.121 0.025 12 1.8 S_front_middle 1760 1179 2438 2.284 0.413 0.098 0.018 9 1.3 S_front_sup 359 271 545 2.203 0.416 0.130 0.026 3 0.4 S_interm_prim-Jensen 3686 2445 4598 1.983 0.379 0.093 0.015 19 2.4 S_intrapariet_and_P_trans 818 557 923 1.972 0.353 0.119 0.022 5 0.9 S_oc_middle_and_Lunatus 1284 865 1655 2.073 0.412 0.115 0.021 8 1.2 S_oc_sup_and_transversal 548 375 740 2.158 0.440 0.122 0.030 4 0.6 S_occipital_ant 679 484 1001 2.308 0.490 0.131 0.045 23 0.7 S_oc-temp_lat 1646 1097 2282 2.326 0.429 0.094 0.016 8 1.1 S_oc-temp_med_and_Lingual 389 299 759 2.216 0.501 0.156 0.036 4 0.7 S_orbital_lateral 617 451 875 2.160 0.715 0.147 0.034 6 1.2 S_orbital_med-olfact 1227 854 2033 2.512 0.506 0.126 0.030 11 1.6 S_orbital-H_Shaped 1863 1233 2313 1.958 0.564 0.111 0.021 14 1.6 S_parieto_occipital 1235 799 933 1.527 0.542 0.124 0.023 20 1.2 S_pericallosal 2364 1559 2674 1.849 0.347 0.098 0.019 14 1.9 S_postcentral 1451 955 2018 2.352 0.434 0.109 0.022 11 1.2 S_precentral-inf-part 1129 748 1524 2.303 0.494 0.092 0.015 5 0.8 S_precentral-sup-part 320 225 435 2.255 0.591 0.119 0.022 3 0.4 S_suborbital 766 558 1156 2.280 0.494 0.134 0.028 7 0.9 S_subparietal 1003 699 1377 2.377 0.455 0.117 0.019 7 1.0 S_temporal_inf 5156 3446 7230 2.327 0.354 0.096 0.018 28 3.9 S_temporal_sup 139 101 211 2.261 0.344 0.117 0.019 1 0.1 S_temporal_transverse PIDs (3854175 3854178) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Nov 22 13:06:13 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 3 rh Fri Nov 22 13:06:13 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh white Waiting for PID 3854471 of (3854471 3854475) to complete... Waiting for PID 3854475 of (3854471 3854475) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189232 Total vertex volume 189020 (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) = 1351565 mm^3 (det: 1.441370 ) 1506 954 2527 2.579 0.622 0.116 0.020 15 1.3 caudalanteriorcingulate 2354 1552 3977 2.492 0.502 0.110 0.022 16 2.2 caudalmiddlefrontal 2852 1755 3606 1.877 0.443 0.133 0.032 37 3.8 cuneus 554 377 1722 3.434 0.770 0.102 0.025 4 0.6 entorhinal 2951 2146 6142 2.646 0.531 0.139 0.032 37 3.7 fusiform 5001 3399 8826 2.340 0.505 0.124 0.025 53 5.1 inferiorparietal 3657 2643 8850 2.776 0.604 0.134 0.032 108 5.0 inferiortemporal 1242 842 1857 2.003 0.722 0.123 0.030 16 1.5 isthmuscingulate 6230 4091 9571 2.118 0.521 0.138 0.031 79 7.9 lateraloccipital 3438 2457 7109 2.749 0.649 0.136 0.037 45 5.0 lateralorbitofrontal 4100 2745 5644 1.911 0.564 0.137 0.033 54 5.7 lingual 2008 1458 3598 2.271 0.578 0.139 0.033 33 2.5 medialorbitofrontal 4853 3223 9642 2.610 0.552 0.117 0.024 50 4.9 middletemporal 894 576 1834 2.682 0.733 0.091 0.020 6 0.6 parahippocampal 2135 1266 3346 2.450 0.540 0.090 0.019 12 1.7 paracentral 1969 1325 3663 2.546 0.465 0.112 0.025 17 2.0 parsopercularis 1008 727 2001 2.466 0.474 0.130 0.028 11 1.2 parsorbitalis 2224 1495 4229 2.496 0.561 0.124 0.027 21 2.5 parstriangularis 1970 1303 2119 1.815 0.498 0.130 0.031 20 2.7 pericalcarine 6272 3957 8148 1.920 0.597 0.108 0.024 56 6.0 postcentral 1504 1007 2494 2.328 0.639 0.123 0.027 18 1.7 posteriorcingulate 6696 4175 11696 2.568 0.602 0.111 0.027 56 7.5 precentral 4304 3035 7396 2.269 0.515 0.131 0.028 51 4.9 precuneus 1188 878 2583 2.731 0.654 0.150 0.039 21 1.9 rostralanteriorcingulate 3986 2932 7762 2.410 0.550 0.146 0.034 54 5.5 rostralmiddlefrontal 9242 6520 19826 2.652 0.553 0.129 0.029 97 11.3 superiorfrontal 5707 3789 8250 2.052 0.477 0.113 0.021 50 4.9 superiorparietal 6937 4724 15112 2.773 0.677 0.114 0.026 63 7.4 superiortemporal 5140 3512 8984 2.396 0.528 0.124 0.025 52 5.4 supramarginal 681 395 992 2.215 0.333 0.105 0.024 6 0.6 transversetemporal 2782 1919 5511 2.832 0.795 0.130 0.039 34 4.8 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189737 Total vertex volume 189533 (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) = 1351565 mm^3 (det: 1.441370 ) 1091 749 2067 2.420 0.772 0.140 0.029 19 1.4 caudalanteriorcingulate 2923 1957 5005 2.347 0.458 0.117 0.022 26 2.7 caudalmiddlefrontal 2706 1696 3181 1.742 0.403 0.124 0.029 31 3.2 cuneus 557 395 2084 3.608 0.728 0.115 0.024 5 0.5 entorhinal 3223 2170 6324 2.570 0.541 0.120 0.033 53 3.7 fusiform 6657 4556 11205 2.312 0.396 0.121 0.024 71 6.7 inferiorparietal 3870 2781 8835 2.720 0.676 0.138 0.033 57 4.9 inferiortemporal 1142 753 1641 1.905 0.714 0.122 0.029 16 1.3 isthmuscingulate 6785 4464 10304 2.110 0.505 0.135 0.031 93 8.0 lateraloccipital 3708 2674 7326 2.545 0.645 0.147 0.043 57 7.0 lateralorbitofrontal 4176 2778 5980 2.031 0.566 0.135 0.032 52 5.7 lingual 1966 1398 3499 2.283 0.654 0.131 0.034 30 2.7 medialorbitofrontal 4713 3247 9551 2.559 0.473 0.114 0.022 47 4.3 middletemporal 940 602 1919 2.698 0.787 0.099 0.022 7 0.9 parahippocampal 1995 1109 3049 2.563 0.588 0.088 0.018 11 1.5 paracentral 1587 1086 2874 2.521 0.396 0.110 0.025 15 1.4 parsopercularis 958 701 2066 2.482 0.516 0.127 0.032 13 1.2 parsorbitalis 1626 1184 3057 2.313 0.502 0.135 0.028 17 2.1 parstriangularis 2419 1537 2455 1.673 0.409 0.113 0.028 25 2.7 pericalcarine 5591 3520 7422 1.911 0.493 0.104 0.019 45 4.6 postcentral 1428 992 2561 2.366 0.675 0.123 0.025 16 1.5 posteriorcingulate 6370 4014 11031 2.508 0.520 0.101 0.020 45 5.6 precentral 4474 3048 7609 2.300 0.518 0.123 0.026 48 4.7 precuneus 848 576 1672 2.775 0.695 0.107 0.023 7 0.8 rostralanteriorcingulate 4500 3457 8914 2.256 0.544 0.150 0.034 70 6.8 rostralmiddlefrontal 10144 7211 21192 2.571 0.578 0.131 0.030 111 13.1 superiorfrontal 6746 4390 10197 2.104 0.417 0.099 0.018 53 5.3 superiorparietal 6057 4070 12894 2.738 0.635 0.110 0.024 56 6.0 superiortemporal 4172 2857 7507 2.383 0.463 0.113 0.024 41 4.1 supramarginal 443 255 705 2.539 0.287 0.101 0.021 4 0.4 transversetemporal 2771 1906 5405 2.750 0.714 0.121 0.034 29 3.6 insula PIDs (3854471 3854475) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Fri Nov 22 13:06:26 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1351565 mm^3 (det: 1.441370 ) Computing euler number orig.nofix lheno = -6, rheno = -16 orig.nofix lhholes = 4, rhholes = 9 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 2024:11:22:13:06:26 mri_segstats N 32 e 79.86 S 0.69 U 291.69 P 366% M 280844 F 2 R 937283 W 0 c 27327 w 189 I 0 O 24 L 27.98 27.37 27.90 @#@FSLOADPOST 2024:11:22:13:07:46 mri_segstats N 32 29.27 27.92 28.06 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri Nov 22 13:07:46 CST 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 3855154 of (3855154 3855157 3855160 3855165 3855168) to complete... Waiting for PID 3855157 of (3855154 3855157 3855160 3855165 3855168) to complete... Waiting for PID 3855160 of (3855154 3855157 3855160 3855165 3855168) to complete... Waiting for PID 3855165 of (3855154 3855157 3855160 3855165 3855168) to complete... Waiting for PID 3855168 of (3855154 3855157 3855160 3855165 3855168) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4204 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8015 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4093 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6055 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 108 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5892 mri_label2label: Done PIDs (3855154 3855157 3855160 3855165 3855168) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 3855287 of (3855287 3855290 3855293 3855296) to complete... Waiting for PID 3855290 of (3855287 3855290 3855293 3855296) to complete... Waiting for PID 3855293 of (3855287 3855290 3855293 3855296) to complete... Waiting for PID 3855296 of (3855287 3855290 3855293 3855296) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4119 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 227 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13816 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4247 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 235 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3657 mri_label2label: Done PIDs (3855287 3855290 3855293 3855296) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 3855409 of (3855409 3855413 3855416 3855419 3855422) to complete... Waiting for PID 3855413 of (3855409 3855413 3855416 3855419 3855422) to complete... Waiting for PID 3855416 of (3855409 3855413 3855416 3855419 3855422) to complete... Waiting for PID 3855419 of (3855409 3855413 3855416 3855419 3855422) to complete... Waiting for PID 3855422 of (3855409 3855413 3855416 3855419 3855422) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 970 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5611 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 1662 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9776 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2077 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1219 mri_label2label: Done PIDs (3855409 3855413 3855416 3855419 3855422) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 3855548 of (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) to complete... Waiting for PID 3855552 of (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) to complete... Waiting for PID 3855555 of (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) to complete... Waiting for PID 3855559 of (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) to complete... Waiting for PID 3855562 of (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) to complete... Waiting for PID 3855565 of (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) to complete... Waiting for PID 3855568 of (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) to complete... Waiting for PID 3855572 of (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 446 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 735 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1909 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 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 PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 801 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4678 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 813 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3732 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 242 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1528 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1168 mri_label2label: Done PIDs (3855548 3855552 3855555 3855559 3855562 3855565 3855568 3855572) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 99675 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.mpm.vpnl.annot @#@FSTIME 2024:11:22:13:08:15 mris_label2annot N 26 e 0.66 S 0.07 U 0.83 P 135% M 133360 F 3 R 36239 W 0 c 89 w 182 I 16 O 1776 L 29.67 28.15 28.13 @#@FSLOADPOST 2024:11:22:13:08:15 mris_label2annot N 26 29.67 28.15 28.13 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3855767 of (3855767 3855771 3855774 3855777 3855782) to complete... Waiting for PID 3855771 of (3855767 3855771 3855774 3855777 3855782) to complete... Waiting for PID 3855774 of (3855767 3855771 3855774 3855777 3855782) to complete... Waiting for PID 3855777 of (3855767 3855771 3855774 3855777 3855782) to complete... Waiting for PID 3855782 of (3855767 3855771 3855774 3855777 3855782) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1031 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2128 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1508 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2011 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2361 mri_label2label: Done PIDs (3855767 3855771 3855774 3855777 3855782) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3855892 of (3855892 3855896 3855899 3855902) to complete... Waiting for PID 3855896 of (3855892 3855896 3855899 3855902) to complete... Waiting for PID 3855899 of (3855892 3855896 3855899 3855902) to complete... Waiting for PID 3855902 of (3855892 3855896 3855899 3855902) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1563 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7201 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1951 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1265 mri_label2label: Done PIDs (3855892 3855896 3855899 3855902) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 3856002 of (3856002 3856005 3856008 3856011 3856015) to complete... Waiting for PID 3856005 of (3856002 3856005 3856008 3856011 3856015) to complete... Waiting for PID 3856008 of (3856002 3856005 3856008 3856011 3856015) to complete... Waiting for PID 3856011 of (3856002 3856005 3856008 3856011 3856015) to complete... Waiting for PID 3856015 of (3856002 3856005 3856008 3856011 3856015) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 709 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4114 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 859 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4193 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 525 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 488 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113479 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 454 mri_label2label: Done PIDs (3856002 3856005 3856008 3856011 3856015) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 77291 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.BA_exvivo.annot @#@FSTIME 2024:11:22:13:08:34 mris_label2annot N 38 e 0.73 S 0.11 U 0.82 P 127% M 133564 F 2 R 36328 W 0 c 89 w 196 I 0 O 1776 L 29.04 28.07 28.10 @#@FSLOADPOST 2024:11:22:13:08:35 mris_label2annot N 38 28.48 27.97 28.07 mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 91191 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2024:11:22:13:08:35 mris_label2annot N 38 e 0.62 S 0.09 U 0.79 P 141% M 133416 F 1 R 36384 W 0 c 85 w 272 I 0 O 1776 L 28.48 27.97 28.07 @#@FSLOADPOST 2024:11:22:13:08:35 mris_label2annot N 38 28.48 27.97 28.07 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189232 Total vertex volume 189020 (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) = 1351565 mm^3 (det: 1.441370 ) 1066 582 1570 2.082 0.562 0.116 0.030 15 1.0 BA1_exvivo 3576 2318 4746 2.003 0.507 0.112 0.022 28 3.5 BA2_exvivo 979 683 900 1.662 0.376 0.132 0.029 9 1.3 BA3a_exvivo 2149 1380 2578 1.714 0.560 0.101 0.023 18 1.9 BA3b_exvivo 1499 818 2598 2.690 0.569 0.095 0.026 12 1.6 BA4a_exvivo 1259 780 2033 2.720 0.567 0.107 0.028 8 1.6 BA4p_exvivo 7725 4941 15315 2.675 0.586 0.108 0.023 59 7.2 BA6_exvivo 1950 1301 3600 2.559 0.428 0.115 0.025 18 1.9 BA44_exvivo 2625 1795 5171 2.497 0.553 0.128 0.029 28 3.1 BA45_exvivo 3522 2231 4081 1.811 0.478 0.127 0.033 41 4.8 V1_exvivo 7307 4861 9846 1.915 0.492 0.147 0.035 101 10.6 V2_exvivo 1453 971 2822 2.473 0.446 0.128 0.028 17 1.6 MT_exvivo 545 394 1389 3.149 0.684 0.116 0.025 4 0.5 perirhinal_exvivo 533 345 1785 3.430 1.048 0.094 0.028 4 0.7 entorhinal_exvivo @#@FSTIME 2024:11:22:13:08:35 mris_anatomical_stats N 12 e 4.00 S 0.30 U 5.81 P 152% M 402040 F 4 R 207660 W 0 c 566 w 328 I 0 O 136 L 28.48 27.97 28.07 @#@FSLOADPOST 2024:11:22:13:08:39 mris_anatomical_stats N 12 28.52 27.99 28.07 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189232 Total vertex volume 189020 (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) = 1351565 mm^3 (det: 1.441370 ) 693 347 984 2.083 0.514 0.127 0.038 10 0.9 BA1_exvivo 1410 882 1820 1.953 0.494 0.094 0.020 8 1.2 BA2_exvivo 816 579 743 1.660 0.366 0.136 0.032 8 1.2 BA3a_exvivo 1321 877 1275 1.418 0.331 0.094 0.018 7 1.1 BA3b_exvivo 1472 824 2586 2.708 0.565 0.095 0.027 11 1.8 BA4a_exvivo 1051 653 1621 2.637 0.586 0.106 0.028 7 1.4 BA4p_exvivo 4635 2901 9453 2.694 0.610 0.106 0.024 35 4.3 BA6_exvivo 1278 855 2351 2.554 0.437 0.119 0.029 13 1.5 BA44_exvivo 1092 734 2391 2.583 0.529 0.126 0.030 12 1.2 BA45_exvivo 3739 2371 4390 1.815 0.475 0.126 0.033 43 5.0 V1_exvivo 3818 2547 4803 1.823 0.459 0.158 0.040 60 6.4 V2_exvivo 391 272 575 2.371 0.320 0.117 0.019 2 0.4 MT_exvivo 236 168 482 3.002 0.545 0.107 0.021 2 0.2 perirhinal_exvivo 336 219 1226 3.825 0.567 0.081 0.016 2 0.2 entorhinal_exvivo @#@FSTIME 2024:11:22:13:08:39 mris_anatomical_stats N 12 e 3.80 S 0.29 U 5.31 P 147% M 402256 F 3 R 191488 W 0 c 530 w 299 I 0 O 136 L 28.52 27.99 28.07 @#@FSLOADPOST 2024:11:22:13:08:43 mris_anatomical_stats N 12 28.52 27.99 28.07 #-------------------------------------------- #@# BA_exvivo Labels rh Fri Nov 22 13:08:43 CST 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 3856340 of (3856340 3856344 3856347 3856350 3856353) to complete... Waiting for PID 3856344 of (3856340 3856344 3856347 3856350 3856353) to complete... Waiting for PID 3856347 of (3856340 3856344 3856347 3856350 3856353) to complete... Waiting for PID 3856350 of (3856340 3856344 3856347 3856350 3856353) to complete... Waiting for PID 3856353 of (3856340 3856344 3856347 3856350 3856353) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 3991 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6726 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4004 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4550 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5796 mri_label2label: Done PIDs (3856340 3856344 3856347 3856350 3856353) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 3856480 of (3856480 3856483 3856486 3856489) to complete... Waiting for PID 3856483 of (3856480 3856483 3856486 3856489) to complete... Waiting for PID 3856486 of (3856480 3856483 3856486 3856489) to complete... Waiting for PID 3856489 of (3856480 3856483 3856486 3856489) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4520 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12348 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7011 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5521 mri_label2label: Done PIDs (3856480 3856483 3856486 3856489) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 3856597 of (3856597 3856600 3856603 3856607 3856610) to complete... Waiting for PID 3856600 of (3856597 3856600 3856603 3856607 3856610) to complete... Waiting for PID 3856603 of (3856597 3856600 3856603 3856607 3856610) to complete... Waiting for PID 3856607 of (3856597 3856600 3856603 3856607 3856610) to complete... Waiting for PID 3856610 of (3856597 3856600 3856603 3856607 3856610) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 1394 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 1811 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9827 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2026 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1071 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 769 mri_label2label: Done PIDs (3856597 3856600 3856603 3856607 3856610) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 3856738 of (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) to complete... Waiting for PID 3856741 of (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) to complete... Waiting for PID 3856745 of (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) to complete... Waiting for PID 3856749 of (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) to complete... Waiting for PID 3856752 of (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) to complete... Waiting for PID 3856756 of (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) to complete... Waiting for PID 3856759 of (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) to complete... Waiting for PID 3856763 of (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 665 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 835 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1593 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1617 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 1156 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4823 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 652 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3371 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1493 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 284 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1309 mri_label2label: Done PIDs (3856738 3856741 3856745 3856749 3856752 3856756 3856759 3856763) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 100584 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.mpm.vpnl.annot @#@FSTIME 2024:11:22:13:09:13 mris_label2annot N 26 e 0.67 S 0.08 U 0.87 P 141% M 134412 F 4 R 36556 W 0 c 89 w 240 I 0 O 1792 L 28.94 28.13 28.12 @#@FSLOADPOST 2024:11:22:13:09:14 mris_label2annot N 26 28.94 28.13 28.12 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3856963 of (3856963 3856967 3856970 3856973 3856976) to complete... Waiting for PID 3856967 of (3856963 3856967 3856970 3856973 3856976) to complete... Waiting for PID 3856970 of (3856963 3856967 3856970 3856973 3856976) to complete... Waiting for PID 3856973 of (3856963 3856967 3856970 3856973 3856976) to complete... Waiting for PID 3856976 of (3856963 3856967 3856970 3856973 3856976) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 890 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2695 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1705 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2197 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1397 mri_label2label: Done PIDs (3856963 3856967 3856970 3856973 3856976) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3857090 of (3857090 3857094 3857098 3857101) to complete... Waiting for PID 3857094 of (3857090 3857094 3857098 3857101) to complete... Waiting for PID 3857098 of (3857090 3857094 3857098 3857101) to complete... Waiting for PID 3857101 of (3857090 3857094 3857098 3857101) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1517 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7001 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1019 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1188 mri_label2label: Done PIDs (3857090 3857094 3857098 3857101) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 3857203 of (3857203 3857206 3857209 3857213 3857216) to complete... Waiting for PID 3857206 of (3857203 3857206 3857209 3857213 3857216) to complete... Waiting for PID 3857209 of (3857203 3857206 3857209 3857213 3857216) to complete... Waiting for PID 3857213 of (3857203 3857206 3857209 3857213 3857216) to complete... Waiting for PID 3857216 of (3857203 3857206 3857209 3857213 3857216) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 1010 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4242 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 869 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4306 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 277 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 718 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114494 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 300 mri_label2label: Done PIDs (3857203 3857206 3857209 3857213 3857216) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 79783 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.BA_exvivo.annot @#@FSTIME 2024:11:22:13:09:32 mris_label2annot N 38 e 0.68 S 0.11 U 0.84 P 140% M 134908 F 1 R 36644 W 0 c 95 w 230 I 0 O 1792 L 30.63 28.58 28.27 @#@FSLOADPOST 2024:11:22:13:09:32 mris_label2annot N 38 30.63 28.58 28.27 mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 94427 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2024:11:22:13:09:32 mris_label2annot N 38 e 0.64 S 0.07 U 0.87 P 146% M 134480 F 3 R 36580 W 0 c 88 w 276 I 0 O 1792 L 30.63 28.58 28.27 @#@FSLOADPOST 2024:11:22:13:09:33 mris_label2annot N 38 30.63 28.58 28.27 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189737 Total vertex volume 189533 (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) = 1351565 mm^3 (det: 1.441370 ) 813 426 1287 2.118 0.455 0.135 0.032 13 1.2 BA1_exvivo 2627 1695 3154 1.870 0.406 0.099 0.020 17 2.1 BA2_exvivo 965 697 978 1.750 0.356 0.126 0.023 6 1.0 BA3a_exvivo 1617 1021 1928 1.731 0.484 0.089 0.015 10 1.0 BA3b_exvivo 1303 663 2220 2.818 0.474 0.073 0.019 7 1.0 BA4a_exvivo 1185 729 1825 2.573 0.480 0.076 0.015 4 0.8 BA4p_exvivo 6219 3870 11826 2.626 0.538 0.106 0.023 50 5.7 BA6_exvivo 2910 1947 5157 2.512 0.428 0.118 0.023 28 2.8 BA44_exvivo 2985 2247 6295 2.387 0.502 0.140 0.032 40 4.1 BA45_exvivo 4165 2585 4732 1.738 0.422 0.120 0.031 48 4.9 V1_exvivo 7448 4868 10296 1.980 0.514 0.142 0.034 106 10.6 V2_exvivo 1590 1086 2685 2.349 0.458 0.121 0.028 17 1.5 MT_exvivo 349 268 936 3.297 0.595 0.147 0.027 4 0.5 perirhinal_exvivo 535 374 2156 3.669 0.797 0.097 0.022 4 0.5 entorhinal_exvivo @#@FSTIME 2024:11:22:13:09:33 mris_anatomical_stats N 12 e 4.31 S 0.62 U 5.85 P 150% M 405696 F 3 R 194021 W 0 c 618 w 288 I 0 O 136 L 30.63 28.58 28.27 @#@FSLOADPOST 2024:11:22:13:09:37 mris_anatomical_stats N 12 30.74 28.63 28.29 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189737 Total vertex volume 189533 (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) = 1351565 mm^3 (det: 1.441370 ) 539 293 768 1.946 0.419 0.129 0.033 8 0.7 BA1_exvivo 1501 945 1890 1.866 0.374 0.088 0.015 8 1.0 BA2_exvivo 870 637 858 1.751 0.373 0.131 0.024 6 1.0 BA3a_exvivo 1290 838 1287 1.573 0.338 0.082 0.012 5 0.7 BA3b_exvivo 770 328 1262 2.930 0.488 0.082 0.025 6 0.7 BA4a_exvivo 982 618 1526 2.579 0.489 0.077 0.015 3 0.7 BA4p_exvivo 4006 2495 7635 2.635 0.546 0.108 0.023 32 3.6 BA6_exvivo 625 436 1291 2.709 0.306 0.126 0.031 8 0.7 BA44_exvivo 731 543 1774 2.616 0.451 0.140 0.029 9 0.8 BA45_exvivo 3994 2497 4466 1.724 0.418 0.119 0.031 45 4.8 V1_exvivo 3985 2596 5303 1.879 0.495 0.154 0.038 69 6.4 V2_exvivo 210 146 417 2.479 0.452 0.138 0.036 2 0.3 MT_exvivo 31 25 69 3.423 0.537 0.176 0.036 0 0.1 perirhinal_exvivo 533 371 1892 3.654 0.723 0.107 0.022 4 0.5 entorhinal_exvivo @#@FSTIME 2024:11:22:13:09:37 mris_anatomical_stats N 12 e 3.93 S 0.26 U 5.51 P 146% M 405356 F 1 R 198923 W 0 c 554 w 295 I 0 O 136 L 30.74 28.63 28.29 @#@FSLOADPOST 2024:11:22:13:09:41 mris_anatomical_stats N 12 30.60 28.64 28.29 Started at Fri Nov 22 11:17:43 CST 2024 Ended at Fri Nov 22 13:09:41 CST 2024 #@#%# recon-all-run-time-hours 1.866 recon-all -s PIB15-273_VYr9_Bay3prisma finished without error at Fri Nov 22 13:09:41 CST 2024 #New# invocation of recon-all Fri Nov 22 14:35:56 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma/ -autorecon2-noaseg -autorecon3 subjid PIB15-273_VYr9_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 143Gi 31Gi 8.0Mi 75Gi 105Gi Swap: 111Gi 230Mi 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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:56-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:57-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:58-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:58-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:58-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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: 2024/11/22-20:35:58-GMT BuildTime: Aug 4 2022 05:48:18 BuildStamp: freesurfer-linux-ubuntu20_x86_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 Fri Nov 22 14:35:58 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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... 