Mon Sep 5 12:42:55 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects /home/marcantf/software/freesurfer/bin/recon-all -all -s P7T_020_001bc -hires -i BC_MPRAGE_iPat2.nii -expert expert-file.opts subjid P7T_020_001bc setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Actual FREESURFER_HOME /home/marcantf/software/freesurfer build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Linux mrphys-gpu1 4.15.0-180-generic #189-Ubuntu SMP Wed May 18 14:13:57 UTC 2022 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 257349 maxlocks unlimited maxsignal 257349 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 62G 22G 5.7G 271M 34G 39G Swap: 0B 0B 0B ######################################## program versions used 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) 7.2.0 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:55-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:56-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:56-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:56-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:56-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:56-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:56-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:56-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:57-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:57-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:57-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:57-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:57-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:58-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:58-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:58-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:58-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:58-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:58-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:58-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:58-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:59-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:59-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:59-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:59-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:42:59-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:00-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:00-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:00-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:00-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:00-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:00-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:00-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:00-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 7.2.0 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:01-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 7.2.0 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:01-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:01-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:01-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:01-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:01-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:01-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:02-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:03-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:04-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:04-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:04-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:04-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:04-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:05-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:05-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:05-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:05-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:05-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:05-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:05-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:06-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:06-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:06-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:06-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:06-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:06-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:07-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:07-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.2.0 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/05-12:43:07-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: marcantf Machine: mrphys-gpu1 Platform: Linux PlatformVersion: 4.15.0-180-generic CompilerName: GCC CompilerVersion: 4.8.5 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 /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/marcantf/software/freesurfer/subjects/P7T_020_001bc mri_convert /home/marcantf/Data/scaifield/P7T_020_001/others-sequences/HighRes+BiasFieldCorr_mprage/BC_MPRAGE_iPat2.nii /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig/001.mgz mri_convert /home/marcantf/Data/scaifield/P7T_020_001/others-sequences/HighRes+BiasFieldCorr_mprage/BC_MPRAGE_iPat2.nii /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig/001.mgz reading from /home/marcantf/Data/scaifield/P7T_020_001/others-sequences/HighRes+BiasFieldCorr_mprage/BC_MPRAGE_iPat2.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999664, 0.017431, 0.0191776) j_ras = (-0.0174342, 0.999848, 0) k_ras = (-0.0191748, -0.000334382, 0.999816) writing to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig/001.mgz... @#@FSTIME 2022:09:05:12:43:08 mri_convert N 2 e 7.96 S 0.20 U 7.74 P 99% M 137916 F 3 R 33123 W 0 c 63 w 5 I 744 O 227544 L 1.68 0.80 0.56 @#@FSLOADPOST 2022:09:05:12:43:16 mri_convert N 2 1.57 0.80 0.56 #-------------------------------------------- #@# MotionCor Mon Sep 5 12:43:19 UTC 2022 Found 1 runs /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig/001.mgz /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/rawavg.mgz /home/marcantf/software/freesurfer/subjects/P7T_020_001bc mri_convert /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/rawavg.mgz /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz --conform_min mri_convert /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/rawavg.mgz /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz --conform_min reading from /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999664, 0.017431, 0.0191776) j_ras = (-0.0174342, 0.999848, 0) k_ras = (-0.0191748, -0.000334382, 0.999816) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 1300.54 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz... @#@FSTIME 2022:09:05:12:43:23 mri_convert N 3 e 14.52 S 0.18 U 14.31 P 99% M 171172 F 0 R 60712 W 0 c 360 w 1 I 0 O 39088 L 1.93 0.89 0.59 @#@FSLOADPOST 2022:09:05:12:43:37 mri_convert N 3 1.79 0.91 0.61 mri_add_xform_to_header -c /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/transforms/talairach.xfm /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2022:09:05:12:43:38 mri_add_xform_to_header N 4 e 3.96 S 0.07 U 3.72 P 95% M 45844 F 14 R 10172 W 0 c 910 w 18 I 3112 O 39088 L 1.79 0.91 0.61 @#@FSLOADPOST 2022:09:05:12:43:42 mri_add_xform_to_header N 4 1.81 0.93 0.61 #-------------------------------------------- #@# Talairach Mon Sep 5 12:43:42 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri /home/marcantf/software/freesurfer/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 7.2.0 Linux mrphys-gpu1 4.15.0-180-generic #189-Ubuntu SMP Wed May 18 14:13:57 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Mon Sep 5 12:43:42 UTC 2022 tmpdir is ./tmp.mri_nu_correct.mni.20110 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.20110/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.20110/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.20110/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.20110/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.72179e-10, 0) j_ras = (-1.5522e-09, 0, -1) k_ras = (4.19126e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Mon Sep 5 12:51:21 UTC 2022 mri_nu_correct.mni done @#@FSTIME 2022:09:05:12:43:42 mri_nu_correct.mni N 12 e 459.00 S 1.69 U 456.43 P 99% M 1176308 F 19 R 852143 W 0 c 14753 w 113 I 4352 O 80520 L 1.81 0.93 0.61 @#@FSLOADPOST 2022:09:05:12:51:21 mri_nu_correct.mni N 12 1.15 1.19 0.91 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Mon Sep 5 12:51:21 UTC 2022 Ended at Mon Sep 5 12:52:01 UTC 2022 talairach_avi done @#@FSTIME 2022:09:05:12:51:21 talairach_avi N 4 e 39.84 S 2.49 U 28.61 P 78% M 599756 F 13 R 713320 W 0 c 768 w 296 I 272152 O 691256 L 1.15 1.19 0.91 @#@FSLOADPOST 2022:09:05:12:52:01 talairach_avi N 4 1.10 1.16 0.92 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /home/marcantf/software/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.2.0 --src: orig.mgz src image (geometry). --trg: /home/marcantf/software/freesurfer/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 1.22950 -0.07548 0.04846 -0.49901; 0.05106 1.16298 0.23662 -13.29578; -0.06208 -0.40619 1.26042 -11.06772; 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 Mon Sep 5 12:52:03 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6790, pval=0.4932 >= threshold=0.0050) @#@FSTIME 2022:09:05:12:52:03 talairach_afd N 4 e 0.24 S 0.00 U 0.00 P 3% M 5948 F 10 R 208 W 0 c 2 w 16 I 2504 O 0 L 1.10 1.16 0.92 @#@FSLOADPOST 2022:09:05:12:52:03 talairach_afd N 4 1.10 1.16 0.92 awk -f /home/marcantf/software/freesurfer/bin/extract_talairach_avi_QA.awk /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/transforms/talairach_avi.log tal_QC_AZS /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/transforms/talairach_avi.log TalAviQA: 0.96789 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Mon Sep 5 12:52:03 UTC 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 /usr/bin/bc /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri /home/marcantf/software/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.2.0 Linux mrphys-gpu1 4.15.0-180-generic #189-Ubuntu SMP Wed May 18 14:13:57 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Mon Sep 5 12:52:04 UTC 2022 tmpdir is ./tmp.mri_nu_correct.mni.20468 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.20468/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.20468/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.20468/ones.mgz 7.2.0 cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.20468/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.20468/ones.mgz sysname Linux hostname mrphys-gpu1 machine x86_64 user marcantf input ./tmp.mri_nu_correct.mni.20468/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.20468/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 39304000 values in range Counting number of voxels in first frame Found 39303999 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.20468/ones.mgz Count: 39303999 8489662.247188 39304000 99.999997 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20468/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20468/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20468/input.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20468/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20468/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20468/input.mean.dat sysname Linux hostname mrphys-gpu1 machine x86_64 user marcantf whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20468/ones.mgz Loading orig.mgz Voxel Volume is 0.216 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 0 Writing to ./tmp.mri_nu_correct.mni.20468/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20468/ones.mgz --i ./tmp.mri_nu_correct.mni.20468/nu0.mgz --sum ./tmp.mri_nu_correct.mni.20468/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20468/output.