537 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 110 gm peak at 75 (75), valley at 42 (42) csf peak at 17, setting threshold to 55 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 76 (76), valley at 36 (36) csf peak at 22, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 20 seconds. @#@FSTIME 2024:11:22:14:35:58 mri_normalize N 9 e 141.58 S 1.59 U 153.81 P 109% M 1209236 F 0 R 1095482 W 0 c 14446 w 156 I 0 O 2400 L 25.04 22.79 23.33 @#@FSLOADPOST 2024:11:22:14:38:20 mri_normalize N 9 23.15 22.66 23.19 #-------------------------------------------- #@# Mask BFS Fri Nov 22 14:38:20 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1392486 voxels in mask (pct= 8.30) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:11:22:14:38:20 mri_mask N 5 e 1.02 S 0.04 U 1.63 P 163% M 74392 F 0 R 17269 W 0 c 158 w 153 I 0 O 2344 L 23.15 22.66 23.19 @#@FSLOADPOST 2024:11:22:14:38:21 mri_mask N 5 23.15 22.66 23.19 #-------------------------------------------- #@# WM Segmentation Fri Nov 22 14:38:21 CST 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/PIB15-273_VYr9_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/PIB15-273_VYr9_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 2024:11:22:14:38:24 AntsDenoiseImageFs N 4 e 37.89 S 0.46 U 37.69 P 100% M 351464 F 0 R 231629 W 0 c 3526 w 57 I 0 O 2392 L 23.06 22.65 23.18 @#@FSLOADPOST 2024:11:22:14:39:02 AntsDenoiseImageFs N 4 22.41 22.60 23.15 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): 100.7 +- 6.4 [79.0 --> 125.0] CCS GM (75.0) : 73.5 +- 10.9 [30.0 --> 95.0] white_mean 100.746 white_sigma 6.39597 gray_mean 73.4639 gray_sigma 10.8757 setting bottom of white matter range wm_low to 84.3 setting top of gray matter range gray_hi to 95.2 wm_low 84.3396 wm_hi 125 gray_low 30 gray_hi 95.2153 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 84.3396 wm_hi 125 gray_low 30 gray_hi 95.2153 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 95.2153, wm_low = 84.3396 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=95.2153, wmlow=84.3396 108732 voxels processed (0.65%) 51629 voxels white (0.31%) 57103 voxels non-white (0.34%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=79.3396, gray_hi=95.2153, wsize=13 216746 voxels tested (1.29%) 40729 voxels changed (0.24%) 38747 multi-scale searches (0.23%) Recovering bright white MRIrecoverBrightWhite() wm_low 84.3396 wm_hi 125 slack 6.39597 pct_thresh 0.33 intensity_thresh 131.396 nvox_thresh 8.58 72 voxels tested (0.00%) 56 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=79.3396, hithr=95.2153 smoothing input volume with sigma = 0.250 91337 voxels tested (0.54%) 14399 voxels changed (0.09%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 1676 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1257 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 3730 filled MRIfindBrightNonWM(): 101 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.2 minutes writing output to wm.seg.mgz... @#@FSTIME 2024:11:22:14:39:02 mri_segment N 6 e 70.86 S 0.43 U 71.41 P 101% M 146500 F 1 R 359190 W 0 c 6639 w 84 I 0 O 736 L 22.41 22.60 23.15 @#@FSLOADPOST 2024:11:22:14:40:13 mri_segment N 6 17.07 20.91 22.52 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 0.56 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2910 additional wm voxels added 0 additional wm voxels added SEG EDIT: 52409 voxels turned on, 30770 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2024:11:22:14:40:13 mri_edit_wm_with_aseg N 5 e 33.91 S 0.42 U 35.44 P 105% M 463896 F 0 R 471333 W 0 c 3345 w 146 I 0 O 680 L 17.07 20.91 22.52 @#@FSLOADPOST 2024:11:22:14:40:47 mri_edit_wm_with_aseg N 5 18.58 20.87 22.45 mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 8 found - 8 modified | TOTAL: 17 pass 2 (xy-): 0 found - 8 modified | TOTAL: 17 pass 1 (yz+): 12 found - 12 modified | TOTAL: 29 pass 2 (yz+): 0 found - 12 modified | TOTAL: 29 pass 1 (yz-): 12 found - 12 modified | TOTAL: 41 pass 2 (yz-): 0 found - 12 modified | TOTAL: 41 pass 1 (xz+): 11 found - 11 modified | TOTAL: 52 pass 2 (xz+): 0 found - 11 modified | TOTAL: 52 pass 1 (xz-): 6 found - 6 modified | TOTAL: 58 pass 2 (xz-): 0 found - 6 modified | TOTAL: 58 Iteration Number : 1 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 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 pass 1 (+++): 6 found - 6 modified | TOTAL: 12 pass 2 (+++): 0 found - 6 modified | TOTAL: 12 Iteration Number : 1 pass 1 (++): 44 found - 44 modified | TOTAL: 44 pass 2 (++): 0 found - 44 modified | TOTAL: 44 pass 1 (+-): 21 found - 21 modified | TOTAL: 65 pass 2 (+-): 0 found - 21 modified | TOTAL: 65 pass 1 (--): 28 found - 28 modified | TOTAL: 93 pass 2 (--): 0 found - 28 modified | TOTAL: 93 pass 1 (-+): 21 found - 21 modified | TOTAL: 114 pass 2 (-+): 0 found - 21 modified | TOTAL: 114 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 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 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 3 found - 3 modified | TOTAL: 7 pass 2 (xz+): 0 found - 3 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 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 (+-): 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 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 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 : 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 = 195 (out of 467426: 0.041718) 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 2024:11:22:14:40:47 mri_pretess N 5 e 4.37 S 0.07 U 5.38 P 124% M 57448 F 0 R 30848 W 0 c 513 w 86 I 0 O 680 L 18.58 20.87 22.45 @#@FSLOADPOST 2024:11:22:14:40:51 mri_pretess N 5 19.25 20.98 22.47 #-------------------------------------------- #@# Fill Fri Nov 22 14:40:51 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 1.09938 0.05633 -0.05324 -15.94841; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47585; 0.00000 0.00000 0.00000 1.00000; Using auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt ndiff 8465 voxel to talairach voxel transform 1.09938 0.05633 -0.05324 -15.94841; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47585; 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] = 1275 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) no need to search using seed (126, 120, 155), TAL = (2.0, 27.0, 8.0) talairach voxel to voxel transform 0.90335 -0.03841 0.05260 13.82314; 0.04583 0.83382 -0.13192 35.09698; -0.08070 0.08907 0.94653 23.01431; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 120, 155) --> (2.0, 27.0, 8.0) done. filling took 1.2 minutes talairach cc position changed to (2.00, 27.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 27.00, 8.00) SRC: (114.93, 119.66, 171.70) search lh wm seed point around talairach space (-16.00, 27.00, 8.00), SRC: (147.45, 121.31, 168.79) 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 8465 edits Writing edits to ../tmp/filled.edits.txt Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2024:11:22:14:40:51 mri_fill N 14 e 69.53 S 1.45 U 69.76 P 102% M 969636 F 0 R 896446 W 0 c 6653 w 94 I 0 O 536 L 19.25 20.98 22.47 @#@FSLOADPOST 2024:11:22:14:42:01 mri_fill N 14 18.03 20.48 22.20 #-------------------------------------------- #@# Tessellate lh Fri Nov 22 14:42:01 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 9 found - 9 modified | TOTAL: 12 pass 2 (yz+): 0 found - 9 modified | TOTAL: 12 pass 1 (yz-): 6 found - 6 modified | TOTAL: 18 pass 2 (yz-): 0 found - 6 modified | TOTAL: 18 pass 1 (xz+): 2 found - 2 modified | TOTAL: 20 pass 2 (xz+): 0 found - 2 modified | TOTAL: 20 pass 1 (xz-): 2 found - 2 modified | TOTAL: 22 pass 2 (xz-): 0 found - 2 modified | TOTAL: 22 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 (+-): 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 (-+): 0 found - 0 modified | TOTAL: 2 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 = 24 (out of 223117: 0.010757) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:22:14:42:01 mri_pretess N 4 e 1.99 S 0.04 U 2.68 P 137% M 40904 F 1 R 8836 W 0 c 257 w 50 I 0 O 224 L 18.03 20.48 22.20 @#@FSLOADPOST 2024:11:22:14:42:03 mri_pretess N 4 18.03 20.48 22.20 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.3.2 7.3.2 slice 50: 23 vertices, 31 faces slice 60: 2872 vertices, 3045 faces slice 70: 9067 vertices, 9302 faces slice 80: 17115 vertices, 17432 faces slice 90: 26163 vertices, 26449 faces slice 100: 35575 vertices, 35913 faces slice 110: 45190 vertices, 45547 faces slice 120: 55009 vertices, 55333 faces slice 130: 64538 vertices, 64875 faces slice 140: 73457 vertices, 73786 faces slice 150: 82272 vertices, 82537 faces slice 160: 89349 vertices, 89597 faces slice 170: 95598 vertices, 95817 faces slice 180: 101316 vertices, 101486 faces slice 190: 105684 vertices, 105823 faces slice 200: 108839 vertices, 108920 faces slice 210: 109328 vertices, 109334 faces slice 220: 109328 vertices, 109334 faces slice 230: 109328 vertices, 109334 faces slice 240: 109328 vertices, 109334 faces slice 250: 109328 vertices, 109334 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 2024:11:22:14:42:03 mri_tessellate N 3 e 1.77 S 0.03 U 2.10 P 120% M 35540 F 0 R 7828 W 0 c 201 w 195 I 0 O 5128 L 18.03 20.48 22.20 @#@FSLOADPOST 2024:11:22:14:42:05 mri_tessellate N 3 18.83 20.60 22.23 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 109328 voxel in cpt #1: X=-6 [v=109328,e=328002,f=218668] located at (-25.467382, -7.447772, 5.227316) For the whole surface: X=-6 [v=109328,e=328002,f=218668] One single component has been found nothing to do done @#@FSTIME 2024:11:22:14:42:05 mris_extract_main_component N 2 e 0.70 S 0.16 U 0.69 P 122% M 218336 F 2 R 57632 W 0 c 82 w 178 I 0 O 7696 L 18.83 20.60 22.23 @#@FSLOADPOST 2024:11:22:14:42:06 mris_extract_main_component N 2 18.83 20.60 22.23 #-------------------------------------------- #@# Tessellate rh Fri Nov 22 14:42:06 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 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+): 9 found - 9 modified | TOTAL: 10 pass 2 (yz+): 0 found - 9 modified | TOTAL: 10 pass 1 (yz-): 8 found - 8 modified | TOTAL: 18 pass 2 (yz-): 0 found - 8 modified | TOTAL: 18 pass 1 (xz+): 4 found - 4 modified | TOTAL: 22 pass 2 (xz+): 0 found - 4 modified | TOTAL: 22 pass 1 (xz-): 2 found - 2 modified | TOTAL: 24 pass 2 (xz-): 0 found - 2 modified | TOTAL: 24 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 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 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 = 28 (out of 226722: 0.012350) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2024:11:22:14:42:06 mri_pretess N 4 e 2.56 S 0.03 U 3.21 P 126% M 40896 F 0 R 13169 W 0 c 293 w 37 I 0 O 224 L 18.83 20.60 22.23 @#@FSLOADPOST 2024:11:22:14:42:08 mri_pretess N 4 18.83 20.60 22.23 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.3.2 7.3.2 slice 60: 1646 vertices, 1781 faces slice 70: 7006 vertices, 7207 faces slice 80: 13574 vertices, 13850 faces slice 90: 22734 vertices, 23048 faces slice 100: 31456 vertices, 31765 faces slice 110: 40679 vertices, 41022 faces slice 120: 50771 vertices, 51125 faces slice 130: 60559 vertices, 60887 faces slice 140: 69959 vertices, 70290 faces slice 150: 78636 vertices, 78927 faces slice 160: 86974 vertices, 87219 faces slice 170: 93735 vertices, 93959 faces slice 180: 99522 vertices, 99732 faces slice 190: 104416 vertices, 104599 faces slice 200: 108595 vertices, 108726 faces slice 210: 109848 vertices, 109866 faces slice 220: 109848 vertices, 109866 faces slice 230: 109848 vertices, 109866 faces slice 240: 109848 vertices, 109866 faces slice 250: 109848 vertices, 109866 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 2024:11:22:14:42:08 mri_tessellate N 3 e 1.68 S 0.03 U 1.96 P 118% M 35744 F 0 R 7836 W 0 c 192 w 199 I 0 O 5152 L 19.32 20.68 22.25 @#@FSLOADPOST 2024:11:22:14:42:10 mri_tessellate N 3 19.32 20.68 22.25 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 109840 voxel in cpt #1: X=-20 [v=109840,e=329580,f=219720] located at (26.311516, -3.227103, 8.884086) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (31.000000, 25.000000, -5.000000) For the whole surface: X=-18 [v=109848,e=329598,f=219732] 2 components have been found keeping component #1 with 109840 vertices done @#@FSTIME 2024:11:22:14:42:10 mris_extract_main_component N 2 e 0.80 S 0.14 U 0.85 P 122% M 219752 F 1 R 57934 W 0 c 101 w 340 I 0 O 7728 L 19.32 20.68 22.25 @#@FSLOADPOST 2024:11:22:14:42:11 mris_extract_main_component N 2 19.32 20.68 22.25 #-------------------------------------------- #@# Smooth1 lh Fri Nov 22 14:42:11 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Fri Nov 22 14:42:11 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 392511 of (392511 392514) to complete... Waiting for PID 392514 of (392511 392514) 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 (392511 392514) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Fri Nov 22 14:42:13 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Fri Nov 22 14:42:13 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 392594 of (392594 392597) to complete... Waiting for PID 392597 of (392594 392597) 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 = 43.8 mm, total surface area = 58730 mm^2 step 000: RMS=0.147 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.054 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.032 (target=0.015) step 060: RMS=0.031 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 28.846733 mris_inflate stimesec 1.175207 mris_inflate ru_maxrss 175176 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 596079 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7720 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2531 mris_inflate ru_nivcsw 2601 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 43.9 mm, total surface area = 59285 mm^2 step 000: RMS=0.146 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.078 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.054 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes inflation complete. Not saving sulc mris_inflate utimesec 28.923195 mris_inflate stimesec 0.656435 mris_inflate ru_maxrss 175840 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 308466 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7752 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3102 mris_inflate ru_nivcsw 2592 PIDs (392594 392597) completed and logs appended. #-------------------------------------------- #@# QSphere lh Fri Nov 22 14:42:28 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Fri Nov 22 14:42:28 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 400607 of (400607 400610) to complete... Waiting for PID 400610 of (400607 400610) 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 0.340... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.60 (0.00-->5.88) (max @ vno 40634 --> 41589) face area 0.03 +- 0.03 (-0.05-->0.56) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.838, avgs=0 005/300: dt: 0.9000, rms radial error=176.579, avgs=0 010/300: dt: 0.9000, rms radial error=176.022, avgs=0 015/300: dt: 0.9000, rms radial error=175.290, avgs=0 020/300: dt: 0.9000, rms radial error=174.457, avgs=0 025/300: dt: 0.9000, rms radial error=173.566, avgs=0 030/300: dt: 0.9000, rms radial error=172.642, avgs=0 035/300: dt: 0.9000, rms radial error=171.702, avgs=0 040/300: dt: 0.9000, rms radial error=170.754, avgs=0 045/300: dt: 0.9000, rms radial error=169.806, avgs=0 050/300: dt: 0.9000, rms radial error=168.861, avgs=0 055/300: dt: 0.9000, rms radial error=167.917, avgs=0 060/300: dt: 0.9000, rms radial error=166.977, avgs=0 065/300: dt: 0.9000, rms radial error=166.042, avgs=0 070/300: dt: 0.9000, rms radial error=165.110, avgs=0 075/300: dt: 0.9000, rms radial error=164.184, avgs=0 080/300: dt: 0.9000, rms radial error=163.262, avgs=0 085/300: dt: 0.9000, rms radial error=162.345, avgs=0 090/300: dt: 0.9000, rms radial error=161.432, avgs=0 095/300: dt: 0.9000, rms radial error=160.525, avgs=0 100/300: dt: 0.9000, rms radial error=159.623, avgs=0 105/300: dt: 0.9000, rms radial error=158.726, avgs=0 110/300: dt: 0.9000, rms radial error=157.833, avgs=0 115/300: dt: 0.9000, rms radial error=156.946, avgs=0 120/300: dt: 0.9000, rms radial error=156.063, avgs=0 125/300: dt: 0.9000, rms radial error=155.185, avgs=0 130/300: dt: 0.9000, rms radial error=154.312, avgs=0 135/300: dt: 0.9000, rms radial error=153.443, avgs=0 140/300: dt: 0.9000, rms radial error=152.579, avgs=0 145/300: dt: 0.9000, rms radial error=151.720, avgs=0 150/300: dt: 0.9000, rms radial error=150.866, avgs=0 155/300: dt: 0.9000, rms radial error=150.016, avgs=0 160/300: dt: 0.9000, rms radial error=149.171, avgs=0 165/300: dt: 0.9000, rms radial error=148.330, avgs=0 170/300: dt: 0.9000, rms radial error=147.494, avgs=0 175/300: dt: 0.9000, rms radial error=146.663, avgs=0 180/300: dt: 0.9000, rms radial error=145.836, avgs=0 185/300: dt: 0.9000, rms radial error=145.014, avgs=0 190/300: dt: 0.9000, rms radial error=144.196, avgs=0 195/300: dt: 0.9000, rms radial error=143.383, avgs=0 200/300: dt: 0.9000, rms radial error=142.574, avgs=0 205/300: dt: 0.9000, rms radial error=141.770, avgs=0 210/300: dt: 0.9000, rms radial error=140.970, avgs=0 215/300: dt: 0.9000, rms radial error=140.175, avgs=0 220/300: dt: 0.9000, rms radial error=139.384, avgs=0 225/300: dt: 0.9000, rms radial error=138.598, avgs=0 230/300: dt: 0.9000, rms radial error=137.815, avgs=0 235/300: dt: 0.9000, rms radial error=137.038, avgs=0 240/300: dt: 0.9000, rms radial error=136.264, avgs=0 245/300: dt: 0.9000, rms radial error=135.495, avgs=0 250/300: dt: 0.9000, rms radial error=134.730, avgs=0 255/300: dt: 0.9000, rms radial error=133.969, avgs=0 260/300: dt: 0.9000, rms radial error=133.213, avgs=0 265/300: dt: 0.9000, rms radial error=132.461, avgs=0 270/300: dt: 0.9000, rms radial error=131.713, avgs=0 275/300: dt: 0.9000, rms radial error=130.970, avgs=0 280/300: dt: 0.9000, rms radial error=130.230, avgs=0 285/300: dt: 0.9000, rms radial error=129.495, avgs=0 290/300: dt: 0.9000, rms radial error=128.764, avgs=0 295/300: dt: 0.9000, rms radial error=128.037, avgs=0 300/300: dt: 0.9000, rms radial error=127.314, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12313.10 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00040 epoch 2 (K=40.0), pass 1, starting sse = 1837.27 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00045 epoch 3 (K=160.0), pass 1, starting sse = 139.82 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.20/20 = 0.00998 epoch 4 (K=640.0), pass 1, starting sse = 4.35 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/16 = 0.00676 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0240 hours FSRUNTIME@ mris_sphere 0.0240 hours 4 threads #VMPC# mris_sphere VmPeak 769780 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 0.337... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.59 (0.00-->6.69) (max @ vno 39442 --> 39443) face area 0.03 +- 0.03 (-0.02-->0.70) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.850, avgs=0 005/300: dt: 0.9000, rms radial error=176.590, avgs=0 010/300: dt: 0.9000, rms radial error=176.034, avgs=0 015/300: dt: 0.9000, rms radial error=175.304, avgs=0 020/300: dt: 0.9000, rms radial error=174.475, avgs=0 025/300: dt: 0.9000, rms radial error=173.588, avgs=0 030/300: dt: 0.9000, rms radial error=172.668, avgs=0 035/300: dt: 0.9000, rms radial error=171.732, avgs=0 040/300: dt: 0.9000, rms radial error=170.789, avgs=0 045/300: dt: 0.9000, rms radial error=169.843, avgs=0 050/300: dt: 0.9000, rms radial error=168.898, avgs=0 055/300: dt: 0.9000, rms radial error=167.955, avgs=0 060/300: dt: 0.9000, rms radial error=167.016, avgs=0 065/300: dt: 0.9000, rms radial error=166.080, avgs=0 070/300: dt: 0.9000, rms radial error=165.149, avgs=0 075/300: dt: 0.9000, rms radial error=164.223, avgs=0 080/300: dt: 0.9000, rms radial error=163.302, avgs=0 085/300: dt: 0.9000, rms radial error=162.385, avgs=0 090/300: dt: 0.9000, rms radial error=161.473, avgs=0 095/300: dt: 0.9000, rms radial error=160.566, avgs=0 100/300: dt: 0.9000, rms radial error=159.664, avgs=0 105/300: dt: 0.9000, rms radial error=158.767, avgs=0 110/300: dt: 0.9000, rms radial error=157.874, avgs=0 115/300: dt: 0.9000, rms radial error=156.987, avgs=0 120/300: dt: 0.9000, rms radial error=156.104, avgs=0 125/300: dt: 0.9000, rms radial error=155.226, avgs=0 130/300: dt: 0.9000, rms radial error=154.353, avgs=0 135/300: dt: 0.9000, rms radial error=153.484, avgs=0 140/300: dt: 0.9000, rms radial error=152.620, avgs=0 145/300: dt: 0.9000, rms radial error=151.761, avgs=0 150/300: dt: 0.9000, rms radial error=150.907, avgs=0 155/300: dt: 0.9000, rms radial error=150.057, avgs=0 160/300: dt: 0.9000, rms radial error=149.212, avgs=0 165/300: dt: 0.9000, rms radial error=148.371, avgs=0 170/300: dt: 0.9000, rms radial error=147.536, avgs=0 175/300: dt: 0.9000, rms radial error=146.704, avgs=0 180/300: dt: 0.9000, rms radial error=145.878, avgs=0 185/300: dt: 0.9000, rms radial error=145.056, avgs=0 190/300: dt: 0.9000, rms radial error=144.238, avgs=0 195/300: dt: 0.9000, rms radial error=143.425, avgs=0 200/300: dt: 0.9000, rms radial error=142.617, avgs=0 205/300: dt: 0.9000, rms radial error=141.813, avgs=0 210/300: dt: 0.9000, rms radial error=141.013, avgs=0 215/300: dt: 0.9000, rms radial error=140.218, avgs=0 220/300: dt: 0.9000, rms radial error=139.427, avgs=0 225/300: dt: 0.9000, rms radial error=138.641, avgs=0 230/300: dt: 0.9000, rms radial error=137.858, avgs=0 235/300: dt: 0.9000, rms radial error=137.081, avgs=0 240/300: dt: 0.9000, rms radial error=136.307, avgs=0 245/300: dt: 0.9000, rms radial error=135.538, avgs=0 250/300: dt: 0.9000, rms radial error=134.774, avgs=0 255/300: dt: 0.9000, rms radial error=134.013, avgs=0 260/300: dt: 0.9000, rms radial error=133.257, avgs=0 265/300: dt: 0.9000, rms radial error=132.505, avgs=0 270/300: dt: 0.9000, rms radial error=131.757, avgs=0 275/300: dt: 0.9000, rms radial error=131.014, avgs=0 280/300: dt: 0.9000, rms radial error=130.275, avgs=0 285/300: dt: 0.9000, rms radial error=129.540, avgs=0 290/300: dt: 0.9000, rms radial error=128.809, avgs=0 295/300: dt: 0.9000, rms radial error=128.082, avgs=0 300/300: dt: 0.9000, rms radial error=127.359, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12385.61 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00047 epoch 2 (K=40.0), pass 1, starting sse = 1836.02 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00057 epoch 3 (K=160.0), pass 1, starting sse = 141.13 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.24/19 = 0.01268 epoch 4 (K=640.0), pass 1, starting sse = 3.12 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.22/32 = 0.00693 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0274 hours FSRUNTIME@ mris_sphere 0.0274 hours 4 threads #VMPC# mris_sphere VmPeak 704608 mris_sphere done PIDs (400607 400610) completed and logs appended. #@# Fix Topology lh Fri Nov 22 14:44:06 CST 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_Bay3prisma lh #@# Fix Topology rh Fri Nov 22 14:44:06 CST 2024 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_Bay3prisma rh Waiting for PID 480992 of (480992 480995) to complete... Waiting for PID 480995 of (480992 480995) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_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=-6 (nv=109328, nf=218668, ne=328002, g=4) 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... 1532 ambiguous faces found in tessellation segmenting defects... 12 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 12 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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: -9.1119 (-4.5560) -vertex loglikelihood: -6.3627 (-3.1814) -normal dot loglikelihood: -3.6156 (-3.6156) -quad curv loglikelihood: -6.0080 (-3.0040) Total Loglikelihood : -25.0982 CORRECTING DEFECT 0 (vertices=12, convex hull=27, v0=19792) After retessellation of defect 0 (v0=19792), euler #=-9 (108421,325006,216576) : difference with theory (-9) = 0 CORRECTING DEFECT 1 (vertices=88, convex hull=46, v0=62284) After retessellation of defect 1 (v0=62284), euler #=-8 (108430,325048,216610) : difference with theory (-8) = 0 CORRECTING DEFECT 2 (vertices=9, convex hull=21, v0=67530) After retessellation of defect 2 (v0=67530), euler #=-7 (108431,325056,216618) : difference with theory (-7) = 0 CORRECTING DEFECT 3 (vertices=130, convex hull=46, v0=70660) After retessellation of defect 3 (v0=70660), euler #=-6 (108448,325127,216673) : difference with theory (-6) = 0 CORRECTING DEFECT 4 (vertices=10, convex hull=24, v0=72159) After retessellation of defect 4 (v0=72159), euler #=-5 (108451,325145,216689) : difference with theory (-5) = 0 CORRECTING DEFECT 5 (vertices=52, convex hull=65, v0=74356) After retessellation of defect 5 (v0=74356), euler #=-4 (108464,325210,216742) : difference with theory (-4) = 0 CORRECTING DEFECT 6 (vertices=13, convex hull=19, v0=75788) After retessellation of defect 6 (v0=75788), euler #=-3 (108465,325218,216750) : difference with theory (-3) = 0 CORRECTING DEFECT 7 (vertices=7, convex hull=17, v0=78723) After retessellation of defect 7 (v0=78723), euler #=-2 (108466,325224,216756) : difference with theory (-2) = 0 CORRECTING DEFECT 8 (vertices=327, convex hull=67, v0=80317) After retessellation of defect 8 (v0=80317), euler #=-1 (108475,325280,216804) : difference with theory (-1) = 0 CORRECTING DEFECT 9 (vertices=44, convex hull=36, v0=88375) After retessellation of defect 9 (v0=88375), euler #=0 (108485,325324,216839) : difference with theory (0) = 0 CORRECTING DEFECT 10 (vertices=197, convex hull=195, v0=93245) After retessellation of defect 10 (v0=93245), euler #=1 (108504,325483,216980) : difference with theory (1) = 0 CORRECTING DEFECT 11 (vertices=19, convex hull=59, v0=105809) After retessellation of defect 11 (v0=105809), euler #=2 (108516,325542,217028) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.13-->7.47) (max @ vno 92573 --> 95929) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.13-->7.47) (max @ vno 92573 --> 95929) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 49 mutations (38.9%), 77 crossovers (61.1%), 78 vertices were eliminated building final representation... 812 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=108516, nf=217028, ne=325542, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 72 intersecting 001: 5 intersecting terminating search with 0 intersecting topology fixing took 0.8 minutes FSRUNTIME@ mris_fix_topology lh 0.0127 hours 4 threads #VMPC# mris_fix_topology VmPeak 946212 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PIB15-273_VYr9_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=-20 (nv=109840, nf=219720, ne=329580, g=11) 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... 642 ambiguous faces found in tessellation segmenting defects... 16 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 16 defects to be corrected 0 vertices coincident reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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: -9.0076 (-4.5038) -vertex loglikelihood: -6.3482 (-3.1741) -normal dot loglikelihood: -3.6968 (-3.6968) -quad curv loglikelihood: -6.2596 (-3.1298) Total Loglikelihood : -25.3122 CORRECTING DEFECT 0 (vertices=15, convex hull=17, v0=30390) After retessellation of defect 0 (v0=30390), euler #=-13 (109399,327901,218489) : difference with theory (-13) = 0 CORRECTING DEFECT 1 (vertices=17, convex hull=29, v0=31345) After retessellation of defect 1 (v0=31345), euler #=-12 (109402,327919,218505) : difference with theory (-12) = 0 CORRECTING DEFECT 2 (vertices=5, convex hull=18, v0=46111) After retessellation of defect 2 (v0=46111), euler #=-11 (109404,327928,218513) : difference with theory (-11) = 0 CORRECTING DEFECT 3 (vertices=36, convex hull=55, v0=67661) After retessellation of defect 3 (v0=67661), euler #=-10 (109425,328015,218580) : difference with theory (-10) = 0 CORRECTING DEFECT 4 (vertices=16, convex hull=27, v0=70626) After retessellation of defect 4 (v0=70626), euler #=-9 (109428,328031,218594) : difference with theory (-9) = 0 CORRECTING DEFECT 5 (vertices=26, convex hull=17, v0=74112) After retessellation of defect 5 (v0=74112), euler #=-8 (109432,328046,218606) : difference with theory (-8) = 0 CORRECTING DEFECT 6 (vertices=52, convex hull=50, v0=83661) After retessellation of defect 6 (v0=83661), euler #=-7 (109441,328094,218646) : difference with theory (-7) = 0 CORRECTING DEFECT 7 (vertices=46, convex hull=83, v0=89286) After retessellation of defect 7 (v0=89286), euler #=-6 (109458,328181,218717) : difference with theory (-6) = 0 CORRECTING DEFECT 8 (vertices=19, convex hull=53, v0=92407) After retessellation of defect 8 (v0=92407), euler #=-5 (109467,328228,218756) : difference with theory (-5) = 0 CORRECTING DEFECT 9 (vertices=27, convex hull=58, v0=96758) After retessellation of defect 9 (v0=96758), euler #=-4 (109479,328284,218801) : difference with theory (-4) = 0 CORRECTING DEFECT 10 (vertices=27, convex hull=54, v0=97844) After retessellation of defect 10 (v0=97844), euler #=-3 (109488,328330,218839) : difference with theory (-3) = 0 CORRECTING DEFECT 11 (vertices=31, convex hull=69, v0=98571) After retessellation of defect 11 (v0=98571), euler #=-2 (109500,328395,218893) : difference with theory (-2) = 0 CORRECTING DEFECT 12 (vertices=29, convex hull=48, v0=102114) After retessellation of defect 12 (v0=102114), euler #=-1 (109509,328441,218931) : difference with theory (-1) = 0 CORRECTING DEFECT 13 (vertices=35, convex hull=79, v0=105045) After retessellation of defect 13 (v0=105045), euler #=0 (109528,328531,219003) : difference with theory (0) = 0 CORRECTING DEFECT 14 (vertices=21, convex hull=59, v0=107174) After retessellation of defect 14 (v0=107174), euler #=1 (109533,328568,219036) : difference with theory (1) = 0 CORRECTING DEFECT 15 (vertices=41, convex hull=72, v0=108854) After retessellation of defect 15 (v0=108854), euler #=2 (109558,328668,219112) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.05-->5.48) (max @ vno 101299 --> 104057) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.05-->5.48) (max @ vno 101299 --> 104057) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 65 mutations (36.9%), 111 crossovers (63.1%), 34 vertices were eliminated building final representation... 282 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=109558, nf=219112, ne=328668, g=0) writing corrected surface to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 65 intersecting 001: 6 intersecting terminating search with 0 intersecting topology fixing took 0.6 minutes FSRUNTIME@ mris_fix_topology rh 0.0097 hours 4 threads #VMPC# mris_fix_topology VmPeak 946732 PIDs (480992 480995) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 108516 - 325542 + 217028 = 2 --> 0 holes F =2V-4: 217028 = 217032-4 (0) 2E=3F: 651084 = 651084 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 109558 - 328668 + 219112 = 2 --> 0 holes F =2V-4: 219112 = 219116-4 (0) 2E=3F: 657336 = 657336 (0) total defect index = 0 Fri Nov 22 14:44:53 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_7_3_Ubuntu20.04/bin/defect2seg --s PIB15-273_VYr9_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 509711 mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 16 non-cortical segments detected only using segment with 7233 vertices erasing segment 1 (vno[0] = 61881) erasing segment 2 (vno[0] = 66650) erasing segment 3 (vno[0] = 69395) erasing segment 4 (vno[0] = 70707) erasing segment 5 (vno[0] = 71183) erasing segment 6 (vno[0] = 79510) erasing segment 7 (vno[0] = 79530) erasing segment 8 (vno[0] = 79682) erasing segment 9 (vno[0] = 80339) erasing segment 10 (vno[0] = 80364) erasing segment 11 (vno[0] = 81152) erasing segment 12 (vno[0] = 81173) erasing segment 13 (vno[0] = 82054) erasing segment 14 (vno[0] = 82774) erasing segment 15 (vno[0] = 84914) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz 1000 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 525164 mris_defects_pointset done mri_label2label --label-cortex /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/aseg.presurf.mgz 0 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 4 non-cortical segments detected only using segment with 7034 vertices erasing segment 1 (vno[0] = 54327) erasing segment 2 (vno[0] = 79211) erasing segment 3 (vno[0] = 83634) mri_label2vol --defects /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz 2000 1 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/surface.defects.mgz mris_defects_pointset -s /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix -d /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels -o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defects.pointset --label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label Reading in surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.nofix Reading in defect segmentation /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.defect_labels Reading in label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 525528 mris_defects_pointset done Started at Fri Nov 22 14:44:53 CST 2024 Ended at Fri Nov 22 14:45:29 CST 2024 Defect2seg-Run-Time-Sec 36 Defect2seg-Run-Time-Min 0.72 Defect2seg-Run-Time-Hours 0.01 tkmeditfv PIB15-273_VYr9_Bay3prisma brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2024:11:22:14:44:53 defect2seg N 3 e 35.52 S 0.94 U 38.38 P 110% M 330360 F 9 R 503375 W 0 c 3644 w 1473 I 0 O 18096 L 28.10 23.85 23.20 @#@FSLOADPOST 2024:11:22:14:45:29 defect2seg N 3 26.93 24.04 23.29 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.708681 remeshing to edge length 0.708681 with 3 iterations avg qual before : 0.893931 after: 0.971172 Removing intersections Remeshed surface quality stats nv0 = 108516 nv = 113725 1.048 Area 227446 0.30082 0.03345 0.089645 0.4837 Corner 682338 60.00000 8.79261 17.375351 145.0652 Edge 341169 0.84144 0.08220 0.481877 1.2317 Hinge 341169 9.69502 9.78915 0.000017 127.9969 mris_remesh done @#@FSTIME 2024:11:22:14:45:29 mris_remesh N 7 e 28.92 S 0.90 U 29.76 P 105% M 637844 F 2 R 801521 W 0 c 2871 w 1069 I 0 O 8000 L 26.93 24.04 23.29 @#@FSLOADPOST 2024:11:22:14:45:58 mris_remesh N 7 28.51 24.72 23.54 mris_remesh --remesh --iters 3 --input /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig.premesh --output /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.708874 remeshing to edge length 0.708874 with 3 iterations avg qual before : 0.891876 after: 0.971205 Removing intersections Remeshed surface quality stats nv0 = 109558 nv = 114467 1.04481 Area 228930 0.30121 0.03349 0.075014 0.4910 Corner 686790 60.00000 8.79528 17.421000 143.5818 Edge 343395 0.84198 0.08215 0.449565 1.2429 Hinge 343395 9.55184 9.86331 0.000000 129.8714 mris_remesh done @#@FSTIME 2024:11:22:14:45:58 mris_remesh N 7 e 30.32 S 1.09 U 30.75 P 105% M 642052 F 1 R 805548 W 0 c 3013 w 759 I 0 O 8056 L 28.51 24.72 23.54 @#@FSLOADPOST 2024:11:22:14:46:28 mris_remesh N 7 31.77 25.92 23.98 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:14:46:28 mris_remove_intersection N 2 e 2.55 S 0.20 U 2.65 P 111% M 288100 F 2 R 135073 W 0 c 265 w 369 I 0 O 8000 L 31.77 25.92 23.98 @#@FSLOADPOST 2024:11:22:14:46:31 mris_remove_intersection N 2 31.39 25.94 24.00 rm -f ../surf/lh.inflated /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:14:46:31 mris_remove_intersection N 2 e 2.68 S 0.23 U 2.71 P 109% M 290448 F 0 R 136292 W 0 c 278 w 364 I 0 O 8056 L 31.39 25.94 24.00 @#@FSLOADPOST 2024:11:22:14:46:33 mris_remove_intersection N 2 31.39 25.94 24.00 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Fri Nov 22 14:46:33 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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: 207370 voxels (1.24%) border gray 223027 voxels (1.33%) 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=22960, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 99.3 +- 7.5 [70.0 --> 110.0] CCS GM (77.0) : 75.9 +- 11.3 [30.0 --> 110.0] white_mean = 99.3299 +/- 7.48873, gray_mean = 75.9186 +/- 11.3356 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=158 nbins=159 intensity peaks found at WM=103+-5.2, GM=73+-8.7 white_mode = 103, gray_mode = 73 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 61.7 (was 70.000000) setting MAX_BORDER_WHITE to 110.5 (was 105.000000) setting MIN_BORDER_WHITE to 73.0 (was 85.000000) setting MAX_CSF to 50.3 (was 40.000000) setting MAX_GRAY to 95.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 61.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 39.0 (was 40.000000) When placing the white surface white_border_hi = 110.489; white_border_low = 73; white_outside_low = 61.6644; white_inside_hi = 120; white_outside_hi = 110.489; When placing the pial surface pial_border_hi = 61.6644; pial_border_low = 38.9932; pial_outside_low = 10; pial_inside_hi = 95.5113; pial_outside_hi = 55.9966; #VMPC# mris_autodet_gwstats VmPeak 563524 mris_autodet_gwstats done @#@FSTIME 2024:11:22:14:46:33 mris_autodet_gwstats N 8 e 4.40 S 0.16 U 5.68 P 132% M 204672 F 2 R 104513 W 0 c 557 w 126 I 0 O 8 L 31.39 25.94 24.00 @#@FSLOADPOST 2024:11:22:14:46:38 mris_autodet_gwstats N 8 31.60 26.07 24.05 #-------------------------------------------- #@# AutoDetGWStats rh Fri Nov 22 14:46:38 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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: 207370 voxels (1.24%) border gray 223027 voxels (1.33%) 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=22960, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 99.3 +- 7.5 [70.0 --> 110.0] CCS GM (77.0) : 75.9 +- 11.3 [30.0 --> 110.0] white_mean = 99.3299 +/- 7.48873, gray_mean = 75.9186 +/- 11.3356 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=158 nbins=159 intensity peaks found at WM=102+-5.2, GM=74+-7.8 white_mode = 102, gray_mode = 74 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70.000000) setting MAX_BORDER_WHITE to 109.5 (was 105.000000) setting MIN_BORDER_WHITE to 74.0 (was 85.000000) setting MAX_CSF to 51.3 (was 40.000000) setting MAX_GRAY to 94.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 40.0 (was 40.000000) When placing the white surface white_border_hi = 109.489; white_border_low = 74; white_outside_low = 62.6644; white_inside_hi = 120; white_outside_hi = 109.489; When placing the pial surface pial_border_hi = 62.6644; pial_border_low = 39.9932; pial_outside_low = 10; pial_inside_hi = 94.5113; pial_outside_hi = 56.9966; #VMPC# mris_autodet_gwstats VmPeak 564392 mris_autodet_gwstats done @#@FSTIME 2024:11:22:14:46:38 mris_autodet_gwstats N 8 e 4.47 S 0.22 U 5.54 P 129% M 206336 F 1 R 108891 W 0 c 540 w 131 I 0 O 8 L 31.60 26.07 24.05 @#@FSLOADPOST 2024:11:22:14:46:42 mris_autodet_gwstats N 8 31.39 26.12 24.08 #-------------------------------------------- #@# WhitePreAparc lh Fri Nov 22 14:46:42 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 227446 0.26594 0.06151 0.001033 0.5776 Corner 682338 60.00000 9.29767 3.959747 142.2395 Edge 341169 0.78745 0.11195 0.022654 1.2791 Hinge 341169 6.44690 6.23970 0.000036 145.9689 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=22960, wmmin=5, clip=110 MRIfindBrightNonWM(): 473 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 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6143, nmarked2=5, nripped=6143 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56863: xyz = (-31.1771,2.11353,9.27216) oxyz = (-31.1771,2.11353,9.27216) wxzy = (-31.1771,2.11353,9.27216) pxyz = (0,0,0) CBVO Creating mask 113725 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=6143 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6143, nmarked2=5, nripped=6143 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 = 110.4887310; border_low = 73.0000000; outside_low = 61.6644060; outside_hi = 110.4887310; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=2 had to be increased for 62 vertices, nripped=6143 mean border=83.3, 109 (109) missing vertices, mean dist 0.3 [0.9 (%36.2)->0.9 (%63.8))] %49 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0498 min Finding expansion regions mean absolute distance = 0.91 +- 1.16 3469 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=2457843.8, rms=10.424 001: dt: 0.5000, sse=1380500.4, rms=7.659 (26.527%) 002: dt: 0.5000, sse=834125.8, rms=5.767 (24.699%) 003: dt: 0.5000, sse=550974.6, rms=4.479 (22.330%) 004: dt: 0.5000, sse=401974.7, rms=3.619 (19.201%) 005: dt: 0.5000, sse=327328.3, rms=3.094 (14.506%) 006: dt: 0.5000, sse=292685.8, rms=2.814 (9.048%) 007: dt: 0.5000, sse=277641.8, rms=2.679 (4.804%) 008: dt: 0.5000, sse=272201.1, rms=2.622 (2.117%) rms = 2.5912/2.6224, sse=270237.0/272201.1, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=270237.0, rms=2.591 (1.193%) 010: dt: 0.2500, sse=177131.3, rms=1.511 (41.691%) 011: dt: 0.2500, sse=166649.4, rms=1.289 (14.719%) rms = 1.2446/1.2885, sse=161207.5/166649.4, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=161207.5, rms=1.245 (3.404%) rms = 1.2045/1.2446, sse=159370.9/161207.5, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=159370.9, rms=1.204 (3.225%) 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=6143 removing 1 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 #FML# MRISripMidline(): nmarked=6293, nmarked2=5, nripped=6293 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 = 110.4887310; border_low = 73.0000000; outside_low = 61.6644060; outside_hi = 110.4887310; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=1 had to be increased for 69 vertices, nripped=6293 mean border=86.0, 130 (45) missing vertices, mean dist -0.3 [0.6 (%67.4)->0.2 (%32.6))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0336 min Finding expansion regions mean absolute distance = 0.46 +- 0.83 3582 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=580287.6, rms=4.367 014: dt: 0.5000, sse=332442.8, rms=2.756 (36.890%) 015: dt: 0.5000, sse=289632.0, rms=2.379 (13.675%) 016: dt: 0.5000, sse=277787.2, rms=2.262 (4.913%) rms = 2.3686/2.2624, sse=288175.4/277787.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=223857.1, rms=1.597 (29.407%) 018: dt: 0.2500, sse=202287.3, rms=1.230 (22.963%) 019: dt: 0.2500, sse=196932.5, rms=1.120 (8.968%) rms = 1.0915/1.1200, sse=195654.5/196932.5, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=195654.5, rms=1.091 (2.547%) rms = 1.0563/1.0915, sse=194173.0/195654.5, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=194173.0, rms=1.056 (3.222%) 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=6293 removing 2 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 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=6321, nmarked2=6, nripped=6321 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 = 110.4887310; border_low = 73.0000000; outside_low = 61.6644060; outside_hi = 110.4887310; 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=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 83 vertices, nripped=6321 mean border=88.6, 147 (38) missing vertices, mean dist -0.2 [0.4 (%70.6)->0.2 (%29.4))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0189 min Finding expansion regions mean absolute distance = 0.36 +- 0.52 3381 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=437935.9, rms=3.565 022: dt: 0.5000, sse=270965.9, rms=2.202 (38.233%) 023: dt: 0.5000, sse=262643.7, rms=2.112 (4.098%) rms = 2.1801/2.1116, sse=267589.0/262643.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=211574.7, rms=1.448 (31.436%) 025: dt: 0.2500, sse=192124.7, rms=1.079 (25.470%) 026: dt: 0.2500, sse=189320.2, rms=1.004 (6.977%) rms = 0.9875/1.0037, sse=188107.6/189320.2, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=188107.6, rms=0.988 (1.616%) rms = 0.9563/0.9875, sse=186664.6/188107.6, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=186664.6, rms=0.956 (3.162%) 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=6321 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 #FML# MRISripMidline(): nmarked=6354, nmarked2=6, nripped=6354 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 = 110.4887310; border_low = 73.0000000; outside_low = 61.6644060; outside_hi = 110.4887310; 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=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 98 vertices, nripped=6354 mean border=89.8, 132 (32) missing vertices, mean dist -0.1 [0.3 (%59.2)->0.2 (%40.8))] %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0121 min Finding expansion regions mean absolute distance = 0.28 +- 0.40 2817 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=233233.9, rms=1.813 029: dt: 0.5000, sse=204626.2, rms=1.356 (25.229%) rms = 1.6700/1.3557, sse=222644.9/204626.