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20468/ones.mgz --i ./tmp.mri_nu_correct.mni.20468/nu0.mgz --sum ./tmp.mri_nu_correct.mni.20468/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20468/output.mean.dat sysname Linux hostname mrphys-gpu1 machine x86_64 user marcantf whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20468/ones.mgz Loading ./tmp.mri_nu_correct.mni.20468/nu0.mgz Voxel Volume is 0.216 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 0 Writing to ./tmp.mri_nu_correct.mni.20468/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.20468/nu0.mgz ./tmp.mri_nu_correct.mni.20468/nu0.mgz mul .91121654416484702822 Saving result to './tmp.mri_nu_correct.mni.20468/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.20468/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.20468/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.20468/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.72179e-10, 0) j_ras = (-1.5522e-09, 0, -1) k_ras = (4.19126e-10, 1, 0) 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 13 seconds. mapping (52, 145) to ( 3, 110) Mon Sep 5 13:00:37 UTC 2022 mri_nu_correct.mni done @#@FSTIME 2022:09:05:12:52:04 mri_nu_correct.mni N 10 e 513.33 S 3.23 U 509.31 P 99% M 1429232 F 29 R 1510341 W 0 c 12495 w 197 I 7224 O 226968 L 1.10 1.16 0.92 @#@FSLOADPOST 2022:09:05:13:00:37 mri_nu_correct.mni N 10 1.25 1.33 1.16 mri_add_xform_to_header -c /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2022:09:05:13:00:37 mri_add_xform_to_header N 4 e 1.47 S 0.06 U 1.35 P 96% M 45968 F 1 R 10186 W 0 c 15 w 3 I 512 O 17024 L 1.25 1.33 1.16 @#@FSLOADPOST 2022:09:05:13:00:38 mri_add_xform_to_header N 4 1.25 1.33 1.16 #-------------------------------------------- #@# Intensity Normalization Mon Sep 5 13:00:38 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_normalize -g 1 -seed 1234 -mprage -noconform 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 not interpolating and embedding volume to be 256^3... reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.22950 -0.07548 0.04846 -0.49901; 0.05106 1.16298 0.23662 -13.29578; -0.06208 -0.40619 1.26042 -11.06772; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 71 (71), valley at 59 (59) csf peak at 10, 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 71 (71), valley at 60 (60) csf peak at 21, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 6 minutes and 12 seconds. @#@FSTIME 2022:09:05:13:00:38 mri_normalize N 8 e 373.46 S 1.49 U 371.77 P 99% M 1282052 F 7 R 723397 W 0 c 2751 w 8 I 1576 O 15872 L 1.25 1.33 1.16 @#@FSLOADPOST 2022:09:05:13:06:52 mri_normalize N 8 1.18 1.43 1.28 #-------------------------------------------- #@# Skull Stripping Mon Sep 5 13:06:52 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_em_register -skull nu.mgz /home/marcantf/software/freesurfer/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 = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/marcantf/software/freesurfer/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 3 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=39.9 skull bounding box = (60, 36, 38) --> (289, 259, 307) finding center of left hemi white matter using (136, 110, 173) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (108,82,140) --> (164, 137,206) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.5 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -308.752 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.695380 @ (10.526, 31.579, 10.526) max log p = -4.623946 @ (15.789, -5.263, -5.263) max log p = -4.592319 @ (-7.895, -7.895, 2.632) max log p = -4.585039 @ (-1.316, -1.316, -1.316) max log p = -4.575253 @ (-0.658, -0.658, -0.658) max log p = -4.546091 @ (0.329, -0.329, 0.329) max log p = -4.546091 @ (0.000, 0.000, 0.000) max log p = -4.539786 @ (0.082, 0.247, -0.082) Found translation: (16.9, 16.4, 6.2): log p = -4.540 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.209, old_max_log_p =-4.540 (thresh=-4.5) 0.74175 0.00000 0.00000 -2.17460; 0.00000 0.68410 0.07832 -2.75582; 0.00000 -0.09682 0.63948 21.55552; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 53 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.209, old_max_log_p =-4.209 (thresh=-4.2) 0.74175 0.00000 0.00000 -2.17460; 0.00000 0.68410 0.07832 -2.75582; 0.00000 -0.09682 0.63948 21.55552; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 51 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.113, old_max_log_p =-4.209 (thresh=-4.2) 0.75243 0.03566 0.05008 -19.18883; -0.04841 0.67546 0.11701 1.32881; -0.05033 -0.14634 0.65532 37.57505; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 43 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.106, old_max_log_p =-4.113 (thresh=-4.1) 0.76900 0.01865 0.02523 -14.68738; -0.02417 0.68910 0.12009 -6.12375; -0.02520 -0.14237 0.64430 33.73535; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 45 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.102, old_max_log_p =-4.106 (thresh=-4.1) 0.75458 0.01830 0.02476 -11.30556; -0.02462 0.70202 0.12234 -7.77439; -0.02520 -0.14237 0.64430 35.61035; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 44 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.101, old_max_log_p =-4.102 (thresh=-4.1) 0.76873 0.01865 0.02522 -14.62396; -0.02462 0.70202 0.12234 -7.77439; -0.02473 -0.13970 0.63222 35.81057; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 47 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.082, old_max_log_p =-4.101 (thresh=-4.1) 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 37 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.082, old_max_log_p =-4.082 (thresh=-4.1) 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 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 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 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: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.082 (old=-308.752) transform before final EM align: 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 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 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 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) = 4.5 tol 0.000000 final transform: 0.77089 0.01401 0.01904 -13.02194; -0.01810 0.70080 0.11697 -8.13742; -0.01860 -0.13439 0.63559 33.80812; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 1006144 FSRUNTIME@ mri_em_register 0.2571 hours 1 threads registration took 15 minutes and 26 seconds. @#@FSTIME 2022:09:05:13:06:52 mri_em_register N 4 e 925.61 S 2.22 U 920.84 P 99% M 833456 F 7 R 245531 W 0 c 19192 w 453 I 151344 O 16 L 1.18 1.43 1.28 @#@FSLOADPOST 2022:09:05:13:22:18 mri_em_register N 4 1.20 1.29 1.31 mri_watershed -T1 -brain_atlas /home/marcantf/software/freesurfer/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 conforming input... updating LTA to account for conformation Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=144 y=122 z=127 r=64 first estimation of the main basin volume: 1146746 voxels Looking for seedpoints 2 found in the cerebellum 11 found in the rest of the brain global maximum in x=159, y=106, z=116, Imax=255 CSF=16, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=1286232892 voxels, voxel volume =1.000 = 1286232892 mmm3 = 1286232.832 cm3 done. PostAnalyze...Basin Prior 877 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=132,y=123, z=120, r=9558 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 45666 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 2646 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1548 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 24642 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 16614 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 216 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 3, 18, 89 after analyzing : 3, 17, 25, 35 RIGHT_CER before analyzing : 3, 3, 12, 61 after analyzing : 3, 17, 25, 28 LEFT_CER before analyzing : 3, 3, 5, 90 after analyzing : 3, 17, 25, 35 RIGHT_BRAIN before analyzing : 3, 3, 17, 89 after analyzing : 3, 17, 25, 35 LEFT_BRAIN before analyzing : 3, 3, 32, 70 after analyzing : 3, 22, 32, 34 OTHER before analyzing : 3, 3, 18, 89 after analyzing : 3, 17, 25, 35 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 66.940, std = 8.127 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.76, sigma = 2.76 after rotation: sse = 1.76, sigma = 2.76 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.80, its var is 2.39 before Erosion-Dilatation 0.06% 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...30 iterations mri_strip_skull: done peeling brain Brain Size = 1441268 voxels, voxel volume = 1.000 mm3 = 1441268 mmm3 = 1441.268 cm3 INFO: MRImask() using MRImaskDifferentGeometry() ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 20.297415 mri_watershed stimesec 0.436297 mri_watershed ru_maxrss 790768 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 223650 mri_watershed ru_majflt 7 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9904 mri_watershed ru_oublock 9272 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 47 mri_watershed ru_nivcsw 755 mri_watershed done @#@FSTIME 2022:09:05:13:22:18 mri_watershed N 6 e 21.07 S 0.47 U 20.29 P 98% M 790768 F 7 R 223651 W 0 c 755 w 48 I 9904 O 9272 L 1.20 1.29 1.31 @#@FSLOADPOST 2022:09:05:13:22:39 mri_watershed N 6 1.14 1.27 1.30 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Sep 5 13:22:40 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/marcantf/software/freesurfer/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 = 1 == reading 1 input volumes... logging results to talairach.log reading '/home/marcantf/software/freesurfer/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 2 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=14.0 skull bounding box = (76, 51, 34) --> (272, 267, 307) finding center of left hemi white matter using (141, 123, 171) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (117,96,137) --> (165, 149,204) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.1 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -356.661 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.141621 @ (31.579, 31.579, 10.526) max log p = -3.993111 @ (-5.263, -5.263, -5.263) max log p = -3.961509 @ (-7.895, -7.895, 2.632) max log p = -3.937413 @ (3.947, 3.947, 3.947) max log p = -3.924160 @ (-3.289, -3.289, -4.605) max log p = -3.912965 @ (2.961, 3.618, 4.934) max log p = -3.910637 @ (0.493, -0.164, 0.493) max log p = -3.907392 @ (-0.576, 0.411, 0.576) Found translation: (22.0, 22.9, 13.2): log p = -3.907 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.657, old_max_log_p =-3.907 (thresh=-3.9) 0.74175 0.00000 0.00000 -5.20413; 0.00000 0.68106 0.10141 -6.00259; 0.00000 -0.06697 0.59791 23.10962; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 42 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.653, old_max_log_p =-3.657 (thresh=-3.7) 0.68612 0.00000 0.00000 7.83657; 0.00000 0.68106 0.10141 -6.00259; 0.00000 -0.06697 0.59791 23.10962; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 40 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.645, old_max_log_p =-3.653 (thresh=-3.6) 0.73758 0.00000 0.00000 -4.22610; 0.00000 0.68106 0.10141 -6.00259; 0.00000 -0.06697 0.59791 23.10962; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 41 seconds. **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.645, old_max_log_p =-3.645 (thresh=-3.6) 0.73758 0.00000 0.00000 -4.22610; 0.00000 0.68106 0.10141 -6.00259; 0.00000 -0.06697 0.59791 23.10962; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 40 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.645 (thresh=-3.6) 0.70818 0.01660 0.03937 -6.93696; -0.02762 0.66215 0.13764 -5.04014; -0.04592 -0.11152 0.59976 39.28590; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 33 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.534, old_max_log_p =-3.534 (thresh=-3.5) 0.70818 0.01660 0.03937 -6.93696; -0.02762 0.66215 0.13764 -5.04014; -0.04592 -0.11152 0.59976 39.28590; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 32 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.530, old_max_log_p =-3.534 (thresh=-3.5) 0.70936 0.01753 0.03451 -6.36717; -0.02759 0.66137 0.13748 -4.38253; -0.04017 -0.11151 0.60077 37.27180; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 27 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.524, old_max_log_p =-3.530 (thresh=-3.5) 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 28 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.524, old_max_log_p =-3.524 (thresh=-3.5) 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 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 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 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: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.524 (old=-356.661) transform before final EM align: 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 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 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 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: 013: -log(p) = 4.0 tol 0.000000 final transform: 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 993588 FSRUNTIME@ mri_em_register 0.2587 hours 1 threads registration took 15 minutes and 31 seconds. @#@FSTIME 2022:09:05:13:22:40 mri_em_register N 7 e 931.44 S 2.41 U 926.68 P 99% M 820824 F 0 R 251203 W 0 c 29951 w 401 I 139952 O 16 L 1.14 1.27 1.30 @#@FSLOADPOST 2022:09:05:13:38:11 mri_em_register N 7 1.54 1.51 1.56 #-------------------------------------- #@# CA Normalize Mon Sep 5 13:38:11 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/marcantf/software/freesurfer/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 '/home/marcantf/software/freesurfer/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=14.0 skull bounding box = (76, 51, 34) --> (272, 267, 307) finding center of left hemi white matter using (141, 123, 171) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (117,96,137) --> (165, 149,204) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.1 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246437 sample points... INFO: compute sample coordinates transform 0.71138 0.00672 0.03233 -4.12162; -0.01596 0.66079 0.13786 -6.09450; -0.04017 -0.11151 0.60077 36.33430; 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 (173, 61, 32) --> (268, 235, 303) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 1292 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (84, 62, 28) --> (176, 232, 301) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 5 of 1479 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (178, 193, 78) --> (245, 263, 165) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 6 of 10 (60.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (113, 193, 70) --> (176, 260, 164) Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 5 of 8 (62.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (151, 178, 134) --> (199, 282, 183) Brain_Stem: limiting intensities to 109.0 --> 132.0 9 of 14 (64.3%) samples deleted using 2803 total control points for intensity normalization... bias field = 0.969 +- 0.047 8 of 2778 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (173, 61, 32) --> (268, 235, 303) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 11 of 1536 (0.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (84, 62, 28) --> (176, 232, 301) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 1878 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (178, 193, 78) --> (245, 263, 165) Left_Cerebellum_White_Matter: limiting intensities to 111.0 --> 132.0 44 of 52 (84.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (113, 193, 70) --> (176, 260, 164) Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0 18 of 48 (37.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (151, 178, 134) --> (199, 282, 183) Brain_Stem: limiting intensities to 94.0 --> 132.0 63 of 81 (77.8%) samples deleted using 3595 total control points for intensity normalization... bias field = 1.009 +- 0.052 24 of 3439 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (173, 61, 32) --> (268, 235, 303) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 20 of 1555 (1.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (84, 62, 28) --> (176, 232, 301) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 12 of 1938 (0.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (178, 193, 78) --> (245, 263, 165) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 34 of 75 (45.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (113, 193, 70) --> (176, 260, 164) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 40 (42.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (151, 178, 134) --> (199, 282, 183) Brain_Stem: limiting intensities to 88.0 --> 132.0 63 of 92 (68.5%) samples deleted using 3700 total control points for intensity normalization... bias field = 1.010 +- 0.051 17 of 3496 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 55 seconds. @#@FSTIME 2022:09:05:13:38:11 mri_ca_normalize N 8 e 175.51 S 1.49 U 173.73 P 99% M 917292 F 6 R 864373 W 0 c 1898 w 7 I 1448 O 12424 L 1.54 1.51 1.56 @#@FSLOADPOST 2022:09:05:13:41:07 mri_ca_normalize N 8 1.22 1.45 1.53 #-------------------------------------- #@# CA Reg Mon Sep 5 13:41:07 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/marcantf/software/freesurfer/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 = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/marcantf/software/freesurfer/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 0.970513 #FOTS# QuadFit found better minimum quadopt=(dt=412.508,rms=0.902927) vs oldopt=(dt=369.92,rms=0.903992) #GCMRL# 0 dt 412.507542 rms 0.903 6.964% neg 0 invalid 762 tFOTS 19.0620 tGradient 7.0060 tsec 27.2470 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.880775) vs oldopt=(dt=369.92,rms=0.882822) #GCMRL# 1 dt 517.888000 rms 0.881 2.453% neg 0 invalid 762 tFOTS 15.7690 tGradient 6.9140 tsec 23.8760 #GCMRL# 2 dt 369.920000 rms 0.870 1.220% neg 0 invalid 762 tFOTS 17.0710 tGradient 7.2160 tsec 25.4600 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.862768) vs oldopt=(dt=369.92,rms=0.862815) #GCMRL# 3 dt 443.904000 rms 0.863 0.834% neg 0 invalid 762 tFOTS 16.2290 tGradient 6.8220 tsec 24.2200 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.858611) vs oldopt=(dt=369.92,rms=0.859176) #GCMRL# 4 dt 221.952000 rms 0.859 0.482% neg 0 invalid 762 tFOTS 19.2520 tGradient 7.9360 tsec 28.3830 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.847498) vs oldopt=(dt=1479.68,rms=0.848387) #GCMRL# 5 dt 2071.552000 rms 0.847 1.294% neg 0 invalid 762 tFOTS 16.5280 tGradient 7.0670 tsec 24.7810 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.843308) vs oldopt=(dt=369.92,rms=0.844838) #GCMRL# 6 dt 221.952000 rms 0.843 0.494% neg 0 invalid 762 tFOTS 16.2830 tGradient 6.6740 tsec 24.1330 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.841852) vs oldopt=(dt=369.92,rms=0.842073) #GCMRL# 7 dt 517.888000 rms 0.842 0.000% neg 0 invalid 762 tFOTS 17.3430 tGradient 6.9240 tsec 25.4790 #GCAMreg# pass 0 level1 5 level2 1 tsec 219.705 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 0.842402 #GCMRL# 9 dt 92.480000 rms 0.842 0.078% neg 0 invalid 762 tFOTS 17.2340 tGradient 6.8650 tsec 25.5950 #FOTS# QuadFit found better minimum quadopt=(dt=27.744,rms=0.84173) vs oldopt=(dt=23.12,rms=0.84173) #GCMRL# 10 dt 27.744000 rms 0.842 0.000% neg 0 invalid 762 tFOTS 19.3430 tGradient 6.8950 tsec 27.9810 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 0.862053 #FOTS# QuadFit found better minimum quadopt=(dt=141.981,rms=0.85454) vs oldopt=(dt=103.68,rms=0.855027) #GCMRL# 12 dt 141.980583 rms 0.855 0.872% neg 0 invalid 762 tFOTS 16.7370 tGradient 6.0870 tsec 24.0900 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.840858) vs oldopt=(dt=414.72,rms=0.841346) #GCMRL# 13 dt 497.664000 rms 0.841 1.601% neg 0 invalid 762 tFOTS 17.5530 tGradient 6.5400 tsec 25.3110 #FOTS# QuadFit found better minimum quadopt=(dt=73.0201,rms=0.839135) vs oldopt=(dt=103.68,rms=0.839396) #GCMRL# 14 dt 73.020134 rms 0.839 0.000% neg 0 invalid 762 tFOTS 19.7630 tGradient 5.5370 tsec 26.5740 #GCMRL# 15 dt 73.020134 rms 0.839 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7790 tsec 7.0220 #GCMRL# 16 dt 73.020134 rms 0.839 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8990 tsec 7.5930 #GCMRL# 17 dt 73.020134 rms 0.838 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3510 tsec 7.6650 #GCMRL# 18 dt 73.020134 rms 0.837 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0930 tsec 7.4400 #GCMRL# 19 dt 73.020134 rms 0.835 0.219% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7620 tsec 8.0900 #GCMRL# 20 dt 73.020134 rms 0.834 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.8940 tsec 8.1580 #GCMRL# 21 dt 73.020134 rms 0.832 0.188% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3530 tsec 7.5830 #GCMRL# 22 dt 73.020134 rms 0.831 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6790 tsec 7.0050 #GCMRL# 23 dt 73.020134 rms 0.830 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0150 tsec 7.6300 #GCMRL# 24 dt 73.020134 rms 0.829 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4110 tsec 6.8740 #GCMRL# 25 dt 73.020134 rms 0.828 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6270 tsec 7.2930 #GCMRL# 26 dt 73.020134 rms 0.827 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6820 tsec 7.3860 #GCMRL# 27 dt 0.450000 rms 0.827 0.000% neg 0 invalid 762 tFOTS 19.9800 tGradient 5.6960 tsec 27.3780 #GCAMreg# pass 0 level1 4 level2 1 tsec 210.152 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 0.827727 #GCMRL# 29 dt 0.000000 rms 0.827 0.072% neg 0 invalid 762 tFOTS 17.0020 tGradient 5.4710 tsec 23.6450 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 0.874854 #FOTS# QuadFit found better minimum quadopt=(dt=5.45251,rms=0.872856) vs oldopt=(dt=8,rms=0.87327) #GCMRL# 31 dt 5.452514 rms 0.873 0.228% neg 0 invalid 762 tFOTS 15.3370 tGradient 4.7920 tsec 21.3010 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.872863) vs oldopt=(dt=0.5,rms=0.872867) #GCAMreg# pass 0 level1 3 level2 1 tsec 53.707 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 0.87342 #GCMRL# 33 dt 0.500000 rms 0.873 0.062% neg 0 invalid 762 tFOTS 16.3260 tGradient 4.7830 tsec 22.2940 #GCMRL# 34 dt 0.125000 rms 0.873 0.000% neg 0 invalid 762 tFOTS 15.4090 tGradient 4.8510 tsec 21.4840 #GCMRL# 35 dt 0.125000 rms 0.873 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8640 tsec 6.0430 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 0.983543 #FOTS# QuadFit found better minimum quadopt=(dt=3.22267,rms=0.959156) vs oldopt=(dt=2.88,rms=0.959425) #GCMRL# 37 dt 3.222672 rms 0.959 2.480% neg 0 invalid 762 tFOTS 15.3040 tGradient 4.5350 tsec 21.0210 #FOTS# QuadFit found better minimum quadopt=(dt=3.61348,rms=0.948361) vs oldopt=(dt=2.88,rms=0.948799) #GCMRL# 38 dt 3.613483 rms 0.948 1.125% neg 0 invalid 762 tFOTS 15.4310 tGradient 4.5460 tsec 21.2330 #FOTS# QuadFit found better minimum quadopt=(dt=2.58116,rms=0.941939) vs oldopt=(dt=2.88,rms=0.942027) #GCMRL# 39 dt 2.581162 rms 0.942 0.677% neg 0 invalid 762 tFOTS 18.3750 tGradient 4.6260 tsec 24.1980 #FOTS# QuadFit found better minimum quadopt=(dt=2.67669,rms=0.938449) vs oldopt=(dt=2.88,rms=0.938474) #GCMRL# 40 dt 2.676692 rms 0.938 0.371% neg 0 invalid 762 tFOTS 15.3810 tGradient 4.3370 tsec 20.9050 #FOTS# QuadFit found better minimum quadopt=(dt=3.49206,rms=0.933986) vs oldopt=(dt=2.88,rms=0.934115) #GCMRL# 41 dt 3.492063 rms 0.934 0.476% neg 0 invalid 762 tFOTS 15.3960 tGradient 4.4760 tsec 21.0530 #FOTS# QuadFit found better minimum quadopt=(dt=1.76,rms=0.931846) vs oldopt=(dt=0.72,rms=0.932596) #GCMRL# 42 dt 1.760000 rms 0.932 0.000% neg 0 invalid 762 tFOTS 15.3890 tGradient 4.4300 tsec 21.0350 #GCMRL# 43 dt 1.760000 rms 0.930 0.196% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2560 tsec 5.4380 #GCMRL# 44 dt 1.760000 rms 0.928 0.257% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3390 tsec 5.5270 #GCMRL# 45 dt 1.760000 rms 0.925 0.231% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0640 tsec 6.5890 #GCMRL# 46 dt 1.760000 rms 0.924 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6630 tsec 5.8510 #GCMRL# 47 dt 1.760000 rms 0.923 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7320 tsec 5.9290 #GCMRL# 48 dt 1.760000 rms 0.923 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5470 tsec 5.8120 #FOTS# QuadFit found better minimum quadopt=(dt=10.2764,rms=0.921792) vs oldopt=(dt=11.52,rms=0.921811) #GCMRL# 49 dt 10.276423 rms 0.922 0.173% neg 0 invalid 762 tFOTS 16.5210 tGradient 4.9130 tsec 22.6280 #FOTS# QuadFit found better minimum quadopt=(dt=2.55556,rms=0.920964) vs oldopt=(dt=2.88,rms=0.920983) #GCMRL# 50 dt 2.555556 rms 0.921 0.000% neg 0 invalid 762 tFOTS 16.8670 tGradient 4.6560 tsec 22.7600 #GCMRL# 51 dt 2.555556 rms 0.921 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8320 tsec 6.0110 #GCMRL# 52 dt 2.555556 rms 0.921 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6080 tsec 5.7830 #GCMRL# 53 dt 2.555556 rms 0.920 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6290 tsec 5.8180 #GCMRL# 54 dt 2.555556 rms 0.920 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1490 tsec 6.3720 #GCAMreg# pass 0 level1 2 level2 1 tsec 246.962 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 