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=182521.0, rms=0.929 (31.468%) 031: dt: 0.2500, sse=177074.5, rms=0.796 (14.279%) 032: dt: 0.2500, sse=174696.3, rms=0.743 (6.643%) rms = 0.7693/0.7435, sse=175379.4/174696.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.7338/0.7435, sse=174211.8/174696.3, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=174211.8, rms=0.734 (1.297%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 2.49 minutes #VMPC# mris_place_surfaces VmPeak 2052760 mris_place_surface done @#@FSTIME 2024:11:22:14:46:42 mris_place_surface N 18 e 156.19 S 1.99 U 289.09 P 186% M 1615780 F 1 R 2245134 W 0 c 26890 w 1890 I 0 O 8000 L 31.39 26.12 24.08 @#@FSLOADPOST 2024:11:22:14:49:19 mris_place_surface N 18 25.20 25.67 24.22 #-------------------------------------------- #@# WhitePreAparc rh Fri Nov 22 14:49:19 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 228930 0.26669 0.06219 0.009439 0.6018 Corner 686790 60.00000 9.38503 15.657350 134.1637 Edge 343395 0.78855 0.11289 0.090435 1.2829 Hinge 343395 6.35476 6.30793 0.000008 120.4290 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=22960, wmmin=5, clip=110 MRIfindBrightNonWM(): 473 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=6099, nmarked2=0, nripped=6099 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57234: xyz = (51.2338,7.22227,11.1731) oxyz = (51.2338,7.22227,11.1731) wxzy = (51.2338,7.22227,11.1731) pxyz = (0,0,0) CBVO Creating mask 114467 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=6099 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6099, nmarked2=0, nripped=6099 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 = 109.4887310; border_low = 74.0000000; outside_low = 62.6644060; outside_hi = 109.4887310; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=2 had to be increased for 33 vertices, nripped=6099 mean border=83.3, 86 (86) missing vertices, mean dist 0.3 [0.8 (%35.8)->0.9 (%64.2))] %44 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0400 min Finding expansion regions mean absolute distance = 0.87 +- 1.08 3749 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=2388736.8, rms=10.227 001: dt: 0.5000, sse=1316907.5, rms=7.431 (27.333%) 002: dt: 0.5000, sse=792293.5, rms=5.570 (25.046%) 003: dt: 0.5000, sse=531631.4, rms=4.354 (21.833%) 004: dt: 0.5000, sse=395343.6, rms=3.553 (18.400%) 005: dt: 0.5000, sse=328380.8, rms=3.080 (13.311%) 006: dt: 0.5000, sse=293540.5, rms=2.798 (9.157%) 007: dt: 0.5000, sse=280623.1, rms=2.675 (4.395%) 008: dt: 0.5000, sse=271667.2, rms=2.592 (3.104%) rms = 2.5750/2.5919, sse=271047.9/271667.2, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=271047.9, rms=2.575 (0.650%) 010: dt: 0.2500, sse=181863.5, rms=1.555 (39.614%) 011: dt: 0.2500, sse=169711.9, rms=1.354 (12.896%) rms = 1.3066/1.3544, sse=167683.7/169711.9, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=167683.7, rms=1.307 (3.529%) rms = 1.2756/1.3066, sse=165368.2/167683.7, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=165368.2, rms=1.276 (2.378%) 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=6099 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 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6269, nmarked2=0, nripped=6269 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 = 109.4887310; border_low = 74.0000000; outside_low = 62.6644060; outside_hi = 109.4887310; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=1 had to be increased for 87 vertices, nripped=6269 mean border=85.9, 67 (24) missing vertices, mean dist -0.3 [0.5 (%67.6)->0.2 (%32.4))] %56 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0284 min Finding expansion regions mean absolute distance = 0.42 +- 0.74 3293 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=547778.7, rms=4.170 014: dt: 0.5000, sse=321495.4, rms=2.632 (36.884%) 015: dt: 0.5000, sse=284696.8, rms=2.272 (13.662%) 016: dt: 0.5000, sse=271517.2, rms=2.153 (5.239%) rms = 2.2729/2.1532, sse=280247.8/271517.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=221065.7, rms=1.530 (28.966%) 018: dt: 0.2500, sse=201296.4, rms=1.192 (22.044%) 019: dt: 0.2500, sse=197874.1, rms=1.102 (7.565%) rms = 1.0763/1.1021, sse=196427.7/197874.1, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=196427.7, rms=1.076 (2.340%) rms = 1.0503/1.0763, sse=195047.7/196427.7, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=195047.7, rms=1.050 (2.417%) 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=6269 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 #FML# MRISripMidline(): nmarked=6322, nmarked2=0, nripped=6322 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 = 109.4887310; border_low = 74.0000000; outside_low = 62.6644060; outside_hi = 109.4887310; 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=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 69 vertices, nripped=6322 mean border=88.8, 58 (20) missing vertices, mean dist -0.2 [0.4 (%73.5)->0.2 (%26.5))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0166 min Finding expansion regions mean absolute distance = 0.33 +- 0.45 3217 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=483240.2, rms=3.824 022: dt: 0.5000, sse=275888.8, rms=2.191 (42.706%) 023: dt: 0.5000, sse=264771.2, rms=2.072 (5.445%) rms = 2.1467/2.0715, sse=268077.2/264771.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=214783.2, rms=1.422 (31.373%) 025: dt: 0.2500, sse=194217.0, rms=1.062 (25.287%) 026: dt: 0.2500, sse=190332.7, rms=0.990 (6.791%) rms = 0.9772/0.9900, sse=190109.9/190332.7, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=190109.9, rms=0.977 (1.292%) rms = 0.9522/0.9772, sse=189934.7/190109.9, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=189934.7, rms=0.952 (2.558%) 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=6322 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=6349, nmarked2=0, nripped=6349 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 = 109.4887310; border_low = 74.0000000; outside_low = 62.6644060; outside_hi = 109.4887310; 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=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 83 vertices, nripped=6349 mean border=89.9, 90 (20) missing vertices, mean dist -0.1 [0.3 (%60.2)->0.2 (%39.8))] %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0111 min Finding expansion regions mean absolute distance = 0.24 +- 0.34 2908 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=230132.9, rms=1.715 029: dt: 0.5000, sse=213575.4, rms=1.373 (19.942%) rms = 1.6997/1.3731, sse=229416.6/213575.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=189724.1, rms=0.922 (32.831%) 031: dt: 0.2500, sse=183091.4, rms=0.790 (14.362%) 032: dt: 0.2500, sse=179893.9, rms=0.739 (6.385%) rms = 0.7590/0.7394, sse=179427.1/179893.9, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.7320/0.7394, sse=179346.0/179893.9, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=179346.0, rms=0.732 (1.007%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 2.50 minutes #VMPC# mris_place_surfaces VmPeak 2083748 mris_place_surface done @#@FSTIME 2024:11:22:14:49:19 mris_place_surface N 18 e 157.05 S 3.42 U 287.29 P 185% M 1646976 F 3 R 3253061 W 0 c 26744 w 2178 I 0 O 8056 L 25.35 25.69 24.24 @#@FSLOADPOST 2024:11:22:14:51:56 mris_place_surface N 18 24.52 25.19 24.27 #-------------------------------------------- #@# CortexLabel lh Fri Nov 22 14:51:56 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 6 non-cortical segments detected only using segment with 7802 vertices erasing segment 1 (vno[0] = 53371) erasing segment 2 (vno[0] = 57524) erasing segment 3 (vno[0] = 68633) erasing segment 4 (vno[0] = 69894) erasing segment 5 (vno[0] = 102543) @#@FSTIME 2024:11:22:14:51:56 mri_label2label N 5 e 17.28 S 0.39 U 18.02 P 106% M 294284 F 2 R 160760 W 0 c 1727 w 285 I 0 O 9168 L 24.52 25.19 24.27 @#@FSLOADPOST 2024:11:22:14:52:13 mri_label2label N 5 23.68 24.97 24.21 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Fri Nov 22 14:52:13 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 5607 vertices erasing segment 1 (vno[0] = 37677) erasing segment 2 (vno[0] = 42188) erasing segment 3 (vno[0] = 43104) erasing segment 4 (vno[0] = 53371) erasing segment 5 (vno[0] = 57524) erasing segment 6 (vno[0] = 61049) erasing segment 7 (vno[0] = 63890) erasing segment 8 (vno[0] = 69894) erasing segment 9 (vno[0] = 98798) erasing segment 10 (vno[0] = 102543) @#@FSTIME 2024:11:22:14:52:13 mri_label2label N 5 e 17.94 S 0.29 U 18.73 P 106% M 313988 F 2 R 168035 W 0 c 1788 w 405 I 0 O 9360 L 23.68 24.97 24.21 @#@FSLOADPOST 2024:11:22:14:52:31 mri_label2label N 5 25.61 25.33 24.35 #-------------------------------------------- #@# CortexLabel rh Fri Nov 22 14:52:31 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 3 non-cortical segments detected only using segment with 7667 vertices erasing segment 0 (vno[0] = 23693) erasing segment 2 (vno[0] = 68203) @#@FSTIME 2024:11:22:14:52:31 mri_label2label N 5 e 17.26 S 0.24 U 18.23 P 107% M 283004 F 3 R 155553 W 0 c 1731 w 260 I 0 O 9024 L 25.61 25.33 24.35 @#@FSLOADPOST 2024:11:22:14:52:49 mri_label2label N 5 26.16 25.46 24.41 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Fri Nov 22 14:52:49 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 6 non-cortical segments detected only using segment with 5733 vertices erasing segment 0 (vno[0] = 23693) erasing segment 2 (vno[0] = 37434) erasing segment 3 (vno[0] = 45206) erasing segment 4 (vno[0] = 49500) erasing segment 5 (vno[0] = 68203) @#@FSTIME 2024:11:22:14:52:49 mri_label2label N 5 e 17.58 S 0.26 U 18.73 P 108% M 295300 F 1 R 173049 W 0 c 1757 w 442 I 0 O 9192 L 26.16 25.46 24.41 @#@FSLOADPOST 2024:11:22:14:53:06 mri_label2label N 5 25.91 25.43 24.42 #-------------------------------------------- #@# Smooth2 lh Fri Nov 22 14:53:06 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Fri Nov 22 14:53:06 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 681988 of (681988 681992) to complete... Waiting for PID 681992 of (681988 681992) 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 (681988 681992) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Fri Nov 22 14:53:09 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Fri Nov 22 14:53:09 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 682076 of (682076 682079) to complete... Waiting for PID 682079 of (682076 682079) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 43.8 mm, total surface area = 68680 mm^2 step 000: RMS=0.168 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.037 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (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 40.808442 mris_inflate stimesec 1.367478 mris_inflate ru_maxrss 176284 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 597984 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8920 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5957 mris_inflate ru_nivcsw 3786 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 43.8 mm, total surface area = 69613 mm^2 step 000: RMS=0.168 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (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 43.404885 mris_inflate stimesec 0.462390 mris_inflate ru_maxrss 178552 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 205495 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8976 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 10406 mris_inflate ru_nivcsw 3850 PIDs (682076 682079) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Fri Nov 22 14:53:30 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Fri Nov 22 14:53:30 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf reconbatchjobs /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 682279 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682283 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682287 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682290 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682293 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682296 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682299 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682302 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682306 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682309 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682312 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... Waiting for PID 682315 of (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 15.792*4pi (198.446) --> -15 handles ICI = 134.7, FI = 1195.2, variation=19329.800 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 186 vertices thresholded to be in k1 ~ [-0.19 0.48], k2 ~ [-0.09 0.06] total integrated curvature = 0.709*4pi (8.907) --> 0 handles ICI = 1.5, FI = 7.7, variation=137.776 114 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 132 vertices thresholded to be in [-0.13 0.23] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.023 done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 16.726*4pi (210.184) --> -16 handles ICI = 131.0, FI = 1239.6, variation=19720.940 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 211 vertices thresholded to be in k1 ~ [-0.18 0.35], k2 ~ [-0.10 0.07] total integrated curvature = 0.688*4pi (8.644) --> 0 handles ICI = 1.5, FI = 7.1, variation=130.744 116 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 138 vertices thresholded to be in [-0.13 0.16] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.022 done. PIDs (682279 682283 682287 682290 682293 682296 682299 682302 682306 682309 682312 682315) completed and logs appended. #-------------------------------------------- #@# Sphere lh Fri Nov 22 14:54:14 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Fri Nov 22 14:54:14 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 682683 of (682683 682686) to complete... Waiting for PID 682686 of (682683 682686) 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 0.313... 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 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %18.91 pass 1: epoch 2 of 3 starting distance error %18.90 unfolding complete - removing small folds... starting distance error %18.87 removing remaining folds... final distance error %18.87 MRISunfold() return, current seed 1234 -01: dt=0.0000, 63 negative triangles VmPeak 773012 076: dt=0.9900, 63 negative triangles 077: dt=0.9900, 24 negative triangles 078: dt=0.9900, 14 negative triangles 079: dt=0.9900, 9 negative triangles 080: dt=0.9900, 9 negative triangles 081: dt=0.9900, 4 negative triangles 082: dt=0.9900, 9 negative triangles 083: dt=0.9900, 3 negative triangles 084: dt=0.9900, 5 negative triangles 085: dt=0.9900, 1 negative triangles 086: dt=0.9900, 2 negative triangles 087: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.0457 hours FSRUNTIME@ mris_sphere 0.0457 hours 4 threads #VMPC# mris_sphere VmPeak 773012 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 0.310... 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.32 pass 1: epoch 2 of 3 starting distance error %19.31 unfolding complete - removing small folds... starting distance error %19.25 removing remaining folds... final distance error %19.25 MRISunfold() return, current seed 1234 -01: dt=0.0000, 120 negative triangles VmPeak 773664 100: dt=0.9900, 120 negative triangles 101: dt=0.9900, 53 negative triangles 102: dt=0.9900, 20 negative triangles 103: dt=0.9900, 14 negative triangles 104: dt=0.9900, 7 negative triangles 105: dt=0.9900, 6 negative triangles 106: dt=0.9900, 4 negative triangles 107: dt=0.9900, 4 negative triangles 108: dt=0.9900, 1 negative triangles 109: dt=0.9900, 1 negative triangles 110: dt=0.9900, 2 negative triangles 111: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.0547 hours FSRUNTIME@ mris_sphere 0.0546 hours 4 threads #VMPC# mris_sphere VmPeak 773664 mris_sphere done PIDs (682683 682686) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Fri Nov 22 14:57:31 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Fri Nov 22 14:57:31 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 684261 of (684261 684264) to complete... Waiting for PID 684264 of (684261 684264) 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/PIB15-273_VYr9_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 = 5.429 curvature mean = 0.022, std = 0.824 curvature mean = 0.015, std = 0.883 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (5.50, -12.00, -2.00) sse = 183496.2, elapsed since starting=0.1323 min MRISrigidBodyAlignGlobal() done 0.13 min curvature mean = -0.004, std = 0.857 curvature mean = 0.006, std = 0.957 curvature mean = -0.006, std = 0.869 curvature mean = 0.002, std = 0.984 curvature mean = -0.006, std = 0.873 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.021, std = 0.254 curvature mean = 0.037, std = 0.252 curvature mean = 0.058, std = 0.414 curvature mean = 0.036, std = 0.311 curvature mean = 0.020, std = 0.637 curvature mean = 0.035, std = 0.338 curvature mean = 0.009, std = 0.776 curvature mean = 0.035, std = 0.350 curvature mean = 0.002, std = 0.868 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... -01: dt=0.0000, 0 negative triangles VmPeak 691268 registration took 0.06 hours #VMPC# mris_register VmPeak 691268 FSRUNTIME@ mris_register 0.0611 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/PIB15-273_VYr9_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 = 5.457 curvature mean = 0.021, std = 0.808 curvature mean = 0.016, std = 0.878 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (16.50, -8.50, 2.00) sse = 230425.8, elapsed since starting=0.1664 min MRISrigidBodyAlignGlobal() done 0.17 min curvature mean = 0.016, std = 0.846 curvature mean = 0.006, std = 0.955 curvature mean = 0.016, std = 0.858 curvature mean = 0.002, std = 0.983 curvature mean = 0.016, std = 0.861 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.022, std = 0.262 curvature mean = 0.038, std = 0.244 curvature mean = 0.061, std = 0.403 curvature mean = 0.036, std = 0.301 curvature mean = 0.025, std = 0.612 curvature mean = 0.035, std = 0.328 curvature mean = 0.011, std = 0.751 curvature mean = 0.035, std = 0.340 curvature mean = 0.002, std = 0.848 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... -01: dt=0.0000, 0 negative triangles VmPeak 773700 registration took 0.06 hours #VMPC# mris_register VmPeak 773700 FSRUNTIME@ mris_register 0.0637 hours 4 threads PIDs (684261 684264) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Fri Nov 22 15:01:20 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri Nov 22 15:01:20 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 699606 of (699606 699609) to complete... Waiting for PID 699609 of (699606 699609) 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 (699606 699609) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Fri Nov 22 15:01:21 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 Fri Nov 22 15:01:21 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 699679 of (699679 699682) to complete... Waiting for PID 699682 of (699679 699682) 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 (699679 699682) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Fri Nov 22 15:01:22 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Fri Nov 22 15:01:22 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 699885 of (699885 699888) to complete... Waiting for PID 699888 of (699885 699888) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 947 labels changed using aseg relabeling using gibbs priors... 000: 2740 changed, 113725 examined... 001: 642 changed, 11610 examined... 002: 140 changed, 3523 examined... 003: 40 changed, 867 examined... 004: 18 changed, 260 examined... 005: 12 changed, 119 examined... 006: 5 changed, 67 examined... 007: 3 changed, 32 examined... 008: 3 changed, 21 examined... 009: 2 changed, 16 examined... 010: 2 changed, 11 examined... 011: 1 changed, 9 examined... 012: 1 changed, 7 examined... 013: 0 changed, 7 examined... 218 labels changed using aseg 000: 90 total segments, 49 labels (167 vertices) changed 001: 43 total segments, 2 labels (2 vertices) changed 002: 41 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... 1541 vertices marked for relabeling... 1541 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 10 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 1006 labels changed using aseg relabeling using gibbs priors... 000: 2431 changed, 114467 examined... 001: 559 changed, 10641 examined... 002: 122 changed, 3176 examined... 003: 50 changed, 756 examined... 004: 19 changed, 291 examined... 005: 12 changed, 124 examined... 006: 5 changed, 77 examined... 007: 2 changed, 31 examined... 008: 2 changed, 14 examined... 009: 1 changed, 9 examined... 010: 1 changed, 8 examined... 011: 0 changed, 7 examined... 229 labels changed using aseg 000: 81 total segments, 36 labels (59 vertices) changed 001: 46 total segments, 1 labels (1 vertices) changed 002: 45 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... 1492 vertices marked for relabeling... 1492 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 11 seconds. PIDs (699885 699888) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Fri Nov 22 15:01:33 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 227446 0.33272 0.11509 0.000783 1.9143 Corner 682338 60.00000 13.82705 0.631326 177.8177 Edge 341169 0.88708 0.19271 0.027651 3.2709 Hinge 341169 10.90318 11.01197 0.000055 179.8996 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=22960, wmmin=5, clip=110 MRIfindBrightNonWM(): 473 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 8084/113725 vertices (105641 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 393 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56863: xyz = (-30.8459,2.32079,9.84438) oxyz = (-30.8459,2.32079,9.84438) wxzy = (-30.8459,2.32079,9.84438) pxyz = (0,0,0) CBVO Creating mask 113725 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4887310; border_low = 73.0000000; outside_low = 61.6644060; outside_hi = 110.4887310; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=2 had to be increased for 98 vertices, nripped=8477 mean border=83.4, 92 (92) missing vertices, mean dist 0.4 [1.8 (%12.9)->0.7 (%87.1))] %47 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0455 min Finding expansion regions mean absolute distance = 0.83 +- 1.11 3127 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=1432209.4, rms=7.784 001: dt: 0.5000, sse=625402.1, rms=4.733 (39.196%) 002: dt: 0.5000, sse=366997.4, rms=3.184 (32.724%) 003: dt: 0.5000, sse=296595.4, rms=2.604 (18.211%) 004: dt: 0.5000, sse=269125.6, rms=2.337 (10.286%) rms = 2.3537/2.3366, sse=271229.9/269125.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=217502.2, rms=1.713 (26.692%) 006: dt: 0.2500, sse=195086.7, rms=1.354 (20.972%) 007: dt: 0.2500, sse=189539.0, rms=1.246 (7.924%) rms = 1.2066/1.2464, sse=187802.4/189539.0, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=187802.4, rms=1.207 (3.195%) rms = 1.1781/1.2066, sse=186556.6/187802.4, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=186556.6, rms=1.178 (2.362%) 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 = 110.4887310; border_low = 73.0000000; outside_low = 61.6644060; outside_hi = 110.4887310; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=1 had to be increased for 52 vertices, nripped=8477 mean border=85.8, 63 (32) missing vertices, mean dist -0.3 [0.6 (%63.7)->0.2 (%36.3))] %57 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0336 min Finding expansion regions mean absolute distance = 0.45 +- 0.82 3116 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=496108.3, rms=3.940 010: dt: 0.5000, sse=298828.8, rms=2.484 (36.944%) 011: dt: 0.5000, sse=264440.9, rms=2.136 (14.004%) 012: dt: 0.5000, sse=259344.7, rms=2.079 (2.675%) rms = 2.2071/2.0792, sse=270499.1/259344.