0.920463 #GCMRL# 56 dt 0.000000 rms 0.920 0.054% neg 0 invalid 762 tFOTS 16.3600 tGradient 4.9610 tsec 22.5360 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 0.945979 #GCMRL# 58 dt 0.000000 rms 0.945 0.051% neg 0 invalid 762 tFOTS 14.5680 tGradient 4.4760 tsec 20.2310 #GCAMreg# pass 0 level1 1 level2 1 tsec 53.875 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 0.945979 #GCMRL# 60 dt 0.000000 rms 0.945 0.051% neg 0 invalid 762 tFOTS 14.4020 tGradient 4.4170 tsec 19.9940 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 0.903052 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.89796) vs oldopt=(dt=0.32,rms=0.899583) #GCMRL# 62 dt 0.192000 rms 0.898 0.564% neg 0 invalid 762 tFOTS 15.3970 tGradient 3.7350 tsec 20.3150 #FOTS# QuadFit found better minimum quadopt=(dt=0.016,rms=0.897839) vs oldopt=(dt=0.02,rms=0.897842) #GCMRL# 63 dt 0.016000 rms 0.898 0.000% neg 0 invalid 762 tFOTS 15.3750 tGradient 3.7330 tsec 20.3200 #GCAMreg# pass 0 level1 0 level2 1 tsec 53.642 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 0.89834 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.897805) vs oldopt=(dt=0.005,rms=0.89781) #GCMRL# 65 dt 0.007000 rms 0.898 0.060% neg 0 invalid 762 tFOTS 15.5170 tGradient 3.7160 tsec 20.4210 #FOTS# QuadFit found better minimum quadopt=(dt=0.00175,rms=0.897782) vs oldopt=(dt=0.00125,rms=0.897783) #GCMRL# 66 dt 0.001750 rms 0.898 0.000% neg 0 invalid 762 tFOTS 17.9790 tGradient 3.7390 tsec 22.9350 #GCMRL# 67 dt 0.001750 rms 0.898 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6920 tsec 4.8740 GCAMregister done in 19.5902 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.09222 (18) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (12413 voxels, overlap=0.690) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (12413 voxels, peak = 12), gca=11.9 gca peak = 0.17690 (16) mri peak = 0.07963 (14) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (8401 voxels, overlap=0.886) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (8401 voxels, peak = 18), gca=17.5 gca peak = 0.28275 (96) mri peak = 0.07229 (98) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (5742 voxels, overlap=0.909) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (5742 voxels, peak = 98), gca=98.4 gca peak = 0.18948 (93) mri peak = 0.07110 (100) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (5059 voxels, overlap=0.825) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (5059 voxels, peak = 99), gca=99.0 gca peak = 0.20755 (55) mri peak = 0.06737 (71) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (5862 voxels, overlap=0.021) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (5862 voxels, peak = 68), gca=68.5 gca peak = 0.31831 (58) mri peak = 0.06472 (70) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (4802 voxels, overlap=0.092) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (4802 voxels, peak = 70), gca=70.5 gca peak = 0.11957 (102) mri peak = 0.08419 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (399267 voxels, overlap=0.645) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (399267 voxels, peak = 108), gca=107.6 gca peak = 0.11429 (102) mri peak = 0.07724 (105) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (401542 voxels, overlap=0.729) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (401542 voxels, peak = 108), gca=107.6 gca peak = 0.14521 (59) mri peak = 0.03392 (72) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (228775 voxels, overlap=0.005) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (228775 voxels, peak = 73), gca=73.5 gca peak = 0.14336 (58) mri peak = 0.02956 (72) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (222685 voxels, overlap=0.004) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (222685 voxels, peak = 71), gca=71.1 gca peak = 0.13305 (70) mri peak = 0.11051 (85) Right_Caudate (50): linear fit = 1.22 x + 0.0 (4139 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.22 x + 0.0 (4139 voxels, peak = 85), gca=85.1 gca peak = 0.15761 (71) mri peak = 0.12474 (87) Left_Caudate (11): linear fit = 1.17 x + 0.0 (4532 voxels, overlap=0.056) Left_Caudate (11): linear fit = 1.17 x + 0.0 (4532 voxels, peak = 83), gca=83.4 gca peak = 0.13537 (57) mri peak = 0.02087 ( 9) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (63811 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (63811 voxels, peak = 65), gca=64.7 gca peak = 0.13487 (56) mri peak = 0.01799 (15) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (66982 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (66982 voxels, peak = 78), gca=77.6 gca peak = 0.19040 (84) mri peak = 0.02371 (78) Left_Cerebellum_White_Matter (7): linear fit = 0.96 x + 0.0 (37061 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 0.96 x + 0.0 (37061 voxels, peak = 81), gca=81.1 gca peak = 0.18871 (83) mri peak = 0.02932 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (30553 voxels, overlap=0.122) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (30553 voxels, peak = 88), gca=87.6 gca peak = 0.24248 (57) mri peak = 0.05291 (75) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (2633 voxels, overlap=0.075) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (2633 voxels, peak = 70), gca=69.8 gca peak = 0.35833 (56) mri peak = 0.05383 (70) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (2858 voxels, overlap=0.036) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (2858 voxels, peak = 69), gca=68.6 gca peak = 0.12897 (85) mri peak = 0.07583 (101) Left_Thalamus (10): linear fit = 1.13 x + 0.0 (23961 voxels, overlap=0.180) Left_Thalamus (10): linear fit = 1.13 x + 0.0 (23961 voxels, peak = 96), gca=96.5 gca peak = 0.13127 (83) mri peak = 0.06781 (97) Right_Thalamus (49): linear fit = 1.15 x + 0.0 (16880 voxels, overlap=0.113) Right_Thalamus (49): linear fit = 1.15 x + 0.0 (16880 voxels, peak = 96), gca=95.9 gca peak = 0.12974 (78) mri peak = 0.08571 (99) Left_Putamen (12): linear fit = 1.26 x + 0.0 (12386 voxels, overlap=0.013) Left_Putamen (12): linear fit = 1.26 x + 0.0 (12386 voxels, peak = 99), gca=98.7 gca peak = 0.17796 (79) mri peak = 0.07102 (98) Right_Putamen (51): linear fit = 1.24 x + 0.0 (13362 voxels, overlap=0.014) Right_Putamen (51): linear fit = 1.24 x + 0.0 (13362 voxels, peak = 98), gca=97.6 gca peak = 0.10999 (80) mri peak = 0.06559 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (41446 voxels, overlap=0.417) Brain_Stem (16): linear fit = 1.10 x + 0.0 (41446 voxels, peak = 88), gca=87.6 gca peak = 0.13215 (88) mri peak = 0.05639 (97) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (7164 voxels, overlap=0.427) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (7164 voxels, peak = 100), gca=99.9 gca peak = 0.11941 (89) mri peak = 0.06353 (100) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (9460 voxels, overlap=0.455) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (9460 voxels, peak = 97), gca=97.5 gca peak = 0.20775 (25) mri peak = 0.08536 (27) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (458 voxels, overlap=0.943) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (458 voxels, peak = 24), gca=23.9 gca peak = 0.13297 (21) mri peak = 0.08460 (16) Fourth_Ventricle (15): linear fit = 0.80 x + 0.0 (2279 voxels, overlap=0.726) Fourth_Ventricle (15): linear fit = 0.80 x + 0.0 (2279 voxels, peak = 17), gca=16.7 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 1.23 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.90 x + 0.0 Left_Putamen too bright - rescaling by 0.982 (from 1.265) to 96.8 (was 98.7) Right_Putamen too bright - rescaling by 0.993 (from 1.235) to 96.8 (was 97.6) saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 7.11212 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 0.947701 #FOTS# QuadFit found better minimum quadopt=(dt=397.169,rms=0.903987) vs oldopt=(dt=369.92,rms=0.904221) #GCMRL# 69 dt 397.168724 rms 0.904 4.613% neg 0 invalid 762 tFOTS 16.3170 tGradient 7.3720 tsec 24.8610 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.878365) vs oldopt=(dt=369.92,rms=0.883993) #GCMRL# 70 dt 517.888000 rms 0.878 2.834% neg 0 invalid 762 tFOTS 15.3910 tGradient 7.7640 tsec 24.3330 #FOTS# QuadFit found better minimum quadopt=(dt=887.808,rms=0.863345) vs oldopt=(dt=1479.68,rms=0.866932) #GCMRL# 71 dt 887.808000 rms 0.863 1.710% neg 0 invalid 762 tFOTS 15.4040 tGradient 7.5290 tsec 24.1110 #GCMRL# 72 dt 369.920000 rms 0.857 0.754% neg 0 invalid 762 tFOTS 16.4800 tGradient 7.6500 tsec 25.3210 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.854091) vs oldopt=(dt=369.92,rms=0.854099) #GCMRL# 73 dt 295.936000 rms 0.854 0.320% neg 0 invalid 762 tFOTS 16.4360 tGradient 8.0580 tsec 25.6770 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.850075) vs oldopt=(dt=369.92,rms=0.850101) #GCMRL# 74 dt 443.904000 rms 0.850 0.470% neg 0 invalid 762 tFOTS 16.4440 tGradient 7.7360 tsec 25.3670 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.848032) vs oldopt=(dt=369.92,rms=0.848537) #GCMRL# 75 dt 221.952000 rms 0.848 0.240% neg 0 invalid 762 tFOTS 16.4790 tGradient 7.7780 tsec 25.4390 #FOTS# QuadFit found better minimum quadopt=(dt=887.808,rms=0.843252) vs oldopt=(dt=1479.68,rms=0.843902) #GCMRL# 76 dt 887.808000 rms 0.843 0.564% neg 0 invalid 762 tFOTS 16.4210 tGradient 7.4400 tsec 25.0430 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.841832) vs oldopt=(dt=92.48,rms=0.842008) #GCMRL# 77 dt 129.472000 rms 0.842 0.168% neg 0 invalid 762 tFOTS 16.4450 tGradient 7.6490 tsec 25.2910 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.840561) vs oldopt=(dt=369.92,rms=0.840784) #GCMRL# 78 dt 517.888000 rms 0.841 0.151% neg 0 invalid 762 tFOTS 16.4880 tGradient 7.7060 tsec 25.3870 #GCMRL# 79 dt 369.920000 rms 0.838 0.272% neg 0 invalid 762 tFOTS 16.5100 tGradient 7.3990 tsec 25.1050 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.837512) vs oldopt=(dt=369.92,rms=0.837597) #GCMRL# 80 dt 221.952000 rms 0.838 0.091% neg 0 invalid 762 tFOTS 16.4350 tGradient 7.7890 tsec 25.4080 #GCMRL# 81 dt 1479.680000 rms 0.834 0.425% neg 0 invalid 762 tFOTS 16.6920 tGradient 7.5530 tsec 25.4230 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.831565) vs oldopt=(dt=92.48,rms=0.831911) #GCMRL# 82 dt 129.472000 rms 0.832 0.286% neg 0 invalid 762 tFOTS 17.2990 tGradient 7.4420 tsec 25.9260 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.831046) vs oldopt=(dt=369.92,rms=0.831065) #GCMRL# 83 dt 295.936000 rms 0.831 0.062% neg 0 invalid 762 tFOTS 16.3410 tGradient 7.6570 tsec 25.1810 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.829826) vs oldopt=(dt=369.92,rms=0.830002) #GCMRL# 84 dt 517.888000 rms 0.830 0.147% neg 0 invalid 762 tFOTS 17.6570 tGradient 7.3810 tsec 26.2280 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.82936) vs oldopt=(dt=92.48,rms=0.829455) #GCMRL# 85 dt 129.472000 rms 0.829 0.056% neg 0 invalid 762 tFOTS 20.5200 tGradient 7.3040 tsec 29.0080 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.827467) vs oldopt=(dt=1479.68,rms=0.827512) #GCMRL# 86 dt 1775.616000 rms 0.827 0.228% neg 0 invalid 762 tFOTS 18.0530 tGradient 7.2810 tsec 26.5200 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.825801) vs oldopt=(dt=92.48,rms=0.826135) #GCMRL# 87 dt 129.472000 rms 0.826 0.201% neg 0 invalid 762 tFOTS 16.3600 tGradient 7.3240 tsec 24.8620 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.825313) vs oldopt=(dt=369.92,rms=0.82542) #GCMRL# 88 dt 221.952000 rms 0.825 0.059% neg 0 invalid 762 tFOTS 16.5500 tGradient 7.2660 tsec 25.0060 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.822976) vs oldopt=(dt=1479.68,rms=0.82335) #GCMRL# 89 dt 2071.552000 rms 0.823 0.283% neg 0 invalid 762 tFOTS 17.4480 tGradient 7.4420 tsec 26.3250 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.821754) vs oldopt=(dt=92.48,rms=0.821984) #GCMRL# 90 dt 129.472000 rms 0.822 0.149% neg 0 invalid 762 tFOTS 17.0960 tGradient 8.8030 tsec 27.1270 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.821544) vs oldopt=(dt=92.48,rms=0.821596) #GCMRL# 91 dt 129.472000 rms 0.822 0.000% neg 0 invalid 762 tFOTS 18.0430 tGradient 7.2630 tsec 26.5320 #GCMRL# 92 dt 129.472000 rms 0.821 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3700 tsec 8.5600 #GCMRL# 93 dt 129.472000 rms 0.821 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5780 tsec 8.7790 #GCMRL# 94 dt 129.472000 rms 0.821 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4630 tsec 8.6450 #GCMRL# 95 dt 129.472000 rms 0.820 