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=212923.3, rms=1.440 (30.755%) 014: dt: 0.2500, sse=195158.8, rms=1.099 (23.649%) 015: dt: 0.2500, sse=191829.9, rms=1.021 (7.094%) rms = 1.0047/1.0213, sse=191259.7/191829.9, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=191259.7, rms=1.005 (1.627%) rms = 0.9833/1.0047, sse=190388.4/191259.7, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=190388.4, rms=0.983 (2.131%) 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 = 110.4887310; border_low = 73.0000000; outside_low = 61.6644060; outside_hi = 110.4887310; 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=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 46 vertices, nripped=8477 mean border=88.6, 80 (22) missing vertices, mean dist -0.2 [0.4 (%70.6)->0.2 (%29.4))] %74 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0185 min Finding expansion regions mean absolute distance = 0.37 +- 0.53 3600 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=439754.8, rms=3.615 018: dt: 0.5000, sse=269820.4, rms=2.194 (39.315%) 019: dt: 0.5000, sse=254905.0, rms=2.051 (6.518%) rms = 2.1039/2.0508, sse=262097.0/254905.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=208558.8, rms=1.404 (31.525%) 021: dt: 0.2500, sse=189828.0, rms=1.030 (26.653%) 022: dt: 0.2500, sse=186817.0, rms=0.945 (8.226%) rms = 0.9311/0.9453, sse=185451.2/186816.9, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=185451.2, rms=0.931 (1.496%) rms = 0.9086/0.9311, sse=184613.8/185451.2, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=184613.8, rms=0.909 (2.416%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 110.4887310; border_low = 73.0000000; outside_low = 61.6644060; outside_hi = 110.4887310; 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=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 84 vertices, nripped=8477 mean border=89.7, 82 (19) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %81 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0143 min Finding expansion regions mean absolute distance = 0.28 +- 0.39 2782 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=230895.8, rms=1.799 025: dt: 0.5000, sse=205261.2, rms=1.315 (26.868%) rms = 1.6125/1.3154, sse=219692.0/205261.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=183797.8, rms=0.893 (32.123%) 027: dt: 0.2500, sse=177452.1, rms=0.747 (16.368%) rms = 0.7017/0.7467, sse=175495.5/177452.1, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=175495.5, rms=0.702 (6.030%) rms = 0.6924/0.7017, sse=175016.8/175495.5, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=175016.8, rms=0.692 (1.321%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 2.33 minutes #VMPC# mris_place_surfaces VmPeak 2033932 mris_place_surface done @#@FSTIME 2024:11:22:15:01:33 mris_place_surface N 25 e 147.97 S 2.17 U 279.52 P 190% M 1608928 F 2 R 1717653 W 0 c 25981 w 1977 I 0 O 8000 L 19.01 25.75 25.64 @#@FSLOADPOST 2024:11:22:15:04:01 mris_place_surface N 25 18.57 23.82 24.99 #-------------------------------------------- #@# WhiteSurfs rh Fri Nov 22 15:04:01 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 228930 0.33439 0.11654 0.002188 2.1436 Corner 686790 60.00000 13.90809 0.902962 175.0156 Edge 343395 0.88916 0.19300 0.035731 3.0559 Hinge 343395 10.61992 11.05488 0.000044 179.9575 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=22960, wmmin=5, clip=110 MRIfindBrightNonWM(): 473 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 7916/114467 vertices (106551 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 339 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 57234: xyz = (51.6062,7.09153,11.2992) oxyz = (51.6062,7.09153,11.2992) wxzy = (51.6062,7.09153,11.2992) pxyz = (0,0,0) CBVO Creating mask 114467 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4887310; border_low = 74.0000000; outside_low = 62.6644060; outside_hi = 109.4887310; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=2 had to be increased for 101 vertices, nripped=8255 mean border=83.4, 82 (82) missing vertices, mean dist 0.4 [1.8 (%11.4)->0.7 (%88.6))] %41 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0367 min Finding expansion regions mean absolute distance = 0.78 +- 1.01 2611 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=1469653.1, rms=7.844 001: dt: 0.5000, sse=610001.4, rms=4.617 (41.145%) 002: dt: 0.5000, sse=349682.6, rms=3.002 (34.979%) 003: dt: 0.5000, sse=287543.2, rms=2.473 (17.601%) 004: dt: 0.5000, sse=265337.9, rms=2.245 (9.227%) rms = 2.2840/2.2452, sse=268916.5/265337.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=218587.0, rms=1.674 (25.437%) 006: dt: 0.2500, sse=199129.8, rms=1.359 (18.797%) 007: dt: 0.2500, sse=194453.8, rms=1.267 (6.814%) rms = 1.2344/1.2668, sse=192575.9/194453.8, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=192575.9, rms=1.234 (2.558%) rms = 1.2092/1.2344, sse=191450.5/192575.9, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=191450.5, rms=1.209 (2.037%) 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 = 109.4887310; border_low = 74.0000000; outside_low = 62.6644060; outside_hi = 109.4887310; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=1 had to be increased for 65 vertices, nripped=8255 mean border=85.7, 40 (12) missing vertices, mean dist -0.3 [0.5 (%63.6)->0.2 (%36.4))] %54 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0337 min Finding expansion regions mean absolute distance = 0.41 +- 0.75 3038 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=477623.7, rms=3.798 010: dt: 0.5000, sse=295730.4, rms=2.410 (36.539%) 011: dt: 0.5000, sse=263860.4, rms=2.064 (14.347%) 012: dt: 0.5000, sse=256528.3, rms=1.989 (3.626%) rms = 2.1250/1.9894, sse=265429.0/256528.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=214062.2, rms=1.400 (29.607%) 014: dt: 0.2500, sse=197127.3, rms=1.102 (21.320%) 015: dt: 0.2500, sse=195757.8, rms=1.038 (5.815%) rms = 1.0287/1.0378, sse=194527.8/195757.8, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=194527.8, rms=1.029 (0.872%) rms = 1.0108/1.0287, sse=193890.3/194527.8, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=193890.3, rms=1.011 (1.740%) 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 = 109.4887310; border_low = 74.0000000; outside_low = 62.6644060; outside_hi = 109.4887310; 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=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 70 vertices, nripped=8255 mean border=88.7, 45 (9) missing vertices, mean dist -0.2 [0.4 (%73.6)->0.2 (%26.4))] %74 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0181 min Finding expansion regions mean absolute distance = 0.33 +- 0.46 3243 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=479462.0, rms=3.832 018: dt: 0.5000, sse=274231.9, rms=2.176 (43.204%) 019: dt: 0.5000, sse=255668.7, rms=2.018 (7.257%) rms = 2.0845/2.0185, sse=261399.4/255668.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=210068.8, rms=1.380 (31.645%) 021: dt: 0.2500, sse=192145.8, rms=1.023 (25.886%) 022: dt: 0.2500, sse=189894.1, rms=0.957 (6.403%) rms = 0.9493/0.9571, sse=188940.6/189894.1, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=188940.6, rms=0.949 (0.811%) rms = 0.9292/0.9493, sse=188025.1/188940.6, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=188025.1, rms=0.929 (2.116%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 109.4887310; border_low = 74.0000000; outside_low = 62.6644060; outside_hi = 109.4887310; 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=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 81 vertices, nripped=8255 mean border=89.8, 69 (7) missing vertices, mean dist -0.1 [0.3 (%60.3)->0.2 (%39.7))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0114 min Finding expansion regions mean absolute distance = 0.24 +- 0.35 2914 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=228218.7, rms=1.715 025: dt: 0.5000, sse=212552.3, rms=1.368 (20.247%) rms = 1.6685/1.3679, sse=225967.7/212552.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=187694.7, rms=0.922 (32.625%) 027: dt: 0.2500, sse=181027.9, rms=0.778 (15.548%) 028: dt: 0.2500, sse=178849.0, rms=0.724 (6.976%) rms = 0.7427/0.7240, sse=178799.3/178849.0, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.7188/0.7240, sse=178328.6/178849.0, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=178328.5, rms=0.719 (0.718%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 2.35 minutes #VMPC# mris_place_surfaces VmPeak 2046852 mris_place_surface done @#@FSTIME 2024:11:22:15:04:02 mris_place_surface N 25 e 147.83 S 2.24 U 267.79 P 182% M 1622084 F 2 R 2406654 W 0 c 25052 w 1741 I 0 O 8056 L 18.57 23.82 24.99 @#@FSLOADPOST 2024:11:22:15:06:29 mris_place_surface N 25 32.00 26.09 25.59 #-------------------------------------------- #@# T1PialSurf lh Fri Nov 22 15:06:29 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 227446 0.33409 0.12764 0.000783 2.1059 Corner 682338 60.00000 15.17165 0.331715 178.8057 Edge 341169 0.89026 0.21067 0.025188 3.5854 Hinge 341169 10.95166 11.09401 0.000050 179.9422 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=22960, wmmin=5, clip=110 MRIfindBrightNonWM(): 473 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 67.2522 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 5893/113725 vertices (107832 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 56863: xyz = (-30.7537,2.31681,9.85973) oxyz = (-30.7537,2.31681,9.85973) wxzy = (-30.7537,2.31681,9.85973) pxyz = (-30.7537,2.31681,9.85973) CBVO Creating mask 113725 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5112690; border_hi = 61.6644060; border_low = 38.9932170; outside_low = 10.0000000; outside_hi = 55.9966090; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=2 had to be increased for 124 vertices, nripped=5893 mean border=58.9, 147 (147) missing vertices, mean dist 1.9 [2.2 (%0.0)->2.6 (%100.0))] %23 local maxima, %47 large gradients and %24 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0400 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=21525518.0, rms=31.497 001: dt: 0.5000, sse=16053673.0, rms=27.166 (13.751%) 002: dt: 0.5000, sse=11853781.0, rms=23.301 (14.227%) 003: dt: 0.5000, sse=8813191.0, rms=20.042 (13.986%) 004: dt: 0.5000, sse=6676224.0, rms=17.389 (13.239%) 005: dt: 0.5000, sse=5101922.0, rms=15.138 (12.941%) 006: dt: 0.5000, sse=3820111.2, rms=13.021 (13.986%) 007: dt: 0.5000, sse=2793314.8, rms=11.035 (15.254%) 008: dt: 0.5000, sse=1991967.2, rms=9.190 (16.719%) 009: dt: 0.5000, sse=1430536.5, rms=7.636 (16.915%) 010: dt: 0.5000, sse=1056832.0, rms=6.393 (16.270%) 011: dt: 0.5000, sse=842838.3, rms=5.556 (13.088%) 012: dt: 0.5000, sse=722174.9, rms=5.023 (9.609%) 013: dt: 0.5000, sse=664381.5, rms=4.744 (5.553%) 014: dt: 0.5000, sse=626229.3, rms=4.549 (4.098%) 015: dt: 0.5000, sse=611315.9, rms=4.469 (1.773%) 016: dt: 0.5000, sse=594008.8, rms=4.374 (2.114%) rms = 4.3420/4.3741, sse=588567.3/594008.7, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=588567.3, rms=4.342 (0.734%) 018: dt: 0.2500, sse=399815.0, rms=3.146 (27.550%) 019: dt: 0.2500, sse=358957.8, rms=2.824 (10.231%) 020: dt: 0.2500, sse=348907.8, rms=2.737 (3.078%) 021: dt: 0.2500, sse=342726.2, rms=2.683 (1.986%) rms = 2.6608/2.6826, sse=340379.2/342726.3, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=340379.2, rms=2.661 (0.814%) 023: dt: 0.1250, sse=323612.6, rms=2.507 (5.798%) rms = 2.4803/2.5066, sse=320884.5/323612.6, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=320884.5, rms=2.480 (1.049%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 95.5112690; border_hi = 61.6644060; border_low = 38.9932170; outside_low = 10.0000000; outside_hi = 55.9966090; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=1 had to be increased for 4715 vertices, nripped=5893 mean border=56.7, 755 (10) missing vertices, mean dist 0.2 [0.1 (%43.2)->0.4 (%56.8))] %40 local maxima, %36 large gradients and %19 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0127 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=589533.3, rms=4.141 025: dt: 0.5000, sse=543713.1, rms=3.869 (6.563%) rms = 4.0330/3.8692, sse=568213.8/543713.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=421670.1, rms=3.049 (21.194%) 027: dt: 0.2500, sse=378779.2, rms=2.707 (11.233%) 028: dt: 0.2500, sse=367297.5, rms=2.605 (3.761%) rms = 2.5760/2.6048, sse=364070.1/367297.5, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=364070.1, rms=2.576 (1.108%) 030: dt: 0.1250, sse=348589.0, rms=2.429 (5.725%) rms = 2.3978/2.4285, sse=345455.0/348589.0, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=345454.9, rms=2.398 (1.264%) 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 = 95.5112690; border_hi = 61.6644060; border_low = 38.9932170; outside_low = 10.0000000; outside_hi = 55.9966090; 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=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 5434 vertices, nripped=5893 mean border=55.5, 978 (8) missing vertices, mean dist 0.1 [0.1 (%45.4)->0.3 (%54.6))] %51 local maxima, %24 large gradients and %19 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0088 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=422442.4, rms=3.027 rms = 3.6930/3.0265, sse=519454.9/422442.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=371922.4, rms=2.607 (13.867%) 033: dt: 0.2500, sse=359162.4, rms=2.489 (4.521%) rms = 2.4749/2.4890, sse=357398.9/359162.4, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=357398.9, rms=2.475 (0.566%) 035: dt: 0.1250, sse=347133.8, rms=2.374 (4.063%) rms = 2.3533/2.3743, sse=344960.0/347133.9, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=344960.0, rms=2.353 (0.887%) 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 = 95.5112690; border_hi = 61.6644060; border_low = 38.9932170; outside_low = 10.0000000; outside_hi = 55.9966090; 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=113725 Gdiag_no=-1 vno start=0, stop=113725 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 4704 vertices, nripped=5893 mean border=54.7, 2045 (7) missing vertices, mean dist 0.1 [0.1 (%48.7)->0.3 (%51.3))] %55 local maxima, %19 large gradients and %18 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0052 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=368153.9, rms=2.571 rms = 3.1729/2.5708, sse=442187.1/368153.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=348883.2, rms=2.388 (7.096%) rms = 2.3491/2.3884, sse=344552.4/348883.2, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=344552.4, rms=2.349 (1.646%) 039: dt: 0.1250, sse=338475.8, rms=2.287 (2.637%) rms = 2.2635/2.2871, sse=336026.1/338475.8, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=336026.1, rms=2.264 (1.033%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 17 intersecting 001: 7 intersecting 002: 2 intersecting step 1 with no progress (num=4, old_num=2) 003: 4 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 2.58 minutes #VMPC# mris_place_surfaces VmPeak 1414100 mris_place_surface done @#@FSTIME 2024:11:22:15:06:29 mris_place_surface N 28 e 162.39 S 1.91 U 312.24 P 193% M 976748 F 2 R 2004179 W 0 c 29326 w 1904 I 0 O 8000 L 32.00 26.09 25.59 @#@FSLOADPOST 2024:11:22:15:09:12 mris_place_surface N 28 27.10 26.87 26.00 #-------------------------------------------- #@# T1PialSurf rh Fri Nov 22 15:09:12 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 228930 0.33645 0.12928 0.000510 2.5374 Corner 686790 60.00000 15.20867 0.228557 178.9709 Edge 343395 0.89332 0.21120 0.025965 3.0559 Hinge 343395 10.66932 11.06478 0.000037 179.8298 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=22960, wmmin=5, clip=110 MRIfindBrightNonWM(): 473 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 67.2522 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 6000/114467 vertices (108467 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 57234: xyz = (51.8045,6.9522,11.2346) oxyz = (51.8045,6.9522,11.2346) wxzy = (51.8045,6.9522,11.2346) pxyz = (51.8045,6.9522,11.2346) CBVO Creating mask 114467 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.5112690; border_hi = 62.6644060; border_low = 39.9932170; outside_low = 10.0000000; outside_hi = 56.9966090; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=2 had to be increased for 134 vertices, nripped=6000 mean border=59.5, 137 (137) missing vertices, mean dist 2.0 [1.6 (%0.0)->2.5 (%100.0))] %24 local maxima, %51 large gradients and %20 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0403 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=20803460.0, rms=30.866 001: dt: 0.5000, sse=15323981.0, rms=26.454 (14.295%) 002: dt: 0.5000, sse=11198616.0, rms=22.569 (14.685%) 003: dt: 0.5000, sse=8262567.5, rms=19.333 (14.337%) 004: dt: 0.5000, sse=6225332.5, rms=16.723 (13.502%) 005: dt: 0.5000, sse=4743640.5, rms=14.532 (13.103%) 006: dt: 0.5000, sse=3537910.8, rms=12.467 (14.210%) 007: dt: 0.5000, sse=2587205.2, rms=10.557 (15.322%) 008: dt: 0.5000, sse=1866920.9, rms=8.837 (16.288%) 009: dt: 0.5000, sse=1362017.2, rms=7.396 (16.307%) 010: dt: 0.5000, sse=1033726.6, rms=6.282 (15.057%) 011: dt: 0.5000, sse=852882.2, rms=5.573 (11.288%) 012: dt: 0.5000, sse=746474.7, rms=5.109 (8.339%) 013: dt: 0.5000, sse=690131.9, rms=4.842 (5.209%) 014: dt: 0.5000, sse=651153.2, rms=4.649 (3.997%) 015: dt: 0.5000, sse=632835.1, rms=4.554 (2.051%) 016: dt: 0.5000, sse=616488.1, rms=4.467 (1.905%) rms = 4.4211/4.4668, sse=608363.2/616488.1, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=608363.2, rms=4.421 (1.021%) 018: dt: 0.2500, sse=401426.2, rms=3.133 (29.145%) 019: dt: 0.2500, sse=357166.9, rms=2.784 (11.125%) 020: dt: 0.2500, sse=346280.8, rms=2.689 (3.399%) rms = 2.6419/2.6895, sse=340884.6/346280.8, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=340884.6, rms=2.642 (1.769%) 022: dt: 0.1250, sse=319004.4, rms=2.439 (7.675%) rms = 2.4060/2.4391, sse=315614.9/319004.4, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=315614.9, rms=2.406 (1.357%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.5112690; border_hi = 62.6644060; border_low = 39.9932170; outside_low = 10.0000000; outside_hi = 56.9966090; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=1 had to be increased for 3421 vertices, nripped=6000 mean border=57.0, 595 (25) missing vertices, mean dist 0.2 [0.1 (%41.5)->0.4 (%58.5))] %43 local maxima, %36 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0216 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=658121.2, rms=4.475 024: dt: 0.5000, sse=573633.6, rms=4.009 (10.415%) rms = 4.1235/4.0089, sse=590412.0/573633.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=430435.5, rms=3.075 (23.289%) 026: dt: 0.2500, sse=381641.9, rms=2.688 (12.598%) 027: dt: 0.2500, sse=369453.0, rms=2.579 (4.034%) rms = 2.5317/2.5794, sse=364144.6/369453.0, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=364144.7, rms=2.532 (1.849%) 029: dt: 0.1250, sse=347102.4, rms=2.368 (6.479%) rms = 2.3374/2.3677, sse=344066.0/347102.4, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=344066.0, rms=2.337 (1.280%) 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 = 94.5112690; border_hi = 62.6644060; border_low = 39.9932170; outside_low = 10.0000000; outside_hi = 56.9966090; 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=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 3877 vertices, nripped=6000 mean border=55.3, 841 (17) missing vertices, mean dist 0.1 [0.1 (%39.1)->0.3 (%60.9))] %58 local maxima, %21 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0079 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=466804.1, rms=3.307 rms = 4.1043/3.3075, sse=595954.0/466804.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=383069.1, rms=2.656 (19.706%) 032: dt: 0.2500, sse=362097.8, rms=2.464 (7.230%) rms = 2.4152/2.4637, sse=356552.5/362097.8, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=356552.5, rms=2.415 (1.967%) 034: dt: 0.1250, sse=344245.5, rms=2.292 (5.093%) rms = 2.2667/2.2922, sse=341709.3/344245.5, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=341709.3, rms=2.267 (1.114%) 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 = 94.5112690; border_hi = 62.6644060; border_low = 39.9932170; outside_low = 10.0000000; outside_hi = 56.9966090; 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=114467 Gdiag_no=-1 vno start=0, stop=114467 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 3542 vertices, nripped=6000 mean border=54.5, 1559 (14) missing vertices, mean dist 0.1 [0.2 (%45.8)->0.2 (%54.2))] %63 local maxima, %16 large gradients and %15 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0055 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=368482.2, rms=2.523 rms = 3.3353/2.5227, sse=471623.9/368482.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=344996.2, rms=2.295 (9.022%) rms = 2.2572/2.2951, sse=341051.6/344996.2, time step reduction 2 of 3 to 0.125 0 0 1 037: dt: 0.2500, sse=341051.6, rms=2.257 (1.654%) 038: dt: 0.1250, sse=335243.2, rms=2.196 (2.704%) rms = 2.1727/2.1961, sse=332863.7/335243.2, time step reduction 3 of 3 to 0.062 0 0 1 039: dt: 0.1250, sse=332863.7, rms=2.173 (1.065%) maximum number of reductions reached, breaking from loop positioning took 0.2 minutes Pinning medial wall to white surface removing intersecting faces 000: 19 intersecting 001: 12 intersecting 002: 5 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 2.45 minutes #VMPC# mris_place_surfaces VmPeak 1419452 mris_place_surface done @#@FSTIME 2024:11:22:15:09:12 mris_place_surface N 28 e 154.41 S 1.21 U 296.71 P 192% M 982832 F 2 R 975983 W 0 c 27281 w 1940 I 0 O 8056 L 27.10 26.87 26.00 @#@FSLOADPOST 2024:11:22:15:11:46 mris_place_surface N 28 27.78 27.25 26.27 #@# white curv lh Fri Nov 22 15:11:46 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:15:11:46 mris_place_surface N 5 e 1.78 S 0.11 U 2.16 P 128% M 157320 F 2 R 42356 W 0 c 215 w 126 I 0 O 896 L 27.78 27.25 26.27 @#@FSLOADPOST 2024:11:22:15:11:48 mris_place_surface N 5 27.78 27.25 26.27 #@# white area lh Fri Nov 22 15:11:48 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2024:11:22:15:11:48 mris_place_surface N 3 e 0.76 S 0.07 U 1.21 P 170% M 157056 F 1 R 42256 W 0 c 118 w 103 I 0 O 896 L 27.78 27.25 26.27 @#@FSLOADPOST 2024:11:22:15:11:49 mris_place_surface N 3 27.78 27.25 26.27 #@# pial curv lh Fri Nov 22 15:11:49 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:15:11:49 mris_place_surface N 5 e 2.05 S 0.08 U 2.46 P 124% M 157276 F 2 R 42381 W 0 c 242 w 106 I 0 O 896 L 27.78 27.25 26.27 @#@FSLOADPOST 2024:11:22:15:11:51 mris_place_surface N 5 28.20 27.35 26.31 #@# pial area lh Fri Nov 22 15:11:51 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2024:11:22:15:11:51 mris_place_surface N 3 e 0.72 S 0.09 U 1.12 P 167% M 157148 F 1 R 42331 W 0 c 117 w 112 I 0 O 896 L 28.20 27.35 26.31 @#@FSLOADPOST 2024:11:22:15:11:52 mris_place_surface N 3 28.20 27.35 26.31 #@# thickness lh Fri Nov 22 15:11:52 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 113725 vertices processed 25000 of 113725 vertices processed 50000 of 113725 vertices processed 75000 of 113725 vertices processed 100000 of 113725 vertices processed 0 of 113725 vertices processed 25000 of 113725 vertices processed 50000 of 113725 vertices processed 75000 of 113725 vertices processed 100000 of 113725 vertices processed thickness calculation complete, 53:373 truncations. 