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7340 tsec 9.3520 #GCMRL# 96 dt 129.472000 rms 0.819 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4090 tsec 9.6430 #GCMRL# 97 dt 129.472000 rms 0.818 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4970 tsec 8.6850 #GCMRL# 98 dt 129.472000 rms 0.817 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3830 tsec 8.5730 #GCMRL# 99 dt 129.472000 rms 0.816 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4840 tsec 8.6690 #GCMRL# 100 dt 129.472000 rms 0.815 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4300 tsec 8.6120 #GCMRL# 101 dt 129.472000 rms 0.814 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3580 tsec 8.5460 #GCMRL# 102 dt 129.472000 rms 0.813 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2560 tsec 8.4440 #GCMRL# 103 dt 129.472000 rms 0.812 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4950 tsec 8.6990 #GCMRL# 104 dt 129.472000 rms 0.811 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3830 tsec 8.5650 #GCMRL# 105 dt 129.472000 rms 0.810 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3230 tsec 8.5130 #GCMRL# 106 dt 129.472000 rms 0.809 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3930 tsec 8.5830 #GCMRL# 107 dt 129.472000 rms 0.808 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4610 tsec 8.6510 #GCMRL# 108 dt 129.472000 rms 0.807 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6000 tsec 8.7880 #GCMRL# 109 dt 129.472000 rms 0.806 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7150 tsec 8.9010 #GCMRL# 110 dt 129.472000 rms 0.805 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4550 tsec 8.6330 #GCMRL# 111 dt 129.472000 rms 0.804 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6630 tsec 8.8500 #GCMRL# 112 dt 129.472000 rms 0.803 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2130 tsec 8.4000 #GCMRL# 113 dt 129.472000 rms 0.802 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4280 tsec 8.7490 #GCMRL# 114 dt 129.472000 rms 0.801 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4050 tsec 8.7210 #GCMRL# 115 dt 129.472000 rms 0.800 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8040 tsec 9.0190 #GCMRL# 116 dt 129.472000 rms 0.800 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3600 tsec 8.5470 #GCMRL# 117 dt 129.472000 rms 0.799 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4400 tsec 8.6430 #GCMRL# 118 dt 129.472000 rms 0.798 0.113% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7390 tsec 8.9390 #GCMRL# 119 dt 129.472000 rms 0.797 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3760 tsec 8.5700 #GCMRL# 120 dt 129.472000 rms 0.796 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4970 tsec 8.6800 #GCMRL# 121 dt 129.472000 rms 0.796 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5400 tsec 9.1790 #GCMRL# 122 dt 129.472000 rms 0.795 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2930 tsec 8.4750 #GCMRL# 123 dt 129.472000 rms 0.794 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5270 tsec 8.7100 #GCMRL# 124 dt 129.472000 rms 0.794 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4040 tsec 8.5890 #GCMRL# 125 dt 129.472000 rms 0.793 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3560 tsec 8.5490 #GCMRL# 126 dt 129.472000 rms 0.792 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3060 tsec 8.4890 #GCMRL# 127 dt 129.472000 rms 0.792 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4100 tsec 8.5920 #GCMRL# 128 dt 129.472000 rms 0.791 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2960 tsec 8.4800 #GCMRL# 129 dt 129.472000 rms 0.791 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4970 tsec 8.6820 #GCMRL# 130 dt 129.472000 rms 0.790 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5940 tsec 8.7760 #GCMRL# 131 dt 129.472000 rms 0.790 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2270 tsec 8.4100 #GCMRL# 132 dt 129.472000 rms 0.789 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3020 tsec 8.4890 #GCMRL# 133 dt 129.472000 rms 0.789 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3090 tsec 8.5010 #GCMRL# 134 dt 129.472000 rms 0.788 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2900 tsec 8.4790 #GCMRL# 135 dt 129.472000 rms 0.788 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2790 tsec 8.4510 #GCMRL# 136 dt 129.472000 rms 0.788 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2180 tsec 8.3930 #GCMRL# 137 dt 129.472000 rms 0.787 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2410 tsec 8.4260 #GCMRL# 138 dt 129.472000 rms 0.787 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2290 tsec 8.4190 #GCMRL# 139 dt 129.472000 rms 0.787 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3680 tsec 8.5390 #GCMRL# 140 dt 129.472000 rms 0.786 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4110 tsec 8.5900 #GCMRL# 141 dt 129.472000 rms 0.786 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3670 tsec 8.5720 #GCMRL# 142 dt 129.472000 rms 0.785 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7020 tsec 8.8820 #GCMRL# 143 dt 129.472000 rms 0.785 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3500 tsec 8.5280 #GCMRL# 144 dt 129.472000 rms 0.784 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3730 tsec 8.5520 #GCMRL# 145 dt 129.472000 rms 0.784 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2570 tsec 8.4380 #GCMRL# 146 dt 129.472000 rms 0.784 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4070 tsec 8.5740 #GCMRL# 147 dt 129.472000 rms 0.783 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1890 tsec 8.3610 #GCMRL# 148 dt 129.472000 rms 0.783 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4060 tsec 8.5770 #GCMRL# 149 dt 129.472000 rms 0.783 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4770 tsec 8.6500 #GCMRL# 150 dt 129.472000 rms 0.783 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3900 tsec 8.6000 #GCMRL# 151 dt 129.472000 rms 0.782 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4370 tsec 8.6150 #GCMRL# 152 dt 129.472000 rms 0.782 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5630 tsec 8.7480 #GCMRL# 153 dt 129.472000 rms 0.782 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2780 tsec 8.4510 #GCMRL# 154 dt 129.472000 rms 0.781 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4250 tsec 8.6130 #GCMRL# 155 dt 129.472000 rms 0.781 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5810 tsec 8.7790 #GCMRL# 156 dt 129.472000 rms 0.781 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4480 tsec 8.6340 #GCMRL# 157 dt 129.472000 rms 0.780 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4680 tsec 8.6690 #GCMRL# 158 dt 129.472000 rms 0.780 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4550 tsec 8.6430 #GCMRL# 159 dt 129.472000 rms 0.780 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3950 tsec 8.5750 #GCMRL# 160 dt 129.472000 rms 0.780 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3160 tsec 8.4940 #GCMRL# 161 dt 129.472000 rms 0.779 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2200 tsec 8.3940 #GCMRL# 162 dt 129.472000 rms 0.779 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2870 tsec 8.4770 #GCMRL# 163 dt 129.472000 rms 0.779 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3460 tsec 8.5270 #GCMRL# 164 dt 129.472000 rms 0.779 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3380 tsec 8.5180 #GCMRL# 165 dt 129.472000 rms 0.778 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3340 tsec 8.5870 #GCMRL# 166 dt 129.472000 rms 0.778 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2240 tsec 8.4030 #GCMRL# 167 dt 129.472000 rms 0.778 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3170 tsec 8.5020 #GCMRL# 168 dt 129.472000 rms 0.778 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2070 tsec 8.3930 #GCMRL# 169 dt 129.472000 rms 0.777 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3910 tsec 8.5710 #GCMRL# 170 dt 129.472000 rms 0.777 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3850 tsec 8.5610 #GCMRL# 171 dt 129.472000 rms 0.777 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3850 tsec 8.5690 #GCMRL# 172 dt 129.472000 rms 0.777 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3980 tsec 8.5840 #GCMRL# 173 dt 129.472000 rms 0.777 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3620 tsec 8.5440 #GCMRL# 174 dt 129.472000 rms 0.777 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4090 tsec 8.5850 #GCMRL# 175 dt 129.472000 rms 0.776 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3110 tsec 8.4870 #GCMRL# 176 dt 129.472000 rms 0.776 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3710 tsec 8.5550 #GCMRL# 177 dt 129.472000 rms 0.776 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4080 tsec 8.5880 #GCMRL# 178 dt 129.472000 rms 0.776 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3290 tsec 8.5060 #GCMRL# 179 dt 129.472000 rms 0.775 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4370 tsec 8.6150 #GCMRL# 180 dt 129.472000 rms 0.775 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3700 tsec 8.5540 #GCMRL# 181 dt 129.472000 rms 0.775 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3160 tsec 8.5490 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.775098) vs oldopt=(dt=92.48,rms=0.775098) #GCMRL# 182 dt 129.472000 rms 0.775 0.000% neg 0 invalid 762 tFOTS 17.2930 tGradient 7.2840 tsec 25.7970 #GCMRL# 183 dt 129.472000 rms 0.775 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2310 tsec 8.4130 #GCMRL# 184 dt 129.472000 rms 0.775 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2510 tsec 8.4260 #GCMRL# 185 dt 129.472000 rms 0.775 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3970 tsec 8.5780 #GCMRL# 186 dt 129.472000 rms 0.775 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3500 tsec 8.5350 #GCMRL# 187 dt 129.472000 rms 0.775 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3910 tsec 8.5840 #GCMRL# 188 dt 129.472000 rms 0.775 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3440 tsec 8.5240 #GCMRL# 189 dt 129.472000 rms 0.775 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2510 tsec 8.4250 #GCMRL# 190 dt 129.472000 rms 0.775 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2350 tsec 8.4080 #GCMRL# 191 dt 129.472000 rms 0.775 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.2260 tsec 8.4160 #GCAMreg# pass 0 level1 5 level2 1 tsec 1482.64 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 0.774873 #FOTS# QuadFit found better minimum quadopt=(dt=0.00338672,rms=0.774432) vs oldopt=(dt=0.00564453,rms=0.774432) #GCMRL# 193 dt 0.003387 rms 0.774 0.057% neg 0 invalid 762 tFOTS 22.9460 tGradient 7.3070 tsec 31.4270 #GCMRL# 194 dt 0.850000 rms 0.774 0.000% neg 0 invalid 762 tFOTS 17.3150 tGradient 7.2440 tsec 26.8280 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 0.780195 #FOTS# QuadFit found better minimum quadopt=(dt=995.328,rms=0.755733) vs oldopt=(dt=1658.88,rms=0.759346) #GCMRL# 196 dt 995.328000 rms 0.756 3.135% neg 0 invalid 762 tFOTS 18.8230 tGradient 5.5980 tsec 25.6040 #FOTS# QuadFit found better minimum quadopt=(dt=159.261,rms=0.748732) vs oldopt=(dt=103.68,rms=0.749493) #GCMRL# 197 dt 159.260726 rms 0.749 0.926% neg 0 invalid 762 tFOTS 16.4730 tGradient 5.9910 tsec 23.6470 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.744954) vs oldopt=(dt=103.68,rms=0.745766) #GCMRL# 198 dt 145.152000 rms 0.745 0.505% neg 0 invalid 762 tFOTS 18.5010 tGradient 5.6870 tsec 25.8050 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.74256) vs oldopt=(dt=414.72,rms=0.742963) #GCMRL# 199 dt 248.832000 rms 0.743 0.321% neg 0 invalid 762 tFOTS 16.7810 tGradient 7.4290 tsec 25.4150 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.739618) vs oldopt=(dt=103.68,rms=0.739951) #GCMRL# 200 dt 145.152000 rms 0.740 0.396% neg 0 invalid 762 tFOTS 17.0080 tGradient 5.7020 tsec 23.8950 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.738137) vs oldopt=(dt=103.68,rms=0.738245) #GCMRL# 201 dt 145.152000 rms 0.738 0.200% neg 0 invalid 762 tFOTS 16.6850 tGradient 5.8360 tsec 23.7090 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.736356) vs oldopt=(dt=103.68,rms=0.736693) #GCMRL# 202 dt 145.152000 rms 0.736 0.241% neg 0 invalid 762 tFOTS 15.6300 tGradient 5.9560 tsec 22.7820 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.735095) vs oldopt=(dt=103.68,rms=0.735227) #GCMRL# 203 dt 145.152000 rms 0.735 0.171% neg 0 invalid 762 tFOTS 17.3090 tGradient 5.8730 tsec 24.3740 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.733473) vs oldopt=(dt=103.68,rms=0.733754) #GCMRL# 204 dt 145.152000 rms 0.733 0.221% neg 0 invalid 762 tFOTS 16.2140 tGradient 5.8310 tsec 23.2330 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.732399) vs oldopt=(dt=103.68,rms=0.732505) #GCMRL# 205 dt 145.152000 rms 0.732 0.146% neg 0 invalid 762 tFOTS 16.4050 tGradient 5.9310 tsec 23.5110 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.730951) vs oldopt=(dt=103.68,rms=0.731206) #GCMRL# 206 dt 145.152000 rms 0.731 0.198% neg 0 invalid 762 tFOTS 15.2920 tGradient 5.7700 tsec 22.2290 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.73001) vs oldopt=(dt=103.68,rms=0.730049) #GCMRL# 207 dt 145.152000 rms 0.730 0.129% neg 0 invalid 762 tFOTS 15.3100 tGradient 5.7970 tsec 22.2740 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.72857) vs oldopt=(dt=103.68,rms=0.728805) #GCMRL# 208 dt 145.152000 rms 0.729 0.197% neg 0 invalid 762 tFOTS 15.2740 tGradient 5.5010 tsec 21.9440 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.727668) vs oldopt=(dt=103.68,rms=0.727689) #GCMRL# 209 dt 124.416000 rms 0.728 0.124% neg 0 invalid 762 tFOTS 15.2970 tGradient 5.9350 tsec 22.4090 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.726382) vs oldopt=(dt=103.68,rms=0.726649) #GCMRL# 210 dt 145.152000 rms 0.726 0.177% neg 0 invalid 762 tFOTS 15.3080 tGradient 5.5400 tsec 22.0270 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.725576) vs oldopt=(dt=103.68,rms=0.725649) #GCMRL# 211 dt 145.152000 rms 0.726 0.111% neg 0 invalid 762 tFOTS 15.2690 tGradient 5.8040 tsec 22.2450 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.724401) vs oldopt=(dt=103.68,rms=0.724614) #GCMRL# 212 dt 145.152000 rms 0.724 0.162% neg 0 invalid 762 tFOTS 15.8980 tGradient 6.0910 tsec 23.1760 #GCMRL# 213 dt 103.680000 rms 0.724 0.094% neg 0 invalid 762 tFOTS 16.3870 tGradient 5.6540 tsec 23.2190 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.722466) vs oldopt=(dt=414.72,rms=0.722789) #GCMRL# 214 dt 248.832000 rms 0.722 0.173% neg 0 invalid 762 tFOTS 15.3620 tGradient 5.8340 tsec 22.3730 #GCMRL# 215 dt 103.680000 rms 0.722 0.121% neg 0 invalid 762 tFOTS 15.3860 tGradient 5.6580 tsec 22.2320 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.720107) vs oldopt=(dt=414.72,rms=0.720499) #GCMRL# 216 dt 248.832000 rms 0.720 0.206% neg 0 invalid 762 tFOTS 15.4960 tGradient 5.8570 tsec 22.5350 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.719351) vs oldopt=(dt=103.68,rms=0.719419) #GCMRL# 217 dt 82.944000 rms 0.719 0.105% neg 0 invalid 762 tFOTS 15.4400 tGradient 5.7240 tsec 22.3410 #FOTS# QuadFit found better minimum quadopt=(dt=1327.1,rms=0.714739) vs oldopt=(dt=1658.88,rms=0.715083) #GCMRL# 218 dt 1327.104000 rms 0.715 0.641% neg 0 invalid 762 tFOTS 16.3390 tGradient 5.9270 tsec 23.4440 #FOTS# QuadFit found better minimum quadopt=(dt=65.9762,rms=0.711495) vs oldopt=(dt=103.68,rms=0.712087) #GCMRL# 219 dt 65.976247 rms 0.711 0.454% neg 0 invalid 762 tFOTS 16.4210 tGradient 5.8480 tsec 23.4510 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.711115) vs oldopt=(dt=103.68,rms=0.711127) #GCMRL# 220 dt 82.944000 rms 0.711 0.053% neg 0 invalid 762 tFOTS 16.3490 tGradient 5.6680 tsec 23.1970 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.709728) vs oldopt=(dt=414.72,rms=0.710021) #GCMRL# 221 dt 580.608000 rms 0.710 0.195% neg 0 invalid 762 tFOTS 16.3800 tGradient 5.6720 tsec 23.2270 #GCMRL# 222 dt 103.680000 rms 0.709 0.076% neg 0 invalid 762 tFOTS 15.3850 tGradient 5.8170 tsec 22.3810 #FOTS# QuadFit found better minimum quadopt=(dt=331.776,rms=0.707735) vs oldopt=(dt=414.72,rms=0.707885) #GCMRL# 223 dt 331.776000 rms 0.708 0.205% neg 0 invalid 762 tFOTS 15.4870 tGradient 5.9780 tsec 22.6520 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.707226) vs oldopt=(dt=25.92,rms=0.707322) #GCMRL# 224 dt 36.288000 rms 0.707 0.072% neg 0 invalid 762 tFOTS 17.2930 tGradient 5.7740 tsec 24.2510 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.707048) vs oldopt=(dt=103.68,rms=0.70708) #GCMRL# 225 dt 62.208000 rms 0.707 0.000% neg 0 invalid 762 tFOTS 16.3330 tGradient 5.6450 tsec 23.1930 #GCMRL# 226 dt 62.208000 rms 0.707 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7430 tsec 6.9350 #GCMRL# 227 dt 62.208000 rms 0.707 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8110 tsec 7.0570 #GCMRL# 228 dt 62.208000 rms 0.706 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0370 tsec 7.2470 #GCMRL# 229 dt 62.208000 rms 0.705 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9920 tsec 7.1820 #GCMRL# 230 dt 62.208000 rms 0.704 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.9860 tsec 7.1770 #GCMRL# 231 dt 62.208000 rms 0.704 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0830 tsec 7.7640 #GCMRL# 232 dt 0.972000 rms 0.704 -0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0530 tsec 11.5360 #GCMRL# 233 dt 1.620000 rms 0.704 0.001% neg 0 invalid 762 tFOTS 12.5180 tGradient 6.0460 tsec 19.7430 #GCMRL# 234 dt 0.006328 rms 0.704 0.001% neg 0 invalid 762 tFOTS 8.7190 tGradient 6.0900 tsec 15.9880 #GCAMreg# pass 0 level1 4 level2 1 tsec 809.53 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 0.704555 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.70393) vs oldopt=(dt=25.92,rms=0.703958) #GCMRL# 236 dt 36.288000 rms 0.704 0.089% neg 0 invalid 762 tFOTS 17.3240 tGradient 6.0950 tsec 24.6000 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.703841) vs oldopt=(dt=25.92,rms=0.703853) #GCMRL# 237 dt 36.288000 rms 0.704 0.000% neg 0 invalid 762 tFOTS 18.3180 tGradient 5.5540 tsec 25.0850 #GCMRL# 238 dt 36.288000 rms 0.704 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5710 tsec 6.7550 #GCMRL# 239 dt 36.288000 rms 0.704 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6260 tsec 6.8120 #GCMRL# 240 dt 36.288000 rms 0.704 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6690 tsec 6.8550 #GCMRL# 241 dt 36.288000 rms 0.704 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6370 tsec 6.8130 #GCMRL# 242 dt 36.288000 rms 0.704 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.7680 tsec 6.9870 #FOTS# QuadFit found better minimum quadopt=(dt=497.664,rms=0.701704) vs oldopt=(dt=414.72,rms=0.701743) #GCMRL# 243 dt 497.664000 rms 0.702 0.265% neg 0 invalid 762 tFOTS 16.4130 tGradient 5.5950 tsec 23.1950 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.701473) vs oldopt=(dt=25.92,rms=0.701526) #GCMRL# 244 dt 36.288000 rms 0.701 0.000% neg 0 invalid 762 tFOTS 15.4500 tGradient 5.7990 tsec 22.4670 #GCMRL# 245 dt 36.288000 rms 0.701 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5720 tsec 6.7570 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 0.721334 #FOTS# QuadFit found better minimum quadopt=(dt=119.569,rms=0.710457) vs oldopt=(dt=128,rms=0.710558) #GCMRL# 247 dt 119.568862 rms 0.710 1.508% neg 0 invalid 762 tFOTS 16.3940 tGradient 4.6250 tsec 22.1950 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.701887) vs oldopt=(dt=32,rms=0.703974) #GCMRL# 248 dt 44.800000 rms 0.702 1.206% neg 0 invalid 762 tFOTS 15.4240 tGradient 4.6940 tsec 21.2960 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.687275) vs oldopt=(dt=128,rms=0.690615) #GCMRL# 249 dt 179.200000 rms 0.687 2.082% neg 0 invalid 762 tFOTS 16.3840 tGradient 4.9160 tsec 22.4750 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.68499) vs oldopt=(dt=32,rms=0.685381) #GCMRL# 250 dt 44.800000 rms 0.685 0.332% neg 0 invalid 762 tFOTS 15.4030 tGradient 4.7420 tsec 21.3350 #GCMRL# 251 dt 128.000000 rms 0.682 0.432% neg 0 invalid 762 tFOTS 15.6900 tGradient 4.8260 tsec 21.7540 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.678663) vs oldopt=(dt=32,rms=0.678942) #GCMRL# 252 dt 44.800000 rms 0.679 0.493% neg 0 invalid 762 tFOTS 16.8710 tGradient 4.8930 tsec 22.9970 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.677066) vs oldopt=(dt=32,rms=0.677315) #GCMRL# 253 dt 44.800000 rms 0.677 0.235% neg 0 invalid 762 tFOTS 15.7220 tGradient 4.9430 tsec 21.8510 #FOTS# QuadFit found better minimum quadopt=(dt=76.8,rms=0.675453) vs oldopt=(dt=128,rms=0.675856) #GCMRL# 254 dt 76.800000 rms 0.675 0.238% neg 0 invalid 762 tFOTS 17.4970 tGradient 4.7410 tsec 23.4290 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.674043) vs oldopt=(dt=32,rms=0.674054) #GCMRL# 255 dt 38.400000 rms 0.674 0.209% neg 0 invalid 762 tFOTS 15.5470 tGradient 5.1130 tsec 21.8450 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.672906) vs oldopt=(dt=32,rms=0.673073) #GCMRL# 256 dt 44.800000 rms 0.673 0.169% neg 0 invalid 762 tFOTS 16.4990 tGradient 4.8430 tsec 22.5270 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.671909) vs oldopt=(dt=32,rms=0.672108) #GCMRL# 257 dt 44.800000 rms 0.672 0.148% neg 0 invalid 762 tFOTS 14.6500 tGradient 4.6990 tsec 20.5480 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.671074) vs oldopt=(dt=32,rms=0.671217) #GCMRL# 258 dt 44.800000 rms 0.671 0.124% neg 0 invalid 762 tFOTS 16.5290 tGradient 4.7610 tsec 22.4780 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.670172) vs oldopt=(dt=32,rms=0.670376) #GCMRL# 259 dt 44.800000 rms 0.670 0.134% neg 0 invalid 762 tFOTS 14.4000 tGradient 4.7170 tsec 20.3050 #FOTS# QuadFit found better minimum quadopt=(dt=76.8,rms=0.669294) vs oldopt=(dt=128,rms=0.669489) #GCMRL# 260 dt 76.800000 rms 0.669 0.131% neg 0 invalid 762 tFOTS 17.2330 tGradient 4.5710 tsec 22.9810 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.668374) vs oldopt=(dt=32,rms=0.668393) #GCMRL# 261 dt 38.400000 rms 0.668 0.138% neg 0 invalid 762 tFOTS 15.3040 tGradient 4.5320 tsec 21.0150 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.667653) vs oldopt=(dt=32,rms=0.667714) #GCMRL# 262 dt 44.800000 rms 0.668 0.108% neg 0 invalid 762 tFOTS 15.4760 tGradient 4.6310 tsec 21.2950 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.666928) vs oldopt=(dt=32,rms=0.667024) #GCMRL# 263 dt 44.800000 rms 0.667 0.109% neg 0 invalid 762 tFOTS 17.1370 tGradient 4.3920 tsec 22.7140 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.666399) vs oldopt=(dt=32,rms=0.666425) #GCMRL# 264 dt 44.800000 rms 0.666 0.079% neg 0 invalid 762 tFOTS 16.5240 tGradient 4.6020 tsec 22.3860 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.66577) vs oldopt=(dt=32,rms=0.665853) #GCMRL# 265 dt 44.800000 rms 0.666 0.094% neg 0 invalid 762 tFOTS 15.3910 tGradient 4.5640 tsec 21.1380 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.665181) vs oldopt=(dt=32,rms=0.665234) #GCMRL# 266 dt 44.800000 rms 0.665 0.088% neg 0 invalid 762 tFOTS 16.3800 tGradient 4.5330 tsec 22.0880 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.664764) vs oldopt=(dt=32,rms=0.664801) #GCMRL# 267 dt 44.800000 rms 0.665 0.063% neg 0 invalid 762 tFOTS 14.5030 tGradient 4.4370 tsec 20.1180 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.664088) vs oldopt=(dt=32,rms=0.664155) #GCMRL# 268 dt 44.800000 rms 0.664 0.102% neg 0 invalid 762 tFOTS 22.9000 tGradient 4.4300 tsec 28.8960 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.663712) vs oldopt=(dt=32,rms=0.66372) #GCMRL# 269 dt 38.400000 rms 0.664 0.057% neg 0 invalid 762 tFOTS 15.4660 tGradient 4.5190 tsec 21.1770 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.663072) vs oldopt=(dt=32,rms=0.663167) #GCMRL# 270 dt 44.800000 rms 0.663 0.096% neg 0 invalid 762 tFOTS 16.4050 tGradient 4.5140 tsec 22.1040 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.662769) vs oldopt=(dt=32,rms=0.662795) #GCMRL# 271 dt 44.800000 rms 0.663 0.000% neg 0 invalid 762 tFOTS 14.5080 tGradient 4.4720 tsec 20.1970 #GCMRL# 272 dt 44.800000 rms 0.662 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5590 tsec 5.7450 #GCMRL# 273 dt 44.800000 rms 0.661 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4890 tsec 5.6670 #GCMRL# 274 dt 44.800000 rms 0.660 0.162% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4890 tsec 5.6750 #GCMRL# 275 dt 44.800000 rms 0.659 0.238% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5020 tsec 5.6850 #GCMRL# 276 dt 44.800000 rms 0.657 0.232% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4940 tsec 5.6860 #GCMRL# 277 dt 44.800000 rms 0.655 0.256% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6930 tsec 5.8840 #GCMRL# 278 dt 44.800000 rms 0.654 0.240% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7030 tsec 5.9020 #GCMRL# 279 dt 44.800000 rms 0.652 0.264% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5040 tsec 5.6870 #GCMRL# 280 dt 