54863 vertices at 0 distance 99713 vertices at 1 distance 48594 vertices at 2 distance 16038 vertices at 3 distance 5221 vertices at 4 distance 1811 vertices at 5 distance 688 vertices at 6 distance 298 vertices at 7 distance 111 vertices at 8 distance 45 vertices at 9 distance 15 vertices at 10 distance 7 vertices at 11 distance 9 vertices at 12 distance 12 vertices at 13 distance 11 vertices at 14 distance 3 vertices at 15 distance 6 vertices at 16 distance 3 vertices at 17 distance 2 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2024:11:22:15:11:52 mris_place_surface N 6 e 30.24 S 0.20 U 30.73 P 102% M 157484 F 1 R 142204 W 0 c 2852 w 177 I 0 O 896 L 28.20 27.35 26.31 @#@FSLOADPOST 2024:11:22:15:12:22 mris_place_surface N 6 27.85 27.34 26.34 #@# area and vertex vol lh Fri Nov 22 15:12:22 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Total face volume 188510 Total vertex volume 188303 (mask=0) #@# PIB15-273_VYr9_Bay3prisma lh 188303 vertexvol Done @#@FSTIME 2024:11:22:15:12:22 vertexvol N 4 e 1.58 S 0.18 U 2.02 P 139% M 261256 F 3 R 77372 W 0 c 211 w 361 I 0 O 2688 L 27.85 27.34 26.34 @#@FSLOADPOST 2024:11:22:15:12:24 vertexvol N 4 27.85 27.34 26.34 #@# white curv rh Fri Nov 22 15:12:24 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:15:12:24 mris_place_surface N 5 e 1.88 S 0.08 U 2.33 P 128% M 158132 F 1 R 42595 W 0 c 233 w 100 I 0 O 896 L 27.85 27.34 26.34 @#@FSLOADPOST 2024:11:22:15:12:26 mris_place_surface N 5 27.86 27.36 26.35 #@# white area rh Fri Nov 22 15:12:26 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2024:11:22:15:12:26 mris_place_surface N 3 e 0.73 S 0.09 U 1.03 P 153% M 158360 F 1 R 42606 W 0 c 109 w 110 I 0 O 896 L 27.86 27.36 26.35 @#@FSLOADPOST 2024:11:22:15:12:27 mris_place_surface N 3 27.86 27.36 26.35 #@# pial curv rh Fri Nov 22 15:12:27 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 2024:11:22:15:12:27 mris_place_surface N 5 e 1.63 S 0.11 U 2.08 P 133% M 158180 F 2 R 42596 W 0 c 197 w 118 I 0 O 896 L 27.86 27.36 26.35 @#@FSLOADPOST 2024:11:22:15:12:28 mris_place_surface N 5 27.86 27.36 26.35 #@# pial area rh Fri Nov 22 15:12:28 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2024:11:22:15:12:28 mris_place_surface N 3 e 0.74 S 0.13 U 1.07 P 162% M 158360 F 2 R 42674 W 0 c 115 w 99 I 0 O 896 L 27.86 27.36 26.35 @#@FSLOADPOST 2024:11:22:15:12:29 mris_place_surface N 3 27.86 27.36 26.35 #@# thickness rh Fri Nov 22 15:12:29 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 114467 vertices processed 25000 of 114467 vertices processed 50000 of 114467 vertices processed 75000 of 114467 vertices processed 100000 of 114467 vertices processed 0 of 114467 vertices processed 25000 of 114467 vertices processed 50000 of 114467 vertices processed 75000 of 114467 vertices processed 100000 of 114467 vertices processed thickness calculation complete, 36:329 truncations. 61148 vertices at 0 distance 101818 vertices at 1 distance 45971 vertices at 2 distance 13779 vertices at 3 distance 4151 vertices at 4 distance 1266 vertices at 5 distance 433 vertices at 6 distance 155 vertices at 7 distance 76 vertices at 8 distance 48 vertices at 9 distance 31 vertices at 10 distance 16 vertices at 11 distance 7 vertices at 12 distance 10 vertices at 13 distance 3 vertices at 14 distance 6 vertices at 15 distance 6 vertices at 16 distance 4 vertices at 17 distance 3 vertices at 18 distance 2 vertices at 19 distance 1 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2024:11:22:15:12:29 mris_place_surface N 6 e 30.23 S 0.21 U 30.65 P 102% M 158300 F 2 R 150916 W 0 c 2872 w 129 I 0 O 896 L 27.86 27.36 26.35 @#@FSLOADPOST 2024:11:22:15:12:59 mris_place_surface N 6 28.44 27.52 26.44 #@# area and vertex vol rh Fri Nov 22 15:12:59 CST 2024 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.volume masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Total face volume 189470 Total vertex volume 189264 (mask=0) #@# PIB15-273_VYr9_Bay3prisma rh 189264 vertexvol Done @#@FSTIME 2024:11:22:15:13:00 vertexvol N 4 e 1.84 S 0.21 U 2.26 P 134% M 262788 F 3 R 74930 W 0 c 240 w 383 I 0 O 2688 L 28.44 27.52 26.44 @#@FSLOADPOST 2024:11:22:15:13:01 vertexvol N 4 28.88 27.63 26.48 #----------------------------------------- #@# Curvature Stats lh Fri Nov 22 15:13:01 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PIB15-273_VYr9_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 [ PIB15-273_VYr9_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 [ 199 ] Gb_filter = 0 WARN: S lookup min: -0.054086 WARN: S explicit min: 0.000000 vertex = 495 @#@FSTIME 2024:11:22:15:13:01 mris_curvature_stats N 11 e 2.62 S 0.19 U 3.05 P 123% M 157340 F 2 R 73640 W 0 c 305 w 429 I 0 O 7208 L 28.88 27.63 26.48 @#@FSLOADPOST 2024:11:22:15:13:04 mris_curvature_stats N 11 28.88 27.63 26.48 #----------------------------------------- #@# Curvature Stats rh Fri Nov 22 15:13:04 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PIB15-273_VYr9_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 [ PIB15-273_VYr9_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 [ 164 ] Gb_filter = 0 WARN: S lookup min: -0.095658 WARN: S explicit min: 0.000000 vertex = 510 @#@FSTIME 2024:11:22:15:13:04 mris_curvature_stats N 11 e 2.76 S 0.24 U 3.08 P 120% M 158140 F 2 R 74161 W 0 c 314 w 449 I 0 O 7208 L 28.88 27.63 26.48 @#@FSLOADPOST 2024:11:22:15:13:07 mris_curvature_stats N 11 28.41 27.55 26.46 #-------------------------------------------- #@# Cortical ribbon mask Fri Nov 22 15:13:07 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 = 30 writing volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz mris_volmask took 6.14 minutes writing ribbon files @#@FSTIME 2024:11:22:15:13:07 mris_volmask N 12 e 368.39 S 1.52 U 368.79 P 100% M 897668 F 2 R 1258851 W 0 c 34181 w 313 I 0 O 752 L 28.41 27.55 26.46 @#@FSLOADPOST 2024:11:22:15:19:15 mris_volmask N 12 27.70 28.27 27.27 #----------------------------------------- #@# Cortical Parc 2 lh Fri Nov 22 15:19:15 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Fri Nov 22 15:19:15 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 829312 of (829312 829316) to complete... Waiting for PID 829316 of (829312 829316) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 99 labels changed using aseg relabeling using gibbs priors... 000: 7575 changed, 113725 examined... 001: 1786 changed, 29622 examined... 002: 545 changed, 9498 examined... 003: 229 changed, 3130 examined... 004: 113 changed, 1335 examined... 005: 57 changed, 655 examined... 006: 33 changed, 336 examined... 007: 12 changed, 174 examined... 008: 7 changed, 81 examined... 009: 6 changed, 45 examined... 010: 4 changed, 39 examined... 011: 4 changed, 28 examined... 012: 4 changed, 26 examined... 013: 2 changed, 19 examined... 014: 2 changed, 13 examined... 015: 1 changed, 8 examined... 016: 1 changed, 7 examined... 017: 2 changed, 8 examined... 018: 0 changed, 14 examined... 72 labels changed using aseg 000: 193 total segments, 111 labels (886 vertices) changed 001: 84 total segments, 2 labels (4 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1095 vertices marked for relabeling... 1095 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 14 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 49 labels changed using aseg relabeling using gibbs priors... 000: 7794 changed, 114467 examined... 001: 1792 changed, 30610 examined... 002: 562 changed, 9607 examined... 003: 218 changed, 3271 examined... 004: 90 changed, 1296 examined... 005: 47 changed, 512 examined... 006: 22 changed, 272 examined... 007: 16 changed, 141 examined... 008: 6 changed, 91 examined... 009: 5 changed, 32 examined... 010: 1 changed, 29 examined... 011: 0 changed, 7 examined... 49 labels changed using aseg 000: 231 total segments, 136 labels (1585 vertices) changed 001: 99 total segments, 9 labels (28 vertices) changed 002: 90 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 41 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1026 vertices marked for relabeling... 1026 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 14 seconds. PIDs (829312 829316) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Fri Nov 22 15:19:30 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 Fri Nov 22 15:19:30 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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 829564 of (829564 829567) to complete... Waiting for PID 829567 of (829564 829567) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 1208 labels changed using aseg relabeling using gibbs priors... 000: 1723 changed, 113725 examined... 001: 403 changed, 8166 examined... 002: 114 changed, 2288 examined... 003: 62 changed, 663 examined... 004: 41 changed, 333 examined... 005: 22 changed, 205 examined... 006: 20 changed, 127 examined... 007: 22 changed, 100 examined... 008: 17 changed, 97 examined... 009: 13 changed, 81 examined... 010: 8 changed, 62 examined... 011: 11 changed, 51 examined... 012: 10 changed, 59 examined... 013: 7 changed, 51 examined... 014: 6 changed, 31 examined... 015: 3 changed, 28 examined... 016: 2 changed, 17 examined... 017: 1 changed, 10 examined... 018: 1 changed, 7 examined... 019: 1 changed, 6 examined... 020: 0 changed, 8 examined... 412 labels changed using aseg 000: 52 total segments, 19 labels (80 vertices) changed 001: 33 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... 729 vertices marked for relabeling... 729 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PIB15-273_VYr9_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... 1276 labels changed using aseg relabeling using gibbs priors... 000: 1756 changed, 114467 examined... 001: 395 changed, 8250 examined... 002: 137 changed, 2288 examined... 003: 73 changed, 791 examined... 004: 40 changed, 400 examined... 005: 20 changed, 220 examined... 006: 16 changed, 105 examined... 007: 16 changed, 67 examined... 008: 11 changed, 82 examined... 009: 10 changed, 61 examined... 010: 11 changed, 58 examined... 011: 6 changed, 55 examined... 012: 7 changed, 33 examined... 013: 5 changed, 36 examined... 014: 5 changed, 35 examined... 015: 6 changed, 30 examined... 016: 2 changed, 27 examined... 017: 1 changed, 15 examined... 018: 1 changed, 8 examined... 019: 1 changed, 7 examined... 020: 1 changed, 7 examined... 021: 1 changed, 7 examined... 022: 1 changed, 8 examined... 023: 0 changed, 7 examined... 386 labels changed using aseg 000: 47 total segments, 14 labels (35 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 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... 795 vertices marked for relabeling... 795 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. PIDs (829564 829567) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Fri Nov 22 15:19:41 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts pctsurfcon --s PIB15-273_VYr9_Bay3prisma --lh-only #----------------------------------------- #@# WM/GM Contrast rh Fri Nov 22 15:19:41 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts pctsurfcon --s PIB15-273_VYr9_Bay3prisma --rh-only Waiting for PID 829740 of (829740 829743) to complete... Waiting for PID 829743 of (829740 829743) to complete... pctsurfcon --s PIB15-273_VYr9_Bay3prisma --lh-only Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts/pctsurfcon.log Fri Nov 22 15:19:41 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829740/lh.wm.mgh --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 72831 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829740/lh.wm.mgh Dim: 113725 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829740/lh.gm.mgh --projfrac 0.3 --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 86269 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829740/lh.gm.mgh Dim: 113725 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829740/lh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829740/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/stats/lh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma lh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Seg base 1000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.w-g.pct.mgh Vertex Area is 0.668161 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 PIB15-273_VYr9_Bay3prisma --rh-only mv: cannot stat '/data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts/pctsurfcon.log': No such file or directory Log file is /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/scripts/pctsurfcon.log Fri Nov 22 15:19:41 CST 2024 setenv SUBJECTS_DIR /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829743/rh.wm.mgh --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 73724 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829743/rh.wm.mgh Dim: 114467 1 1 mri_vol2surf --mov /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829743/rh.gm.mgh --projfrac 0.3 --regheader PIB15-273_VYr9_Bay3prisma --cortex srcvol = /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/orig.mgz as target reference. -------- original matrix ----------- -0.06828 0.99745 -0.02076 0.00005; -0.99714 -0.06890 -0.03106 -0.00002; -0.03241 0.01858 0.99930 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Reading surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Done reading source surface Reading thickness /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 = 87691 Masking with /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Writing to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829743/rh.gm.mgh Dim: 114467 1 1 mri_concat /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829743/rh.wm.mgh /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/tmp.pctsurfcon.829743/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/stats/rh.w-g.pct.stats --snr 7.3.2 cwd cmdline mri_segstats --in /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh --annot PIB15-273_VYr9_Bay3prisma rh aparc --sum /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Seg base 2000 Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.w-g.pct.mgh Vertex Area is 0.672885 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 (829740 829743) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Fri Nov 22 15:19:46 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1165 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1786 voxels changed to hypointensity... 2938 hypointense voxels neighboring cortex changed @#@FSTIME 2024:11:22:15:19:46 mri_relabel_hypointensities N 3 e 17.13 S 0.68 U 18.34 P 111% M 444456 F 4 R 522973 W 0 c 1734 w 151 I 0 O 608 L 28.64 28.45 27.36 @#@FSLOADPOST 2024:11:22:15:20:03 mri_relabel_hypointensities N 3 28.80 28.50 27.39 #----------------------------------------- #@# APas-to-ASeg Fri Nov 22 15:20:03 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz --threads 4 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/mri/ribbon.mgz Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Done loading 0 64 128 192 193 65 1 194 66 2 195 67 3 196 68 4 129 197 69 5 198 70 6 199 200 71 7 201 8 72 202 9 130 203 73 10 204 205 11 74 206 12 207 75 13 208 131 14 209 76 210 15 211 16 212 77 17 213 214 18 215 132 19 78 216 20 217 79 218 21 219 22 220 80 23 133 221 222 24 81 223 25 224 82 26 225 134 27 226 83 227 28 228 29 135 229 84 30 230 231 31 85 232 32 136 233 33 86 234 34 235 87 236 35 137 237 36 238 88 239 37 240 38 89 241 39 242 40 138 243 41 90 244 42 245 43 139 246 44 247 45 248 91 46 249 140 47 250 251 48 252 49 253 50 254 92 51 255 141 52 53 54 93 55 142 56 57 58 94 59 143 60 61 95 62 144 63 96 145 97 146 147 98 148 99 149 100 150 151 101 152 102 153 103 154 155 104 156 105 157 106 158 107 159 160 108 161 109 162 110 163 164 111 165 112 166 167 113 168 169 170 114 171 172 173 115 174 175 176 116 177 178 179 117 180 181 182 118 183 184 185 186 119 187 188 189 190 120 191 121 122 123 124 125 126 127 nrelabeled = 91834 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 987100 mri_surf2volseg done @#@FSTIME 2024:11:22:15:20:03 mri_surf2volseg N 20 e 8.25 S 1.08 U 15.01 P 195% M 799736 F 2 R 511737 W 0 c 1501 w 4072 I 0 O 632 L 28.80 28.50 27.39 @#@FSLOADPOST 2024:11:22:15:20:11 mri_surf2volseg N 20 27.37 28.21 27.31 mri_brainvol_stats PIB15-273_VYr9_Bay3prisma ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1434297.0 #CBVS2 BrainSegVol 945070.0 #CBVS2 BrainSegVolNotVent 918320.0 #CBVS2 SupraTentVol 827595.0 #CBVS2 SupraTentVolNotVent 800845.0 #CBVS2 lhCtxGM 188506.1 #CBVS2 rhCtxGM 189574.8 #CBVS2 lhCerebralWM 188195.0 #CBVS2 rhCerebralWM 187192.0 #CBVS2 SubCortGMVol 48351.0 #CBVS2 CerebellumVol 117475.0 #CBVS2 CerebellumGMVol 94295.0 #CBVS2 VentChorVol 23753.0 #CBVS2 3rd4th5thCSF 2997.0 #CBVS2 AllCSF 26750.0 #CBVS2 CCVol 2950.0 @#@FSTIME 2024:11:22:15:20:11 mri_brainvol_stats N 1 e 4.10 S 0.47 U 7.36 P 190% M 207800 F 2 R 186597 W 0 c 696 w 4969 I 0 O 8 L 27.37 28.21 27.31 @#@FSLOADPOST 2024:11:22:15:20:15 mri_brainvol_stats N 1 27.98 28.33 27.35 #----------------------------------------- #@# AParc-to-ASeg aparc Fri Nov 22 15:20:15 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8084 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7916 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Done loading 0 64 192 128 1 65 193 2 66 194 3 195 4 67 5 196 6 197 7 198 8 199 9 10 68 200 11 201 12 202 13 14 203 15 204 16 205 17 69 18 206 19 207 20 208 21 22 209 23 210 24 211 25 26 212 27 213 28 214 29 215 30 216 31 32 217 33 70 218 34 219 35 36 220 37 221 38 222 39 40 223 41 224 42 225 43 44 226 45 227 46 228 47 48 229 49 230 50 51 231 52 232 53 233 54 55 234 56 235 57 236 58 71 237 59 238 60 239 61 62 240 63 241 242 243 244 245 246 247 248 249 250 251 252 253 72 254 255 129 73 74 130 75 131 76 132 77 133 78 134 79 80 135 81 136 82 137 83 84 138 85 139 86 140 87 141 88 142 89 143 90 144 145 91 146 92 147 148 93 149 94 150 95 151 96 152 153 97 154 98 155 99 156 100 157 101 158 102 103 159 104 160 105 106 161 107 162 108 109 163 110 111 164 112 165 113 114 166 115 167 116 117 168 118 169 119 170 120 171 121 172 122 123 173 124 174 125 175 126 176 127 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 377082 ndotcheck = 13295 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 971152 mri_surf2volseg done @#@FSTIME 2024:11:22:15:20:15 mri_surf2volseg N 25 e 63.20 S 1.34 U 119.77 P 191% M 784920 F 2 R 862642 W 0 c 11284 w 2544 I 0 O 728 L 27.98 28.33 27.35 @#@FSLOADPOST 2024:11:22:15:21:18 mri_surf2volseg N 25 29.02 28.59 27.51 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Fri Nov 22 15:21:18 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8084 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.a2009s.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7916 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.a2009s.annot Done loading 0 192 64 128 65 193 1 66 194 2 195 3 67 196 4 197 5 198 6 199 7 200 68 201 8 202 9 203 10 204 205 11 206 12 207 13 208 69 209 14 210 15 211 16 212 213 17 214 18 215 19 216 20 217 218 21 219 22 220 23 221 222 24 70 223 25 224 26 225 27 226 227 28 228 29 229 30 230 231 31 232 32 233 33 234 235 34 236 35 237 36 238 37 239 240 38 241 39 242 40 243 244 41 245 42 246 43 247 248 71 44 249 45 250 251 46 252 47 253 48 254 255 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 72 129 73 130 74 75 131 76 132 77 133 78 79 134 80 135 81 136 82 137 83 84 138 85 139 86 140 87 141 88 142 89 143 90 144 145 91 146 92 147 148 93 149 94 150 95 151 152 96 153 97 154 98 155 99 156 100 157 101 158 102 159 103 104 160 105 161 106 107 162 108 163 109 110 164 111 165 112 113 166 114 167 115 116 168 117 169 118 170 119 171 120 172 121 122 173 123 174 124 175 125 176 126 177 127 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 377082 ndotcheck = 13295 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 971232 mri_surf2volseg done @#@FSTIME 2024:11:22:15:21:19 mri_surf2volseg N 25 e 61.26 S 1.20 U 116.93 P 192% M 785052 F 2 R 782978 W 0 c 11118 w 3998 I 0 O 784 L 29.02 28.59 27.51 @#@FSLOADPOST 2024:11:22:15:22:20 mri_surf2volseg N 25 26.73 28.09 27.41 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Fri Nov 22 15:22:20 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8084 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.DKTatlas.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7916 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.DKTatlas.annot Done loading 0 192 128 64 65 1 193 2 66 194 3 195 4 67 5 196 6 197 7 8 198 9 199 68 10 200 11 12 201 13 202 14 203 15 204 16 17 69 205 18 206 19 207 20 21 208 22 209 23 210 24 211 25 26 212 27 213 28 214 29 215 30 31 216 70 32 217 33 218 34 35 219 36 220 37 221 38 39 222 40 223 41 224 42 43 225 44 226 45 227 46 228 47 48 229 49 230 50 231 51 232 52 53 233 54 234 55 235 56 57 236 58 237 59 238 60 61 239 62 240 63 241 71 242 243 244 245 246 247 248 249 250 251 252 253 254 255 72 129 73 130 74 75 131 76 132 77 133 78 79 134 80 135 81 136 82 83 137 84 138 85 86 139 87 140 88 141 89 142 90 143 144 91 145 92 146 93 147 148 94 149 95 150 96 151 152 97 153 98 154 99 155 100 156 101 157 102 158 103 104 159 105 160 106 107 161 108 162 109 110 163 111 164 112 113 165 114 115 166 116 167 117 118 168 119 169 120 170 121 171 122 172 123 173 124 174 125 175 126 176 127 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 377082 ndotcheck = 13295 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 971152 mri_surf2volseg done @#@FSTIME 2024:11:22:15:22:20 mri_surf2volseg N 25 e 65.40 S 1.48 U 123.43 P 190% M 784804 F 1 R 1105538 W 0 c 11630 w 7342 I 0 O 720 L 26.73 28.09 27.41 @#@FSLOADPOST 2024:11:22:15:23:25 mri_surf2volseg N 25 28.55 28.47 27.60 #----------------------------------------- #@# WMParc Fri Nov 22 15:23:25 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot 3000 --lh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label --lh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white --lh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial --rh-annot /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot 4000 --rh-cortex-mask /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label --rh-white /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white --rh-pial /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8084 vertices from lh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.aparc.annot Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7916 vertices from rh hemi Loading /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.aparc.annot Done loading 192 0 128 64 193 1 65 194 2 66 195 3 67 196 4 68 197 5 69 198 6 199 7 70 200 8 201 9 71 202 10 203 11 72 129 204 12 205 13 206 14 207 15 208 16 209 17 73 210 18 211 19 212 20 213 21 214 22 74 130 215 23 216 24 217 25 218 26 219 27 220 28 75 221 29 222 30 223 31 224 32 225 33 226 34 131 227 35 228 36 76 229 37 230 38 231 39 40 232 41 233 234 42 235 43 236 44 45 237 46 238 47 239 77 48 240 132 49 241 50 242 51 243 52 244 53 245 54 246 55 247 56 248 57 249 58 250 78 59 251 60 252 61 253 62 254 63 255 133 79 80 134 81 135 82 136 83 84 137 85 138 86 87 139 88 89 140 90 91 141 92 93 94 142 95 96 143 97 98 144 99 145 100 101 146 102 147 103 104 148 105 149 106 150 107 151 108 152 109 153 154 110 155 111 156 112 157 113 158 114 159 115 160 116 161 117 162 118 163 119 164 120 165 121 166 122 123 167 124 168 125 169 126 127 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 372437 ndotcheck = 3958 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 971152 mri_surf2volseg done @#@FSTIME 2024:11:22:15:23:25 mri_surf2volseg N 25 e 26.95 S 1.03 U 50.06 P 189% M 784740 F 2 R 610912 W 0 c 4715 w 10083 I 0 O 808 L 28.55 28.47 27.60 @#@FSLOADPOST 2024:11:22:15:23:52 mri_surf2volseg N 25 28.62 28.50 27.63 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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) = 1351565 mm^3 (det: 1.441370 ) 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 2024:11:22:15:23:52 mri_segstats N 24 e 261.24 S 1.21 U 536.59 P 205% M 240104 F 0 R 1475276 W 0 c 49956 w 4651 I 0 O 24 L 28.62 28.50 27.63 @#@FSLOADPOST 2024:11:22:15:28:14 mri_segstats N 24 29.44 28.40 27.75 #----------------------------------------- #@# Parcellation Stats lh Fri Nov 22 15:28:14 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh pial #----------------------------------------- #@# Parcellation Stats rh Fri Nov 22 15:28:14 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh pial Waiting for PID 1097385 of (1097385 1097389 1097392 1097395) to complete... Waiting for PID 1097389 of (1097385 1097389 1097392 1097395) to complete... Waiting for PID 1097392 of (1097385 1097389 1097392 1097395) to complete... Waiting for PID 1097395 of (1097385 1097389 1097392 1097395) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 188510 Total vertex volume 188303 (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) = 