44.800000 rms 0.651 0.205% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6550 tsec 5.8420 #GCMRL# 281 dt 44.800000 rms 0.650 0.197% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5330 tsec 5.7170 #GCMRL# 282 dt 44.800000 rms 0.648 0.171% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5270 tsec 5.7100 #GCMRL# 283 dt 44.800000 rms 0.647 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5410 tsec 5.7430 #GCMRL# 284 dt 44.800000 rms 0.646 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5330 tsec 5.7040 #GCMRL# 285 dt 44.800000 rms 0.646 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4160 tsec 6.0780 #GCMRL# 286 dt 44.800000 rms 0.646 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4090 tsec 5.6180 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.646024) vs oldopt=(dt=8,rms=0.646027) #GCAMreg# pass 0 level1 3 level2 1 tsec 670.133 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 0.646471 #GCMRL# 288 dt 0.000000 rms 0.646 0.067% neg 0 invalid 762 tFOTS 15.4100 tGradient 4.4890 tsec 21.0740 #GCMRL# 289 dt 0.250000 rms 0.646 0.000% neg 0 invalid 762 tFOTS 16.6620 tGradient 4.4990 tsec 23.4720 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 0.703084 #GCMRL# 291 dt 0.000000 rms 0.703 0.057% neg 0 invalid 762 tFOTS 14.5480 tGradient 4.1470 tsec 19.8810 #GCMRL# 292 dt 0.150000 rms 0.703 0.000% neg 0 invalid 762 tFOTS 14.5620 tGradient 4.2010 tsec 21.0610 #GCAMreg# pass 0 level1 2 level2 1 tsec 54.355 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 0.703084 #GCMRL# 294 dt 0.000000 rms 0.703 0.057% neg 0 invalid 762 tFOTS 14.4350 tGradient 4.1360 tsec 19.7510 #GCMRL# 295 dt 0.150000 rms 0.703 0.000% neg 0 invalid 762 tFOTS 15.3680 tGradient 4.1280 tsec 21.7660 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 0.81036 #FOTS# QuadFit found better minimum quadopt=(dt=3.0354,rms=0.792071) vs oldopt=(dt=1.28,rms=0.79874) #GCMRL# 297 dt 3.035398 rms 0.792 2.257% neg 0 invalid 762 tFOTS 14.5600 tGradient 3.9320 tsec 19.7030 #FOTS# QuadFit found better minimum quadopt=(dt=1.94737,rms=0.788847) vs oldopt=(dt=1.28,rms=0.789486) #GCMRL# 298 dt 1.947368 rms 0.789 0.407% neg 0 invalid 762 tFOTS 15.5570 tGradient 3.9530 tsec 21.0820 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.787765) vs oldopt=(dt=1.28,rms=0.787865) #GCMRL# 299 dt 1.792000 rms 0.788 0.137% neg 0 invalid 762 tFOTS 16.5100 tGradient 4.5620 tsec 22.3500 #GCMRL# 300 dt 1.280000 rms 0.787 0.000% neg 0 invalid 762 tFOTS 15.3890 tGradient 3.9770 tsec 20.5790 #GCMRL# 301 dt 1.280000 rms 0.787 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0450 tsec 5.2200 #GCAMreg# pass 0 level1 1 level2 1 tsec 102.15 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 0.7876 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.785917) vs oldopt=(dt=1.28,rms=0.786171) #GCMRL# 303 dt 1.792000 rms 0.786 0.214% neg 0 invalid 762 tFOTS 15.2980 tGradient 3.9250 tsec 20.3940 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.785083) vs oldopt=(dt=1.28,rms=0.785249) #GCMRL# 304 dt 1.792000 rms 0.785 0.106% neg 0 invalid 762 tFOTS 17.2550 tGradient 3.9450 tsec 22.7400 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.784535) vs oldopt=(dt=1.28,rms=0.784638) #GCMRL# 305 dt 1.792000 rms 0.785 0.070% neg 0 invalid 762 tFOTS 15.3480 tGradient 3.9470 tsec 20.4710 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.784211) vs oldopt=(dt=1.28,rms=0.784263) #GCMRL# 306 dt 1.792000 rms 0.784 0.000% neg 0 invalid 762 tFOTS 15.4720 tGradient 4.0260 tsec 20.7310 #GCMRL# 307 dt 1.792000 rms 0.784 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9990 tsec 5.1720 #GCMRL# 308 dt 1.792000 rms 0.784 -0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9830 tsec 6.2500 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.783826) vs oldopt=(dt=1.28,rms=0.783873) #GCMRL# 309 dt 1.792000 rms 0.784 0.024% neg 0 invalid 762 tFOTS 16.8720 tGradient 4.2580 tsec 22.3160 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.78362) vs oldopt=(dt=1.28,rms=0.783664) #GCMRL# 310 dt 1.792000 rms 0.784 0.026% neg 0 invalid 762 tFOTS 16.4340 tGradient 3.9460 tsec 21.5640 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.783451) vs oldopt=(dt=1.28,rms=0.783495) 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 0.724916 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.662282) vs oldopt=(dt=1.28,rms=0.670222) #GCMRL# 312 dt 1.536000 rms 0.662 8.640% neg 0 invalid 762 tFOTS 15.4360 tGradient 3.2360 tsec 20.1730 #GCMRL# 313 dt 0.050000 rms 0.662 0.000% neg 0 invalid 762 tFOTS 13.5650 tGradient 3.2620 tsec 18.0440 #GCAMreg# pass 0 level1 0 level2 1 tsec 50.698 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 0.662671 #GCMRL# 315 dt 0.000000 rms 0.662 0.062% neg 0 invalid 762 tFOTS 13.5450 tGradient 3.2010 tsec 17.9350 #GCMRL# 316 dt 0.050000 rms 0.662 0.000% neg 0 invalid 762 tFOTS 13.4700 tGradient 3.2600 tsec 19.0030 GCAMregister done in 61.8813 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 0.648362 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.646349) vs oldopt=(dt=92.48,rms=0.646433) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 318 dt 129.472000 rms 0.646 0.310% neg 0 invalid 762 tFOTS 19.0360 tGradient 7.0010 tsec 28.3710 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.645664) vs oldopt=(dt=92.48,rms=0.645707) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 319 dt 129.472000 rms 0.646 0.000% neg 0 invalid 762 tFOTS 17.7030 tGradient 7.0530 tsec 27.1510 #GCMRL# 320 dt 129.472000 rms 0.646 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1110 tsec 8.2930 #GCAMreg# pass 0 level1 5 level2 1 tsec 81.143 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 0.646048 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.644877) vs oldopt=(dt=92.48,rms=0.644932) #GCMRL# 322 dt 129.472000 rms 0.645 0.181% neg 0 invalid 762 tFOTS 17.4060 tGradient 7.2430 tsec 25.8250 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.644334) vs oldopt=(dt=92.48,rms=0.644418) #GCMRL# 323 dt 129.472000 rms 0.644 0.000% neg 0 invalid 762 tFOTS 17.5010 tGradient 7.0700 tsec 25.7870 #GCMRL# 324 dt 129.472000 rms 0.644 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.1160 tsec 8.2910 #GCMRL# 325 dt 129.472000 rms 0.644 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.0650 tsec 8.2480 #GCMRL# 326 dt 129.472000 rms 0.643 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.9590 tsec 8.1380 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 0.643396 #FOTS# QuadFit found better minimum quadopt=(dt=143.622,rms=0.637393) vs oldopt=(dt=103.68,rms=0.637745) iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 328 dt 143.622047 rms 0.637 0.933% neg 0 invalid 762 tFOTS 18.2670 tGradient 5.4330 tsec 27.0940 #FOTS# QuadFit found better minimum quadopt=(dt=158.785,rms=0.633649) vs oldopt=(dt=103.68,rms=0.634032) iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 329 dt 158.784810 rms 0.634 0.586% neg 0 invalid 762 tFOTS 19.1070 tGradient 6.9340 tsec 28.4380 #FOTS# QuadFit found better minimum quadopt=(dt=66.7119,rms=0.63214) vs oldopt=(dt=103.68,rms=0.632441) iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 330 dt 66.711864 rms 0.632 0.000% neg 0 invalid 762 tFOTS 18.2730 tGradient 5.3170 tsec 25.9260 #GCMRL# 331 dt 66.711864 rms 0.631 0.162% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3810 tsec 6.5600 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 332 dt 66.711864 rms 0.630 0.173% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3800 tsec 7.7080 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 333 dt 66.711864 rms 0.629 0.204% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4160 tsec 8.4130 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 334 dt 66.711864 rms 0.628 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.6010 tsec 11.7550 #GCMRL# 335 dt 66.711864 rms 0.627 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4550 tsec 6.6320 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 336 dt 66.711864 rms 0.627 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4060 tsec 7.7730 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.626072) vs oldopt=(dt=103.68,rms=0.62615) #GCMRL# 337 dt 145.152000 rms 0.626 0.108% neg 0 invalid 762 tFOTS 17.4140 tGradient 5.4810 tsec 24.0730 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.625491) vs oldopt=(dt=103.68,rms=0.625531) #GCMRL# 338 dt 82.944000 rms 0.625 0.000% neg 0 invalid 762 tFOTS 17.4300 tGradient 5.3490 tsec 24.0020 #GCMRL# 339 dt 82.944000 rms 0.625 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3690 tsec 6.5810 #GCMRL# 340 dt 82.944000 rms 0.625 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3890 tsec 6.5750 #GCMRL# 341 dt 82.944000 rms 0.624 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3010 tsec 6.4750 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 342 dt 82.944000 rms 0.623 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3940 tsec 7.7140 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 343 dt 82.944000 rms 0.622 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3070 tsec 7.6240 #GCMRL# 344 dt 82.944000 rms 0.622 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2940 tsec 6.4930 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 345 dt 82.944000 rms 0.621 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3340 tsec 8.2120 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 346 dt 82.944000 rms 0.620 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4730 tsec 11.5980 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.620127) vs oldopt=(dt=103.68,rms=0.620131) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 347 dt 82.944000 rms 0.620 0.000% neg 0 invalid 762 tFOTS 17.3550 tGradient 5.3160 tsec 25.6020 #GCMRL# 348 dt 82.944000 rms 0.620 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3160 tsec 6.4990 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 349 dt 82.944000 rms 0.620 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3210 tsec 10.9150 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 350 dt 82.944000 rms 0.619 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4590 tsec 7.8010 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 351 dt 82.944000 rms 0.619 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3260 tsec 8.1690 #GCMRL# 352 dt 82.944000 rms 0.619 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3020 tsec 6.4830 #GCMRL# 353 dt 82.944000 rms 0.618 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5270 tsec 6.7090 #GCMRL# 354 dt 82.944000 rms 0.618 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3120 tsec 6.4900 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 355 dt 82.944000 rms 0.617 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4020 tsec 7.7230 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 356 dt 82.944000 rms 0.617 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2830 tsec 8.1220 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 357 dt 82.944000 rms 0.616 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2870 tsec 9.8190 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 4 level2 1 tsec 360.483 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 0.616436 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.614836) vs oldopt=(dt=103.68,rms=0.614877) #GCMRL# 359 dt 124.416000 rms 0.615 0.260% neg 0 invalid 762 tFOTS 17.4770 tGradient 6.2810 tsec 24.9810 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.613798) vs oldopt=(dt=103.68,rms=0.613937) #GCMRL# 360 dt 145.152000 rms 0.614 0.000% neg 0 invalid 762 tFOTS 17.4360 tGradient 5.4010 tsec 24.0680 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 0.619282 #FOTS# QuadFit found better minimum quadopt=(dt=114.387,rms=0.609004) vs oldopt=(dt=128,rms=0.609173) iter 0, gcam->neg = 23 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 362 dt 114.386740 rms 0.609 1.657% neg 0 invalid 762 tFOTS 18.3930 tGradient 4.4660 tsec 30.0010 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.602355) vs oldopt=(dt=32,rms=0.603059) iter 0, gcam->neg = 11 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 363 dt 44.800000 rms 0.602 1.089% neg 0 invalid 762 tFOTS 18.4680 tGradient 4.4560 tsec 32.2080 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.599306) vs oldopt=(dt=32,rms=0.599653) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 364 dt 44.800000 rms 0.599 0.512% neg 0 invalid 762 tFOTS 18.2330 tGradient 4.4430 tsec 25.5130 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.597172) vs oldopt=(dt=32,rms=0.597401) iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 365 dt 44.800000 rms 0.597 0.352% neg 0 invalid 762 tFOTS 18.1920 tGradient 4.4580 tsec 29.8640 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.595468) vs oldopt=(dt=32,rms=0.595543) iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 366 dt 38.400000 rms 0.595 0.288% neg 0 invalid 762 tFOTS 18.1700 tGradient 4.3590 tsec 25.3690 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.594017) vs oldopt=(dt=32,rms=0.594149) iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 367 dt 44.800000 rms 0.594 0.000% neg 0 invalid 762 tFOTS 18.1540 tGradient 4.3930 tsec 29.0980 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 368 dt 44.800000 rms 0.593 0.233% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3380 tsec 7.1770 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 369 dt 44.800000 rms 0.590 0.445% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3980 tsec 7.2740 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 370 dt 44.800000 rms 0.587 0.438% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4040 tsec 11.5240 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 371 dt 44.800000 rms 0.584 0.566% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3690 tsec 6.6720 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 372 dt 44.800000 rms 0.582 0.397% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2290 tsec 10.3010 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 373 dt 44.800000 rms 0.579 0.474% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3610 tsec 10.9950 iter 0, gcam->neg = 24 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 374 dt 44.800000 rms 0.577 0.290% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3950 tsec 12.1570 iter 0, gcam->neg = 35 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 375 dt 44.800000 rms 0.575 0.331% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5520 tsec 12.2100 iter 0, gcam->neg = 20 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 376 dt 44.800000 rms 0.574 0.187% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4060 tsec 13.8930 iter 0, gcam->neg = 27 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 377 dt 44.800000 rms 0.573 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4600 tsec 12.2880 iter 0, gcam->neg = 25 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 378 dt 44.800000 rms 0.572 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4150 tsec 12.6470 iter 0, gcam->neg = 22 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 379 dt 44.800000 rms 0.571 0.186% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4860 tsec 11.6630 iter 0, gcam->neg = 9 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 380 dt 44.800000 rms 0.571 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7530 tsec 8.9620 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 381 dt 44.800000 rms 0.571 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4050 tsec 11.0370 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 382 dt 44.800000 rms 0.570 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3130 tsec 7.1990 #GCMRL# 383 dt 32.000000 rms 0.570 0.128% neg 0 invalid 762 tFOTS 18.2020 tGradient 4.3710 tsec 23.7480 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.569317) vs oldopt=(dt=32,rms=0.569347) #GCMRL# 384 dt 44.800000 rms 0.569 0.000% neg 0 invalid 762 tFOTS 17.2300 tGradient 4.3130 tsec 22.7460 #GCAMreg# pass 0 level1 3 level2 1 tsec 388.253 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 0.569735 #GCMRL# 386 dt 32.000000 rms 0.568 0.220% neg 0 invalid 762 tFOTS 18.9520 tGradient 4.4860 tsec 24.6070 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.567816) vs oldopt=(dt=32,rms=0.567884) #GCMRL# 387 dt 44.800000 rms 0.568 0.000% neg 0 invalid 762 tFOTS 18.1230 tGradient 4.2880 tsec 23.6160 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 0.59122 #FOTS# QuadFit found better minimum quadopt=(dt=2.7,rms=0.590577) vs oldopt=(dt=2.88,rms=0.590579) #GCMRL# 389 dt 2.700000 rms 0.591 0.109% neg 0 invalid 762 tFOTS 18.2520 tGradient 4.0140 tsec 23.4410 #GCMRL# 390 dt 0.720000 rms 0.591 0.000% neg 0 invalid 762 tFOTS 18.2040 tGradient 4.0330 tsec 23.4430 #GCMRL# 391 dt 0.720000 rms 0.591 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0100 tsec 5.1830 #GCAMreg# pass 0 level1 2 level2 1 tsec 65.309 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 0.59097 #FOTS# QuadFit found better minimum quadopt=(dt=1.93548,rms=0.590428) vs oldopt=(dt=2.88,rms=0.590458) #GCMRL# 393 dt 1.935484 rms 0.590 0.092% neg 0 invalid 762 tFOTS 18.4100 tGradient 4.0940 tsec 23.6880 #FOTS# QuadFit found better minimum quadopt=(dt=0.576,rms=0.590416) vs oldopt=(dt=0.72,rms=0.590416) #GCMRL# 394 dt 0.576000 rms 0.590 0.000% neg 0 invalid 762 tFOTS 18.4240 tGradient 4.0840 tsec 23.7280 #GCMRL# 395 dt 0.576000 rms 0.590 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0480 tsec 5.2330 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 0.626854 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.623643) vs oldopt=(dt=1.28,rms=0.623725) #GCMRL# 397 dt 1.536000 rms 0.624 0.512% neg 0 invalid 762 tFOTS 18.5380 tGradient 3.8480 tsec 23.5630 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.623527) vs oldopt=(dt=0.32,rms=0.623532) #GCMRL# 398 dt 0.384000 rms 0.624 0.000% neg 0 invalid 762 tFOTS 18.4560 tGradient 3.9510 tsec 23.6170 #GCAMreg# pass 0 level1 1 level2 1 tsec 60.162 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 0.623945 #FOTS# QuadFit found better minimum quadopt=(dt=1.024,rms=0.622763) vs oldopt=(dt=1.28,rms=0.622798) #GCMRL# 400 dt 1.024000 rms 0.623 0.189% neg 0 invalid 762 tFOTS 21.6320 tGradient 3.8380 tsec 26.6690 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.622648) vs oldopt=(dt=0.32,rms=0.622662) #GCMRL# 401 dt 0.448000 rms 0.623 0.000% neg 0 invalid 762 tFOTS 18.4030 tGradient 3.8580 tsec 23.8060 #GCMRL# 402 dt 0.448000 rms 0.623 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0930 tsec 5.3300 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 0.590685 #FOTS# QuadFit found better minimum quadopt=(dt=2.69843,rms=0.535738) vs oldopt=(dt=1.28,rms=0.550421) iter 0, gcam->neg = 559 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 404 dt 2.698428 rms 0.538 8.916% neg 0 invalid 762 tFOTS 18.4900 tGradient 3.1680 tsec 32.6570 #FOTS# QuadFit found better minimum quadopt=(dt=0.210443,rms=0.536012) vs oldopt=(dt=0.32,rms=0.536315) #GCMRL# 405 dt 0.210443 rms 0.536 0.373% neg 0 invalid 762 tFOTS 18.4260 tGradient 3.2500 tsec 22.8570 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.536003) vs oldopt=(dt=0.005,rms=0.536004) #GCMRL# 406 dt 0.007000 rms 0.536 0.000% neg 0 invalid 762 tFOTS 18.7240 tGradient 3.3150 tsec 23.2500 #GCAMreg# pass 0 level1 0 level2 1 tsec 91.566 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 0.536515 #FOTS# QuadFit found better minimum quadopt=(dt=0.096,rms=0.535757) vs oldopt=(dt=0.08,rms=0.535762) #GCMRL# 408 dt 0.096000 rms 0.536 0.141% neg 0 invalid 762 tFOTS 18.2330 tGradient 3.2070 tsec 22.6100 label assignment complete, 0 changed (0.00%) GCAMregister done in 23.9576 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 0.508982 #GCMRL# 410 dt 5.780000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 17.6920 tGradient 6.1010 tsec 24.9410 #GCAMreg# pass 0 level1 5 level2 1 tsec 56.93 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 0.508981 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.508967) vs oldopt=(dt=23.12,rms=0.508969) #GCMRL# 412 dt 32.368000 rms 0.509 0.003% neg 0 invalid 762 tFOTS 17.7820 tGradient 6.0860 tsec 25.0210 #GCMRL# 413 dt 23.120000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 17.6560 tGradient 6.1630 tsec 25.0070 #GCMRL# 414 dt 23.120000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1000 tsec 7.2440 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 0.509286 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.509008) vs oldopt=(dt=25.92,rms=0.509034) #GCMRL# 416 dt 36.288000 rms 0.509 0.055% neg 0 invalid 762 tFOTS 16.7640 tGradient 4.1730 tsec 22.0780 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.508949) vs oldopt=(dt=25.92,rms=0.50895) #GCMRL# 417 dt 31.104000 rms 0.509 0.000% neg 0 invalid 762 tFOTS 17.6710 tGradient 4.1740 tsec 23.0220 #GCMRL# 418 dt 31.104000 rms 0.509 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.1690 tsec 5.3130 #GCAMreg# pass 0 level1 4 level2 1 tsec 63.647 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 0.50892 #FOTS# QuadFit found better minimum quadopt=(dt=67.8788,rms=0.508291) vs oldopt=(dt=103.68,rms=0.50846) #GCMRL# 420 dt 67.878788 rms 0.508 0.124% neg 0 invalid 762 tFOTS 17.6390 tGradient 4.1640 tsec 22.9450 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.507557) vs oldopt=(dt=103.68,rms=0.507675) #GCMRL# 421 dt 145.152000 rms 0.508 0.144% neg 0 invalid 762 tFOTS 16.7350 tGradient 4.1680 tsec 22.0520 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.507474) vs oldopt=(dt=25.92,rms=0.507484) #GCMRL# 422 dt 36.288000 rms 0.507 0.000% neg 0 invalid 762 tFOTS 18.0270 tGradient 4.2060 tsec 23.4570 #GCMRL# 423 dt 36.288000 rms 0.507 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2380 tsec 5.3980 #GCMRL# 424 dt 36.288000 rms 0.507 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2360 tsec 5.3910 #GCMRL# 425 dt 36.288000 rms 0.507 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2260 tsec 5.3830 #GCMRL# 426 dt 36.288000 rms 0.507 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2250 tsec 5.3810 #GCMRL# 427 dt 36.288000 rms 0.507 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2170 tsec 5.3740 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 0.507721 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.505317) vs oldopt=(dt=32,rms=0.505382) #GCMRL# 429 dt 38.400000 rms 0.505 0.474% neg 0 invalid 762 tFOTS 17.8960 tGradient 3.4370 tsec 22.4910 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.50373) vs oldopt=(dt=32,rms=0.503996) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 430 dt 44.800000 rms 0.504 0.314% neg 0 invalid 762 tFOTS 17.9180 tGradient 3.4400 tsec 23.6930 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.502959) vs oldopt=(dt=32,rms=0.503076) #GCMRL# 431 dt 44.800000 rms 0.503 0.000% neg 0 invalid 762 tFOTS 18.0210 tGradient 3.4980 tsec 22.7150 #GCMRL# 432 dt 44.800000 rms 0.502 0.162% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4880 tsec 4.6560 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 433 dt 44.800000 rms 0.501 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4820 tsec 10.0540 iter 0, gcam->neg = 18 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 434 dt 44.800000 rms 0.501 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4450 tsec 12.2370 iter 0, gcam->neg = 34 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 435 dt 44.800000 rms 0.501 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6910 tsec 11.3330 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 436 dt 128.000000 rms 0.500 0.240% neg 0 invalid 762 tFOTS 16.7600 tGradient 3.4390 tsec 26.6740 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.499261) vs oldopt=(dt=32,rms=0.499342) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 437 dt 25.600000 rms 0.499 0.000% neg 0 invalid 762 tFOTS 17.7060 tGradient 3.4150 tsec 23.9640 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 438 dt 25.600000 rms 0.499 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4370 tsec 7.8070 #GCMRL# 439 dt 25.600000 rms 0.499 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4100 tsec 4.5530 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 440 dt 25.600000 rms 0.499 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4550 tsec 5.7310 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 441 dt 25.600000 rms 0.498 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4530 tsec 7.8580 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 442 dt 25.600000 rms 0.498 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4320 tsec 6.7600 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 443 dt 25.600000 rms 0.498 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4510 tsec 7.3400 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 444 dt 25.600000 rms 0.498 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4330 tsec 9.8940 iter