1351565 mm^3 (det: 1.441370 ) 1148 753 1624 2.249 0.378 0.082 0.013 5 0.7 bankssts 793 504 1305 2.528 0.641 0.121 0.019 9 0.7 caudalanteriorcingulate 2198 1447 3706 2.478 0.501 0.110 0.022 15 2.1 caudalmiddlefrontal 2111 1305 2617 1.871 0.398 0.140 0.035 31 3.1 cuneus 619 420 1871 3.401 0.753 0.102 0.024 4 0.6 entorhinal 3179 2330 7362 2.706 0.575 0.139 0.033 42 4.1 fusiform 4806 3246 8064 2.271 0.484 0.123 0.025 50 4.9 inferiorparietal 3665 2578 7768 2.689 0.551 0.131 0.029 43 4.6 inferiortemporal 1262 849 1890 1.984 0.722 0.121 0.030 16 1.4 isthmuscingulate 6102 4004 9324 2.110 0.505 0.140 0.032 78 7.9 lateraloccipital 3085 2156 6144 2.728 0.585 0.130 0.034 34 4.2 lateralorbitofrontal 4064 2701 5629 1.928 0.555 0.137 0.033 55 5.6 lingual 2508 1789 4331 2.294 0.567 0.136 0.034 40 3.3 medialorbitofrontal 3772 2492 7810 2.665 0.557 0.121 0.026 44 3.9 middletemporal 898 567 1805 2.660 0.722 0.092 0.020 6 0.7 parahippocampal 1854 1062 2847 2.431 0.532 0.089 0.019 10 1.4 paracentral 2160 1438 4043 2.560 0.489 0.111 0.025 19 2.2 parsopercularis 910 679 2130 2.673 0.534 0.149 0.037 14 1.5 parsorbitalis 1876 1274 3408 2.364 0.539 0.122 0.025 17 2.0 parstriangularis 2012 1328 2215 1.831 0.517 0.130 0.032 21 2.7 pericalcarine 5607 3491 7234 1.904 0.594 0.107 0.024 54 5.2 postcentral 1403 937 2360 2.303 0.613 0.122 0.026 16 1.6 posteriorcingulate 6752 4202 11778 2.566 0.594 0.109 0.025 52 7.0 precentral 4359 3078 7224 2.212 0.522 0.128 0.027 49 5.0 precuneus 854 622 2035 2.832 0.668 0.151 0.038 15 1.4 rostralanteriorcingulate 5827 4251 11578 2.409 0.524 0.143 0.034 76 8.4 rostralmiddlefrontal 8512 5867 17552 2.671 0.543 0.122 0.026 78 9.3 superiorfrontal 7241 4759 10485 2.054 0.461 0.115 0.022 66 6.7 superiorparietal 5380 3625 11244 2.749 0.627 0.115 0.026 49 5.8 superiortemporal 5778 3878 10074 2.397 0.516 0.121 0.025 56 5.8 supramarginal 315 261 936 2.782 0.421 0.185 0.044 7 0.6 frontalpole 613 475 2528 3.545 0.678 0.126 0.030 7 0.7 temporalpole 721 409 1047 2.240 0.335 0.099 0.022 6 0.6 transversetemporal 3257 2272 6337 2.836 0.787 0.137 0.040 39 5.6 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 PIB15-273_VYr9_Bay3prisma lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 188510 Total vertex volume 188303 (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) = 1351565 mm^3 (det: 1.441370 ) 1148 695 1624 2.249 0.378 0.091 0.018 22 0.9 bankssts 793 563 1305 2.528 0.641 0.164 0.042 131 1.0 caudalanteriorcingulate 2198 1523 3706 2.478 0.501 0.122 0.027 37 2.3 caudalmiddlefrontal 2111 1594 2617 1.871 0.398 0.127 0.031 29 2.5 cuneus 619 715 1871 3.401 0.753 0.256 0.087 24 3.2 entorhinal 3179 3032 7362 2.706 0.575 0.165 0.045 75 5.8 fusiform 4806 3772 8064 2.271 0.484 0.131 0.026 55 5.3 inferiorparietal 3665 3208 7768 2.689 0.551 0.154 0.039 104 5.7 inferiortemporal 1262 1084 1890 1.984 0.722 0.171 0.047 81 2.4 isthmuscingulate 6102 4830 9324 2.110 0.505 0.137 0.032 91 8.0 lateraloccipital 3085 2357 6144 2.728 0.585 0.132 0.038 52 4.2 lateralorbitofrontal 4064 3352 5629 1.928 0.555 0.140 0.035 55 5.4 lingual 2508 2040 4331 2.294 0.567 0.143 0.039 64 3.9 medialorbitofrontal 3772 3229 7810 2.665 0.557 0.139 0.037 80 4.9 middletemporal 898 804 1805 2.660 0.722 0.160 0.045 10 1.9 parahippocampal 1854 1278 2847 2.431 0.532 0.090 0.016 10 1.2 paracentral 2160 1734 4043 2.560 0.489 0.129 0.028 46 2.2 parsopercularis 910 918 2130 2.673 0.534 0.181 0.039 20 1.6 parsorbitalis 1876 1549 3408 2.364 0.539 0.141 0.027 21 2.3 parstriangularis 2012 1146 2215 1.831 0.517 0.104 0.030 21 2.1 pericalcarine 5607 4215 7234 1.904 0.594 0.117 0.022 368 5.0 postcentral 1403 1096 2360 2.303 0.613 0.146 0.038 61 2.2 posteriorcingulate 6752 4887 11778 2.566 0.594 0.108 0.022 86 6.0 precentral 4359 3425 7224 2.212 0.522 0.137 0.030 59 5.7 precuneus 854 807 2035 2.832 0.668 0.189 0.059 40 2.2 rostralanteriorcingulate 5827 5255 11578 2.409 0.524 0.166 0.040 111 9.0 rostralmiddlefrontal 8512 7073 17552 2.671 0.543 0.136 0.031 128 9.9 superiorfrontal 7241 5436 10485 2.054 0.461 0.121 0.023 81 6.9 superiorparietal 5380 4390 11244 2.749 0.627 0.128 0.028 89 6.1 superiortemporal 5778 4454 10074 2.397 0.516 0.128 0.028 123 6.4 supramarginal 315 419 936 2.782 0.421 0.197 0.033 3 0.5 frontalpole 613 928 2528 3.545 0.678 0.209 0.040 8 1.1 temporalpole 721 550 1047 2.240 0.335 0.102 0.020 4 0.6 transversetemporal 3257 2155 6337 2.836 0.787 0.156 0.048 105 6.7 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189470 Total vertex volume 189264 (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) = 1351565 mm^3 (det: 1.441370 ) 1013 675 1554 2.349 0.323 0.084 0.016 5 0.7 bankssts 891 622 1628 2.418 0.818 0.145 0.027 16 1.1 caudalanteriorcingulate 2833 1890 4877 2.348 0.453 0.116 0.022 25 2.6 caudalmiddlefrontal 2288 1404 2729 1.781 0.414 0.127 0.032 29 3.0 cuneus 590 427 2188 3.631 0.711 0.129 0.032 7 0.8 entorhinal 3591 2449 7330 2.596 0.582 0.128 0.032 47 4.4 fusiform 6645 4561 11317 2.312 0.404 0.122 0.024 74 6.5 inferiorparietal 3562 2520 7730 2.680 0.656 0.134 0.031 50 4.7 inferiortemporal 1173 765 1663 1.931 0.715 0.124 0.028 18 1.2 isthmuscingulate 6813 4513 10508 2.128 0.498 0.135 0.030 87 8.1 lateraloccipital 3131 2202 5907 2.524 0.624 0.133 0.037 39 4.5 lateralorbitofrontal 4261 2813 6125 2.049 0.565 0.133 0.034 53 5.8 lingual 2619 1846 4750 2.315 0.674 0.122 0.030 37 3.1 medialorbitofrontal 3807 2650 8091 2.593 0.485 0.121 0.025 46 3.7 middletemporal 924 582 1844 2.658 0.731 0.098 0.020 7 0.7 parahippocampal 1889 1041 2886 2.569 0.600 0.088 0.019 11 1.5 paracentral 1428 990 2637 2.526 0.382 0.111 0.025 13 1.4 parsopercularis 1084 820 2437 2.348 0.519 0.138 0.034 16 1.7 parsorbitalis 1630 1179 3078 2.324 0.505 0.128 0.028 16 1.9 parstriangularis 2406 1529 2397 1.642 0.388 0.113 0.027 26 2.6 pericalcarine 5097 3190 6664 1.910 0.484 0.102 0.019 39 4.1 postcentral 1392 960 2527 2.346 0.682 0.122 0.025 17 1.5 posteriorcingulate 6578 4159 11309 2.503 0.525 0.102 0.020 47 5.8 precentral 4248 2923 7059 2.266 0.541 0.125 0.026 43 4.5 precuneus 635 426 1238 2.785 0.687 0.109 0.023 7 0.6 rostralanteriorcingulate 6524 5037 13445 2.329 0.550 0.151 0.035 102 10.1 rostralmiddlefrontal 7795 5395 15892 2.612 0.566 0.126 0.028 79 9.3 superiorfrontal 7933 5183 11899 2.083 0.439 0.101 0.019 62 6.2 superiorparietal 4723 3178 9656 2.663 0.579 0.108 0.023 44 4.4 superiortemporal 4346 2973 7789 2.376 0.470 0.115 0.024 43 4.2 supramarginal 366 329 1168 2.782 0.537 0.205 0.058 10 1.0 frontalpole 637 457 2142 3.559 0.563 0.136 0.036 8 1.0 temporalpole 422 238 678 2.558 0.321 0.105 0.023 4 0.4 transversetemporal 3277 2249 6121 2.757 0.703 0.130 0.038 38 4.7 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 PIB15-273_VYr9_Bay3prisma rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189470 Total vertex volume 189264 (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) = 1351565 mm^3 (det: 1.441370 ) 1013 647 1554 2.349 0.323 0.094 0.022 9 0.9 bankssts 891 737 1628 2.418 0.818 0.177 0.056 36 1.6 caudalanteriorcingulate 2833 2196 4877 2.348 0.453 0.122 0.023 49 2.8 caudalmiddlefrontal 2288 1792 2729 1.781 0.414 0.129 0.025 34 2.5 cuneus 590 819 2188 3.631 0.711 0.319 0.084 26 2.7 entorhinal 3591 3123 7330 2.596 0.582 0.151 0.037 123 5.3 fusiform 6645 5149 11317 2.312 0.404 0.131 0.027 88 7.2 inferiorparietal 3562 3098 7730 2.680 0.656 0.149 0.037 81 5.2 inferiortemporal 1173 967 1663 1.931 0.715 0.175 0.060 37 2.6 isthmuscingulate 6813 5368 10508 2.128 0.498 0.135 0.031 137 8.6 lateraloccipital 3131 2460 5907 2.524 0.624 0.148 0.044 66 5.2 lateralorbitofrontal 4261 3348 6125 2.049 0.565 0.135 0.036 71 5.8 lingual 2619 2258 4750 2.315 0.674 0.154 0.037 88 3.9 medialorbitofrontal 3807 3501 8091 2.593 0.485 0.145 0.028 68 4.4 middletemporal 924 805 1844 2.658 0.731 0.165 0.043 14 1.8 parahippocampal 1889 1212 2886 2.569 0.600 0.094 0.017 13 1.4 paracentral 1428 1119 2637 2.526 0.382 0.121 0.024 14 1.5 parsopercularis 1084 1249 2437 2.348 0.519 0.182 0.033 15 1.7 parsorbitalis 1630 1416 3078 2.324 0.505 0.146 0.031 22 2.1 parstriangularis 2406 1495 2397 1.642 0.388 0.105 0.024 37 2.0 pericalcarine 5097 3836 6664 1.910 0.484 0.110 0.019 40 3.9 postcentral 1392 1167 2527 2.346 0.682 0.177 0.058 355 4.0 posteriorcingulate 6578 4792 11309 2.503 0.525 0.103 0.018 87 4.7 precentral 4248 3251 7059 2.266 0.541 0.132 0.029 76 4.8 precuneus 635 493 1238 2.785 0.687 0.126 0.022 7 0.6 rostralanteriorcingulate 6524 6447 13445 2.329 0.550 0.179 0.039 123 10.9 rostralmiddlefrontal 7795 6610 15892 2.612 0.566 0.141 0.030 98 9.5 superiorfrontal 7933 6183 11899 2.083 0.439 0.114 0.019 65 6.2 superiorparietal 4723 3936 9656 2.663 0.579 0.124 0.024 65 4.7 superiortemporal 4346 3451 7789 2.376 0.470 0.125 0.025 48 4.5 supramarginal 366 523 1168 2.782 0.537 0.235 0.048 6 0.7 frontalpole 637 800 2142 3.559 0.563 0.183 0.029 7 0.9 temporalpole 422 295 678 2.558 0.321 0.089 0.017 2 0.2 transversetemporal 3277 2214 6121 2.757 0.703 0.145 0.041 79 5.1 insula PIDs (1097385 1097389 1097392 1097395) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Nov 22 15:28:28 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 2 rh Fri Nov 22 15:28:28 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh white Waiting for PID 1102504 of (1102504 1102508) to complete... Waiting for PID 1102508 of (1102504 1102508) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 188510 Total vertex volume 188303 (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) = 1351565 mm^3 (det: 1.441370 ) 872 671 1704 2.410 0.455 0.159 0.036 14 1.3 G_and_S_frontomargin 1231 862 2500 2.467 0.481 0.150 0.032 16 1.7 G_and_S_occipital_inf 1522 827 2365 2.340 0.575 0.100 0.023 14 1.3 G_and_S_paracentral 1155 778 2375 2.655 0.423 0.124 0.027 12 1.1 G_and_S_subcentral 594 502 1658 2.662 0.520 0.196 0.055 13 1.6 G_and_S_transv_frontopol 1680 1229 3462 2.682 0.526 0.140 0.033 25 2.5 G_and_S_cingul-Ant 1104 730 1881 2.646 0.506 0.102 0.016 6 0.8 G_and_S_cingul-Mid-Ant 1161 771 1949 2.451 0.494 0.108 0.024 8 1.1 G_and_S_cingul-Mid-Post 415 293 1031 2.631 0.533 0.149 0.036 7 0.6 G_cingul-Post-dorsal 254 172 462 2.205 0.766 0.159 0.040 5 0.4 G_cingul-Post-ventral 2005 1200 2628 1.892 0.428 0.141 0.038 31 3.1 G_cuneus 1072 737 2495 2.624 0.368 0.134 0.032 15 1.4 G_front_inf-Opercular 449 327 1185 2.704 0.351 0.147 0.033 7 0.7 G_front_inf-Orbital 1069 716 2502 2.666 0.503 0.139 0.031 14 1.3 G_front_inf-Triangul 3019 2197 7163 2.567 0.515 0.145 0.034 44 4.2 G_front_middle 5815 3941 13500 2.800 0.547 0.125 0.028 61 6.8 G_front_sup 640 420 1430 3.158 0.658 0.134 0.039 9 0.8 G_Ins_lg_and_S_cent_ins 777 571 2242 3.112 0.890 0.157 0.055 15 1.7 G_insular_short 1411 928 2839 2.410 0.494 0.133 0.030 19 1.6 G_occipital_middle 1569 973 2415 2.102 0.516 0.133 0.030 20 1.9 G_occipital_sup 1216 865 3017 2.776 0.580 0.135 0.035 17 1.6 G_oc-temp_lat-fusifor 2710 1778 3906 1.929 0.573 0.151 0.040 44 4.5 G_oc-temp_med-Lingual 1048 668 2853 3.096 0.809 0.096 0.023 7 0.9 G_oc-temp_med-Parahip 2020 1491 5056 2.742 0.623 0.149 0.040 33 3.2 G_orbital 2165 1459 4754 2.571 0.512 0.140 0.032 33 2.8 G_pariet_inf-Angular 2666 1824 5376 2.473 0.519 0.128 0.028 30 3.1 G_pariet_inf-Supramar 2768 1825 4627 2.123 0.489 0.115 0.023 29 2.5 G_parietal_sup 2177 1238 2951 1.943 0.539 0.107 0.028 27 2.3 G_postcentral 2486 1393 5453 2.870 0.581 0.106 0.028 23 2.6 G_precentral 2023 1475 4176 2.317 0.506 0.142 0.034 33 2.8 G_precuneus 1026 733 2081 2.321 0.525 0.156 0.040 22 1.5 G_rectus 581 374 812 2.255 0.759 0.114 0.043 7 1.0 G_subcallosal 591 344 957 2.297 0.340 0.094 0.021 4 0.4 G_temp_sup-G_T_transv 1800 1225 5414 3.168 0.542 0.134 0.036 24 2.5 G_temp_sup-Lateral 550 369 1325 3.402 0.530 0.092 0.023 3 0.6 G_temp_sup-Plan_polar 815 540 1523 2.372 0.586 0.092 0.022 6 0.6 G_temp_sup-Plan_tempo 2013 1421 5377 2.825 0.557 0.141 0.035 33 2.8 G_temporal_inf 1957 1226 4777 2.786 0.540 0.121 0.027 28 2.1 G_temporal_middle 394 261 435 1.944 0.398 0.100 0.017 2 0.3 Lat_Fis-ant-Horizont 387 265 526 2.391 0.588 0.098 0.022 2 0.4 Lat_Fis-ant-Vertical 953 630 1170 2.322 0.509 0.117 0.025 6 1.0 Lat_Fis-post 1918 1243 2547 1.869 0.426 0.147 0.037 28 2.9 Pole_occipital 1326 1035 5071 3.424 0.616 0.154 0.040 20 2.2 Pole_temporal 2405 1638 2747 1.906 0.559 0.126 0.028 23 3.0 S_calcarine 3007 2045 3467 1.938 0.666 0.108 0.022 17 3.1 S_central 1011 663 1185 1.973 0.423 0.090 0.013 4 0.6 S_cingul-Marginalis 482 332 718 2.566 0.375 0.105 0.024 2 0.5 S_circular_insula_ant 1555 1046 2254 2.655 0.677 0.100 0.023 9 1.6 S_circular_insula_inf 1507 1026 2006 2.366 0.468 0.116 0.025 8 1.8 S_circular_insula_sup 794 544 1343 2.602 0.393 0.106 0.017 6 0.6 S_collat_transv_ant 507 354 540 1.921 0.352 0.141 0.030 4 0.7 S_collat_transv_post 1802 1200 2598 2.258 0.496 0.109 0.024 13 1.7 S_front_inf 957 664 1280 2.167 0.456 0.120 0.027 6 1.1 S_front_middle 1976 1356 3158 2.405 0.502 0.114 0.024 14 2.0 S_front_sup 666 441 788 2.263 0.304 0.101 0.017 4 0.5 S_interm_prim-Jensen 2782 1847 3223 1.981 0.398 0.108 0.019 18 2.3 S_intrapariet_and_P_trans 660 453 767 1.932 0.268 0.117 0.021 5 0.6 S_oc_middle_and_Lunatus 970 645 1237 2.135 0.343 0.116 0.022 6 1.0 S_oc_sup_and_transversal 584 391 817 2.150 0.351 0.118 0.021 5 0.5 S_occipital_ant 586 430 965 2.460 0.358 0.136 0.031 6 0.8 S_oc-temp_lat 1841 1266 2715 2.283 0.508 0.117 0.021 16 1.7 S_oc-temp_med_and_Lingual 297 215 419 2.224 0.437 0.127 0.022 2 0.3 S_orbital_lateral 534 385 761 2.362 0.578 0.134 0.032 7 0.7 S_orbital_med-olfact 1014 695 1856 2.923 0.515 0.124 0.029 7 1.3 S_orbital-H_Shaped 1876 1238 2567 2.120 0.543 0.111 0.022 14 1.7 S_parieto_occipital 1139 693 866 1.666 0.617 0.113 0.024 17 1.0 S_pericallosal 2770 1848 3282 1.947 0.447 0.116 0.023 20 2.7 S_postcentral 1248 824 1815 2.507 0.390 0.097 0.019 6 1.0 S_precentral-inf-part 1494 969 2033 2.268 0.421 0.101 0.019 9 1.2 S_precentral-sup-part 568 385 696 2.210 0.491 0.110 0.019 4 0.4 S_suborbital 714 498 930 2.131 0.455 0.131 0.023 6 0.7 S_subparietal 1186 859 1693 2.406 0.455 0.126 0.022 9 1.2 S_temporal_inf 4938 3327 7151 2.308 0.480 0.106 0.019 34 4.1 S_temporal_sup 367 242 454 2.229 0.394 0.136 0.024 4 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189470 Total vertex volume 189264 (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) = 1351565 mm^3 (det: 1.441370 ) 823 667 1845 2.362 0.530 0.169 0.045 18 1.7 G_and_S_frontomargin 1069 739 1802 2.306 0.504 0.146 0.031 17 1.4 G_and_S_occipital_inf 1144 599 1914 2.533 0.557 0.096 0.021 9 0.9 G_and_S_paracentral 1213 820 2387 2.475 0.424 0.125 0.020 12 1.1 G_and_S_subcentral 1041 882 2902 2.663 0.584 0.179 0.049 19 2.3 G_and_S_transv_frontopol 2436 1718 4624 2.570 0.625 0.122 0.028 24 2.7 G_and_S_cingul-Ant 1195 840 2274 2.597 0.565 0.130 0.028 13 1.5 G_and_S_cingul-Mid-Ant 1090 729 1991 2.542 0.455 0.105 0.021 8 1.0 G_and_S_cingul-Mid-Post 398 284 1049 2.695 0.528 0.154 0.032 7 0.6 G_cingul-Post-dorsal 249 157 468 2.270 0.746 0.138 0.037 5 0.3 G_cingul-Post-ventral 2238 1340 2730 1.805 0.403 0.131 0.036 34 3.2 G_cuneus 970 688 2424 2.759 0.385 0.123 0.026 11 1.1 G_front_inf-Opercular 414 322 1108 2.562 0.462 0.166 0.043 8 0.9 G_front_inf-Orbital 620 451 1455 2.528 0.492 0.141 0.032 9 0.8 G_front_inf-Triangul 3836 2854 8715 2.424 0.529 0.150 0.033 63 5.7 G_front_middle 4985 3321 11585 2.784 0.576 0.130 0.031 63 6.4 G_front_sup 541 369 1289 3.080 0.701 0.130 0.037 8 0.6 G_Ins_lg_and_S_cent_ins 549 400 1468 2.911 0.668 0.145 0.046 9 0.9 G_insular_short 1934 1324 4315 2.523 0.424 0.136 0.031 31 2.1 G_occipital_middle 1726 1110 2631 2.060 0.408 0.121 0.027 20 1.9 G_occipital_sup 1542 995 3590 2.701 0.503 0.125 0.033 22 1.9 G_oc-temp_lat-fusifor 2656 1729 4374 2.200 0.605 0.144 0.037 40 3.9 G_oc-temp_med-Lingual 1215 819 3662 3.218 0.859 0.125 0.039 17 1.7 G_oc-temp_med-Parahip 2233 1640 5391 2.521 0.713 0.141 0.040 38 3.4 G_orbital 2334 1619 5099 2.500 0.398 0.140 0.032 40 2.8 G_pariet_inf-Angular 1855 1274 4044 2.589 0.474 0.127 0.028 22 2.0 G_pariet_inf-Supramar 2234 1448 4232 2.326 0.380 0.110 0.022 25 1.9 G_parietal_sup 1846 1070 2559 1.881 0.432 0.108 0.023 19 1.8 G_postcentral 2518 1424 5044 2.704 0.406 0.103 0.023 24 2.3 G_precentral 1786 1251 3890 2.435 0.476 0.127 0.029 23 2.0 G_precuneus 699 505 1336 2.145 0.574 0.132 0.041 19 0.9 G_rectus 384 249 654 2.571 0.754 0.103 0.029 3 0.5 G_subcallosal 346 178 610 2.642 0.314 0.103 0.027 5 0.3 G_temp_sup-G_T_transv 1616 1111 4541 3.001 0.516 0.138 0.032 25 2.2 G_temp_sup-Lateral 774 537 1695 3.163 0.705 0.080 0.018 3 0.5 G_temp_sup-Plan_polar 805 523 1491 2.481 0.484 0.104 0.022 7 0.7 G_temp_sup-Plan_tempo 2015 1450 5465 2.877 0.722 0.161 0.044 44 3.5 G_temporal_inf 2294 1600 5560 2.675 0.460 0.128 0.027 35 2.3 G_temporal_middle 377 250 402 1.907 0.317 0.093 0.014 2 0.2 Lat_Fis-ant-Horizont 172 123 276 2.534 0.433 0.118 0.020 1 0.1 Lat_Fis-ant-Vertical 1217 811 1535 2.226 0.402 0.105 0.019 7 1.0 Lat_Fis-post 3489 2187 4348 1.816 0.456 0.136 0.033 49 4.6 Pole_occipital 1515 1128 4814 3.171 0.594 0.140 0.035 22 2.1 Pole_temporal 2346 1586 2548 1.755 0.502 0.112 0.026 20 2.5 S_calcarine 2764 1883 3229 1.970 0.613 0.093 0.017 11 2.1 S_central 1072 715 1394 2.180 0.451 0.089 0.012 4 0.6 S_cingul-Marginalis 594 425 1001 2.553 0.552 0.130 0.036 5 0.9 S_circular_insula_ant 1223 789 1666 2.508 0.689 0.085 0.019 6 1.1 S_circular_insula_inf 1223 799 1623 2.516 0.362 0.102 0.024 7 1.3 S_circular_insula_sup 1032 718 1628 2.451 0.444 0.101 0.020 6 0.8 S_collat_transv_ant 380 253 397 1.930 0.308 0.135 0.028 3 0.5 S_collat_transv_post 1240 883 1764 2.186 0.404 0.115 0.025 10 1.3 S_front_inf 1803 1323 2658 2.102 0.426 0.130 0.027 17 2.2 S_front_middle 1759 1188 2502 2.291 0.420 0.100 0.019 9 1.4 S_front_sup 327 243 455 2.163 0.416 0.133 0.019 2 0.4 S_interm_prim-Jensen 3718 2465 4649 1.985 0.383 0.093 0.015 19 2.5 S_intrapariet_and_P_trans 871 598 1023 1.990 0.398 0.119 0.022 6 0.9 S_oc_middle_and_Lunatus 1310 865 1638 2.039 0.407 0.112 0.020 8 1.2 S_oc_sup_and_transversal 572 399 786 2.231 0.359 0.122 0.027 4 0.7 S_occipital_ant 607 441 905 2.360 0.427 0.125 0.023 6 0.5 S_oc-temp_lat 1659 1114 2302 2.322 0.412 0.096 0.015 8 1.1 S_oc-temp_med_and_Lingual 338 265 610 2.077 0.555 0.159 0.043 4 0.6 S_orbital_lateral 784 548 1054 2.168 0.651 0.136 0.032 9 1.0 S_orbital_med-olfact 1188 841 1991 2.531 0.484 0.128 0.030 11 1.5 S_orbital-H_Shaped 1851 1218 2256 1.940 0.557 0.111 0.021 14 1.7 S_parieto_occipital 1220 782 914 1.534 0.557 0.123 0.020 22 1.1 S_pericallosal 2273 1522 2531 1.833 0.336 0.098 0.018 13 1.8 S_postcentral 1479 975 2090 2.355 0.429 0.108 0.022 10 1.3 S_precentral-inf-part 1133 759 1536 2.288 0.484 0.093 0.015 5 0.8 S_precentral-sup-part 281 202 417 2.399 0.599 0.126 0.022 3 0.3 S_suborbital 767 561 1160 2.280 0.493 0.133 0.028 6 0.9 S_subparietal 953 655 1229 2.304 0.391 0.114 0.018 6 0.9 S_temporal_inf 5255 3529 7518 2.331 0.359 0.098 0.018 30 4.1 S_temporal_sup 136 98 200 2.253 0.344 0.120 0.020 1 0.1 S_temporal_transverse PIDs (1102504 1102508) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Nov 22 15:28:41 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma lh white #----------------------------------------- #@# Parcellation Stats 3 rh Fri Nov 22 15:28:41 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma rh white Waiting for PID 1102806 of (1102806 1102809) to complete... Waiting for PID 1102809 of (1102806 1102809) 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 PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 188510 Total vertex volume 188303 (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) = 1351565 mm^3 (det: 1.441370 ) 1352 861 2186 2.594 0.545 0.116 0.020 14 1.2 caudalanteriorcingulate 2326 1533 3934 2.473 0.499 0.111 0.022 17 2.2 caudalmiddlefrontal 2873 1756 3595 1.883 0.424 0.133 0.033 39 3.8 cuneus 535 356 1610 3.387 0.771 0.097 0.021 3 0.4 entorhinal 2970 2125 6091 2.614 0.524 0.136 0.031 37 3.6 fusiform 5019 3372 8697 2.318 0.500 0.123 0.025 52 5.2 inferiorparietal 3719 2672 8917 2.758 0.616 0.132 0.030 48 4.8 inferiortemporal 1239 834 1849 1.993 0.719 0.121 0.029 16 1.4 isthmuscingulate 6104 4024 9374 2.109 0.505 0.139 0.032 78 7.9 lateraloccipital 3404 2429 7046 2.740 0.623 0.136 0.037 44 5.1 lateralorbitofrontal 4108 2729 5654 1.924 0.554 0.137 0.033 56 5.7 lingual 2032 1431 3536 2.279 0.577 0.136 0.034 32 2.5 medialorbitofrontal 4837 3212 9511 2.589 0.560 0.118 0.025 52 5.0 middletemporal 927 588 1860 2.654 0.725 0.093 0.021 6 0.7 parahippocampal 2168 1271 3369 2.453 0.528 0.089 0.019 12 1.7 paracentral 1999 1335 3701 2.527 0.467 0.112 0.025 18 2.0 parsopercularis 1008 726 2021 2.475 0.475 0.132 0.029 11 1.4 parsorbitalis 2198 1476 4169 2.471 0.569 0.124 0.026 21 2.4 parstriangularis 1992 1325 2188 1.828 0.519 0.129 0.031 20 2.7 pericalcarine 6338 3983 8193 1.927 0.583 0.109 0.024 60 6.0 postcentral 1528 1023 2527 2.313 0.617 0.122 0.026 17 1.7 posteriorcingulate 6747 4193 11767 2.574 0.589 0.109 0.025 52 6.9 precentral 4289 3015 7290 2.244 0.506 0.130 0.028 49 5.0 precuneus 1173 856 2564 2.750 0.653 0.148 0.037 20 1.8 rostralanteriorcingulate 4016 2925 7744 2.410 0.555 0.141 0.033 50 5.4 rostralmiddlefrontal 9349 6592 20053 2.633 0.551 0.129 0.029 100 11.6 superiorfrontal 5786 3846 8322 2.045 0.463 0.114 0.022 51 5.1 superiorparietal 6987 4734 15088 2.773 0.675 0.114 0.026 62 7.6 superiortemporal 5160 3500 8919 2.376 0.511 0.123 0.025 51 5.4 supramarginal 691 392 1004 2.236 0.323 0.099 0.022 6 0.5 transversetemporal 2767 1933 5525 2.824 0.774 0.134 0.039 34 4.4 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 PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 189470 Total vertex volume 189264 (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) = 1351565 mm^3 (det: 1.441370 ) 1030 722 1958 2.428 0.802 0.142 0.028 19 1.2 caudalanteriorcingulate 2958 1971 5033 2.347 0.457 0.116 0.022 26 2.8 caudalmiddlefrontal 2679 1677 3144 1.740 0.404 0.124 0.029 32 3.2 cuneus 567 404 2034 3.609 0.715 0.124 0.033 6 0.8 entorhinal 3229 2182 6354 2.558 0.548 0.121 0.030 40 3.6 fusiform 6484 4464 11040 2.311 0.401 0.123 0.024 73 6.5 inferiorparietal 3895 2786 8855 2.717 0.667 0.139 0.033 57 5.3 inferiortemporal 1160 758 1656 1.938 0.712 0.123 0.027 18 1.2 isthmuscingulate 6826 4508 10353 2.107 0.501 0.135 0.030 87 8.1 lateraloccipital 3704 2664 7324 2.534 0.628 0.142 0.040 53 6.0 lateralorbitofrontal 4179 2768 5974 2.044 0.562 0.134 0.034 53 5.7 lingual 1904 1349 3469 2.308 0.648 0.128 0.033 33 2.4 medialorbitofrontal 4726 3258 9534 2.554 0.471 0.114 0.023 50 4.3 middletemporal 957 608 1911 2.665 0.739 0.100 0.021 8 0.8 parahippocampal 2004 1113 3052 2.553 0.596 0.090 0.019 12 1.7 paracentral 1584 1094 2883 2.518 0.401 0.111 0.025 14 1.4 parsopercularis 970 715 2086 2.444 0.510 0.129 0.031 12 1.3 parsorbitalis 1562 1138 2935 2.300 0.503 0.133 0.030 16 2.1 parstriangularis 2438 1538 2460 1.661 0.407 0.112 0.028 26 2.6 pericalcarine 5602 3534 7403 1.910 0.492 0.104 0.019 44 4.6 postcentral 1438 992 2563 2.360 0.660 0.124 0.024 17 1.5 posteriorcingulate 6311 3991 10943 2.505 0.523 0.102 0.020 44 5.5 precentral 4454 3049 7551 2.291 0.516 0.124 0.026 47 4.8 precuneus 867 580 1669 2.742 0.700 0.104 0.022 8 0.8 rostralanteriorcingulate 4542 3493 8924 2.256 0.536 0.150 0.034 72 6.9 rostralmiddlefrontal 10229 7281 21371 2.569 0.582 0.131 0.030 113 13.0 superiorfrontal 6717 4379 10169 2.100 0.420 0.099 0.018 51 5.2 superiorparietal 6099 4127 13061 2.744 0.644 0.111 0.025 59 6.2 superiortemporal 4202 2863 7493 2.382 0.463 0.112 0.024 40 3.9 supramarginal 434 246 703 2.560 0.315 0.104 0.023 4 0.4 transversetemporal 2800 1922 5361 2.772 0.681 0.125 0.035 30 3.8 insula PIDs (1102806 1102809) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Fri Nov 22 15:28:54 CST 2024 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma sysname Linux hostname chopin machine x86_64 user grossens whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1351565 mm^3 (det: 1.441370 ) Computing euler number orig.nofix lheno = -6, rheno = -20 orig.nofix lhholes = 4, rhholes = 11 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 2024:11:22:15:28:54 mri_segstats N 32 e 79.14 S 1.13 U 294.65 P 373% M 281204 F 2 R 1175476 W 0 c 27641 w 263 I 0 O 24 L 29.83 28.70 27.88 @#@FSLOADPOST 2024:11:22:15:30:13 mri_segstats N 32 31.37 29.33 28.17 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri Nov 22 15:30:13 CST 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 1157062 of (1157062 1157065 1157068 1157071 1157074) to complete... Waiting for PID 1157065 of (1157062 1157065 1157068 1157071 1157074) to complete... Waiting for PID 1157068 of (1157062 1157065 1157068 1157071 1157074) to complete... Waiting for PID 1157071 of (1157062 1157065 1157068 1157071 1157074) to complete... Waiting for PID 1157074 of (1157062 1157065 1157068 1157071 1157074) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4229 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8030 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4105 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6069 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5889 mri_label2label: Done PIDs (1157062 1157065 1157068 1157071 1157074) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 1170794 of (1170794 1170797 1170800 1170803) to complete... Waiting for PID 1170797 of (1170794 1170797 1170800 1170803) to complete... Waiting for PID 1170800 of (1170794 1170797 1170800 1170803) to complete... Waiting for PID 1170803 of (1170794 1170797 1170800 1170803) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4125 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13809 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4253 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3683 mri_label2label: Done PIDs (1170794 1170797 1170800 1170803) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 1181134 of (1181134 1181137 1181140 1181143 1181147) to complete... Waiting for PID 1181137 of (1181134 1181137 1181140 1181143 1181147) to complete... Waiting for PID 1181140 of (1181134 1181137 1181140 1181143 1181147) to complete... Waiting for PID 1181143 of (1181134 1181137 1181140 1181143 1181147) to complete... Waiting for PID 1181147 of (1181134 1181137 1181140 1181143 1181147) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 1000 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5641 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 1644 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9758 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2065 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1313 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1210 mri_label2label: Done PIDs (1181134 1181137 1181140 1181143 1181147) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 1181356 of (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) to complete... Waiting for PID 1181359 of (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) to complete... Waiting for PID 1181362 of (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) to complete... Waiting for PID 1181366 of (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) to complete... Waiting for PID 1181369 of (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) to complete... Waiting for PID 1181372 of (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) to complete... Waiting for PID 1181375 of (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) to complete... Waiting for PID 1181379 of (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 452 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 739 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1901 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2171 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 824 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4701 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 801 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3720 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 237 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1523 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 151 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1157 mri_label2label: Done PIDs (1181356 1181359 1181362 1181366 1181369 1181372 1181375 1181379) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 99911 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.mpm.vpnl.annot @#@FSTIME 2024:11:22:15:30:45 mris_label2annot N 26 e 0.71 S 0.10 U 0.89 P 139% M 133468 F 1 R 36289 W 0 c 94 w 154 I 0 O 1784 L 32.11 29.68 28.32 @#@FSLOADPOST 2024:11:22:15:30:46 mris_label2annot N 26 32.50 29.80 28.37 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 1188392 of (1188392 1188395 1188398 1188401 1188405) to complete... Waiting for PID 1188395 of (1188392 1188395 1188398 1188401 1188405) to complete... Waiting for PID 1188398 of (1188392 1188395 1188398 1188401 1188405) to complete... Waiting for PID 1188401 of (1188392 1188395 1188398 1188401 1188405) to complete... Waiting for PID 1188405 of (1188392 1188395 1188398 1188401 1188405) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1032 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2129 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1513 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2014 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2367 mri_label2label: Done PIDs (1188392 1188395 1188398 1188401 1188405) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 1197337 of (1197337 1197340 1197343 1197346) to complete... Waiting for PID 1197340 of (1197337 1197340 1197343 1197346) to complete... Waiting for PID 1197343 of (1197337 1197340 1197343 1197346) to complete... Waiting for PID 1197346 of (1197337 1197340 1197343 1197346) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1570 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 169 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7204 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1944 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1282 mri_label2label: Done PIDs (1197337 1197340 1197343 1197346) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 1200222 of (1200222 1200225 1200228 1200231 1200234) to complete... Waiting for PID 1200225 of (1200222 1200225 1200228 1200231 1200234) to complete... Waiting for PID 1200228 of (1200222 1200225 1200228 1200231 1200234) to complete... Waiting for PID 1200231 of (1200222 1200225 1200228 1200231 1200234) to complete... Waiting for PID 1200234 of (1200222 1200225 1200228 1200231 1200234) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 741 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4146 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 835 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4169 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 8 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 521 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 481 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/lh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 113725 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 453 mri_label2label: Done PIDs (1200222 1200225 1200228 1200231 1200234) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 77495 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.BA_exvivo.annot @#@FSTIME 2024:11:22:15:31:07 mris_label2annot N 38 e 0.69 S 0.11 U 0.84 P 137% M 134056 F 3 R 36405 W 0 c 88 w 237 I 0 O 1784 L 34.15 30.36 28.58 @#@FSLOADPOST 2024:11:22:15:31:08 mris_label2annot N 38 34.15 30.36 28.58 mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 91335 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2024:11:22:15:31:08 mris_label2annot N 38 e 0.69 S 0.08 U 0.87 P 137% M 133544 F 2 R 36327 W 0 c 90 w 291 I 0 O 1784 L 34.15 30.36 28.58 @#@FSLOADPOST 2024:11:22:15:31:08 mris_label2annot N 38 34.15 30.36 28.58 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 188510 Total vertex volume 188303 (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) = 1351565 mm^3 (det: 1.441370 ) 1098 595 1597 2.066 0.537 0.114 0.031 14 1.0 BA1_exvivo 3567 2325 4768 2.016 0.496 0.112 0.022 27 3.5 BA2_exvivo 965 681 917 1.718 0.372 0.133 0.029 7 1.2 BA3a_exvivo 2185 1378 2590 1.720 0.557 0.102 0.022 22 1.9 BA3b_exvivo 1521 799 2613 2.737 0.531 0.093 0.023 12 1.4 BA4a_exvivo 1260 792 2069 2.732 0.555 0.105 0.027 7 1.5 BA4p_exvivo 7782 4964 15337 2.669 0.581 0.108 0.022 60 7.3 BA6_exvivo 1942 1300 3557 2.511 0.426 0.115 0.025 18 2.0 BA44_exvivo 2630 1787 5164 2.494 0.540 0.127 0.029 27 3.1 BA45_exvivo 3551 2220 4117 1.826 0.490 0.127 0.034 44 4.8 V1_exvivo 7222 4788 9745 1.926 0.479 0.147 0.035 101 10.5 V2_exvivo 1437 959 2782 2.453 0.448 0.129 0.028 17 1.6 MT_exvivo 540 386 1328 3.116 0.655 0.115 0.027 5 0.5 perirhinal_exvivo 530 345 1727 3.344 1.086 0.095 0.021 4 0.5 entorhinal_exvivo @#@FSTIME 2024:11:22:15:31:08 mris_anatomical_stats N 12 e 4.55 S 0.41 U 6.83 P 159% M 403292 F 3 R 198744 W 0 c 684 w 306 I 0 O 136 L 34.15 30.36 28.58 @#@FSLOADPOST 2024:11:22:15:31:13 mris_anatomical_stats N 12 32.30 30.04 28.49 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB15-273_VYr9_Bay3prisma lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 188510 Total vertex volume 188303 (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) = 1351565 mm^3 (det: 1.441370 ) 700 348 991 2.066 0.496 0.130 0.040 11 0.9 BA1_exvivo 1399 873 1806 1.975 0.499 0.094 0.020 8 1.2 BA2_exvivo 818 584 773 1.717 0.364 0.136 0.031 6 1.1 BA3a_exvivo 1346 884 1290 1.422 0.338 0.094 0.018 8 1.1 BA3b_exvivo 1488 801 2599 2.771 0.533 0.091 0.024 10 1.4 BA4a_exvivo 1047 656 1640 2.649 0.559 0.101 0.024 6 1.1 BA4p_exvivo 4683 2928 9501 2.691 0.606 0.106 0.024 36 4.4 BA6_exvivo 1264 854 2320 2.489 0.427 0.120 0.029 13 1.5 BA44_exvivo 1111 734 2403 2.587 0.529 0.125 0.029 12 1.2 BA45_exvivo 3783 2366 4452 1.830 0.487 0.125 0.033 45 5.0 V1_exvivo 3790 2520 4776 1.835 0.450 0.158 0.041 61 6.4 V2_exvivo 392 271 566 2.341 0.306 0.117 0.019 3 0.4 MT_exvivo 240 168 480 2.933 0.565 0.104 0.021 2 0.2 perirhinal_exvivo 329 216 1194 3.750 0.590 0.082 0.016 2 0.2 entorhinal_exvivo @#@FSTIME 2024:11:22:15:31:13 mris_anatomical_stats N 12 e 4.52 S 0.51 U 6.29 P 150% M 402716 F 1 R 204064 W 0 c 638 w 299 I 0 O 136 L 32.30 30.04 28.49 @#@FSLOADPOST 2024:11:22:15:31:18 mris_anatomical_stats N 12 30.83 29.78 28.41 #-------------------------------------------- #@# BA_exvivo Labels rh Fri Nov 22 15:31:18 CST 2024 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 1206119 of (1206119 1206122 1206126 1206130 1206133) to complete... Waiting for PID 1206122 of (1206119 1206122 1206126 1206130 1206133) to complete... Waiting for PID 1206126 of (1206119 1206122 1206126 1206130 1206133) to complete... Waiting for PID 1206130 of (1206119 1206122 1206126 1206130 1206133) to complete... Waiting for PID 1206133 of (1206119 1206122 1206126 1206130 1206133) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 3985 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6718 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4001 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4538 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5798 mri_label2label: Done PIDs (1206119 1206122 1206126 1206130 1206133) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 1207013 of (1207013 1207016 1207020 1207023) to complete... Waiting for PID 1207016 of (1207013 1207016 1207020 1207023) to complete... Waiting for PID 1207020 of (1207013 1207016 1207020 1207023) to complete... Waiting for PID 1207023 of (1207013 1207016 1207020 1207023) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4520 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12357 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 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 PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 145 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5500 mri_label2label: Done PIDs (1207013 1207016 1207020 1207023) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 1207133 of (1207133 1207137 1207140 1207143 1207147) to complete... Waiting for PID 1207137 of (1207133 1207137 1207140 1207143 1207147) to complete... Waiting for PID 1207140 of (1207133 1207137 1207140 1207143 1207147) to complete... Waiting for PID 1207143 of (1207133 1207137 1207140 1207143 1207147) to complete... Waiting for PID 1207147 of (1207133 1207137 1207140 1207143 1207147) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 1381 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6108 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 1861 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9877 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2012 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1071 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 768 mri_label2label: Done PIDs (1207133 1207137 1207140 1207143 1207147) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 1216597 of (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) to complete... Waiting for PID 1216600 of (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) to complete... Waiting for PID 1216604 of (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) to complete... Waiting for PID 1216607 of (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) to complete... Waiting for PID 1216610 of (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) to complete... Waiting for PID 1216614 of (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) to complete... Waiting for PID 1216617 of (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) to complete... Waiting for PID 1216621 of (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 661 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 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 PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1607 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1619 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 1128 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4795 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 685 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3404 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 271 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1499 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 292 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1317 mri_label2label: Done PIDs (1216597 1216600 1216604 1216607 1216610 1216614 1216617 1216621) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 100543 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.mpm.vpnl.annot @#@FSTIME 2024:11:22:15:31:48 mris_label2annot N 26 e 0.73 S 0.09 U 1.00 P 148% M 134308 F 2 R 36532 W 0 c 103 w 226 I 0 O 1792 L 32.09 30.18 28.59 @#@FSLOADPOST 2024:11:22:15:31:48 mris_label2annot N 26 32.09 30.18 28.59 mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 1217080 of (1217080 1217083 1217086 1217089 1217092) to complete... Waiting for PID 1217083 of (1217080 1217083 1217086 1217089 1217092) to complete... Waiting for PID 1217086 of (1217080 1217083 1217086 1217089 1217092) to complete... Waiting for PID 1217089 of (1217080 1217083 1217086 1217089 1217092) to complete... Waiting for PID 1217092 of (1217080 1217083 1217086 1217089 1217092) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 886 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2692 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1707 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2190 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1399 mri_label2label: Done PIDs (1217080 1217083 1217086 1217089 1217092) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 1217217 of (1217217 1217220 1217224 1217227) to complete... Waiting for PID 1217220 of (1217217 1217220 1217224 1217227) to complete... Waiting for PID 1217224 of (1217217 1217220 1217224 1217227) to complete... Waiting for PID 1217227 of (1217217 1217220 1217224 1217227) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1513 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7006 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1019 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1188 mri_label2label: Done PIDs (1217217 1217220 1217224 1217227) 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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_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 PIB15-273_VYr9_Bay3prisma --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 1217347 of (1217347 1217351 1217354 1217357 1217361) to complete... Waiting for PID 1217351 of (1217347 1217351 1217354 1217357 1217361) to complete... Waiting for PID 1217354 of (1217347 1217351 1217354 1217357 1217361) to complete... Waiting for PID 1217357 of (1217347 1217351 1217354 1217357 1217361) to complete... Waiting for PID 1217361 of (1217347 1217351 1217354 1217357 1217361) to complete... mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 1001 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4233 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 899 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 8 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 276 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 711 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PIB15-273_VYr9_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 = PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/surf/rh.white Reading target registration /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_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 114467 Number of reverse mapping hits = 5 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 296 mri_label2label: Done PIDs (1217347 1217351 1217354 1217357 1217361) completed and logs appended. mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 79790 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.BA_exvivo.annot @#@FSTIME 2024:11:22:15:32:08 mris_label2annot N 38 e 0.76 S 0.09 U 0.92 P 132% M 134804 F 1 R 36655 W 0 c 99 w 225 I 0 O 1792 L 33.42 30.61 28.76 @#@FSLOADPOST 2024:11:22:15:32:09 mris_label2annot N 38 33.42 30.61 28.76 mris_label2annot --s PIB15-273_VYr9_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/PIB15-273_VYr9_Bay3prisma/label cmdline mris_label2annot --s PIB15-273_VYr9_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 PIB15-273_VYr9_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/PIB15-273_VYr9_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 94410 unhit vertices Writing annot to /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2024:11:22:15:32:09 mris_label2annot N 38 e 0.70 S 0.10 U 0.87 P 137% M 134400 F 2 R 36566 W 0 c 88 w 203 I 0 O 1792 L 33.42 30.61 28.76 @#@FSLOADPOST 2024:11:22:15:32:09 mris_label2annot N 38 33.42 30.61 28.76 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189470 Total vertex volume 189264 (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) = 1351565 mm^3 (det: 1.441370 ) 825 437 1298 2.101 0.448 0.131 0.031 12 1.1 BA1_exvivo 2609 1695 3149 1.870 0.407 0.101 0.020 17 2.2 BA2_exvivo 967 695 986 1.755 0.354 0.126 0.023 6 1.0 BA3a_exvivo 1611 1027 1928 1.724 0.479 0.090 0.014 9 1.0 BA3b_exvivo 1304 665 2196 2.796 0.475 0.076 0.020 7 1.1 BA4a_exvivo 1202 737 1839 2.575 0.520 0.076 0.015 4 0.7 BA4p_exvivo 6195 3871 11811 2.626 0.539 0.107 0.023 51 5.6 BA6_exvivo 2862 1942 5129 2.509 0.427 0.119 0.023 26 2.9 BA44_exvivo 2939 2203 6108 2.367 0.500 0.139 0.033 39 4.2 BA45_exvivo 4169 2571 4718 1.736 0.428 0.118 0.032 49 4.9 V1_exvivo 7528 4919 10419 1.980 0.513 0.142 0.035 103 10.7 V2_exvivo 1560 1072 2651 2.387 0.427 0.122 0.027 17 1.4 MT_exvivo 348 263 888 3.222 0.560 0.140 0.026 3 0.4 perirhinal_exvivo 558 388 2072 3.528 1.047 0.108 0.029 7 0.7 entorhinal_exvivo @#@FSTIME 2024:11:22:15:32:09 mris_anatomical_stats N 12 e 4.61 S 0.38 U 6.92 P 158% M 405284 F 1 R 167676 W 0 c 677 w 323 I 0 O 136 L 33.42 30.61 28.76 @#@FSLOADPOST 2024:11:22:15:32:14 mris_anatomical_stats N 12 33.63 30.70 28.80 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PIB15-273_VYr9_Bay3prisma rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/mri/wm.mgz... reading input surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... reading input pial surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.pial... reading input white surface /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189470 Total vertex volume 189264 (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) = 1351565 mm^3 (det: 1.441370 ) 538 289 759 1.946 0.409 0.128 0.031 7 0.7 BA1_exvivo 1480 938 1850 1.852 0.368 0.087 0.015 8 1.0 BA2_exvivo 877 641 870 1.751 0.368 0.131 0.024 6 1.0 BA3a_exvivo 1276 842 1294 1.565 0.329 0.083 0.013 5 0.7 BA3b_exvivo 765 323 1238 2.925 0.493 0.086 0.028 7 0.9 BA4a_exvivo 999 619 1519 2.588 0.530 0.076 0.016 3 0.7 BA4p_exvivo 3990 2497 7638 2.632 0.547 0.109 0.022 33 3.6 BA6_exvivo 614 434 1271 2.679 0.328 0.127 0.033 7 0.7 BA44_exvivo 718 539 1743 2.608 0.444 0.141 0.031 9 0.9 BA45_exvivo 3994 2473 4443 1.722 0.424 0.117 0.032 47 4.8 V1_exvivo 4023 2626 5362 1.878 0.489 0.154 0.040 64 6.7 V2_exvivo 206 140 400 2.455 0.454 0.135 0.036 3 0.2 MT_exvivo 34 25 65 3.432 0.442 0.170 0.038 0 0.1 perirhinal_exvivo 543 374 1883 3.597 0.753 0.110 0.025 6 0.6 entorhinal_exvivo @#@FSTIME 2024:11:22:15:32:14 mris_anatomical_stats N 12 e 4.51 S 0.49 U 6.51 P 155% M 405768 F 3 R 197093 W 0 c 649 w 309 I 0 O 136 L 33.63 30.70 28.80 @#@FSLOADPOST 2024:11:22:15:32:19 mris_anatomical_stats N 12 33.34 30.69 28.81 Started at Fri Nov 22 14:35:56 CST 2024 Ended at Fri Nov 22 15:32:19 CST 2024 #@#%# recon-all-run-time-hours 0.940 recon-all -s PIB15-273_VYr9_Bay3prisma finished without error at Fri Nov 22 15:32:19 CST 2024 #New# invocation of recon-all Wed Jan 8 15:52:26 CST 2025 cd /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma_AT_test1 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 PIB15-273_VYr9_Bay3prisma_AT_test1 -autorecon2-wm -autorecon3 subjid PIB15-273_VYr9_Bay3prisma_AT_test1 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 155Gi 15Gi 133Mi 80Gi 93Gi 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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:26-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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: 2025/01/08-21:52:27-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 Wed Jan 8 15:52:27 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma_AT_test1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1392486 voxels in mask (pct= 8.30) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2025:01:08:15:52:27 mri_mask N 5 e 0.94 S 0.05 U 1.36 P 150% M 74292 F 0 R 17272 W 0 c 135 w 93 I 4752 O 2344 L 13.95 14.05 12.50 @#@FSLOADPOST 2025:01:08:15:52:28 mri_mask N 5 14.36 14.13 12.53 #-------------------------------------------- #@# Fill Wed Jan 8 15:52:28 CST 2025 /data/jsp/human/PIB/PIB_FreeSurfer7.3/Processing/PIB15-273_VYr9_Bay3prisma_AT_test1/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 1.09938 0.05633 -0.05324 -15.94841; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47585; 0.00000 0.00000 0.00000 1.00000; Using auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt ndiff 9202 voxel to talairach voxel transform 1.09938 0.05633 -0.05324 -15.94841; -0.04493 1.17940 0.16688 -44.61295; 0.09796 -0.10619 1.03625 -21.47585; 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] = 1275 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) no need to search using seed (126, 120, 155), TAL = (2.0, 27.0, 8.0) free(): double free detected in tcache 2 Command terminated by signal 6 @#@FSTIME 2025:01:08:15:52:28 mri_fill N 14 e 34.65 S 1.17 U 34.52 P 103% M 969524 F 0 R 849011 W 0 c 3155 w 79 I 1920 O 0 L 14.36 14.13 12.53 @#@FSLOADPOST 2025:01:08:15:53:03 mri_fill N 14 16.22 14.64 12.75 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 PIB15-273_VYr9_Bay3prisma_AT_test1 exited with ERRORS at Wed Jan 8 15:53:03 CST 2025 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting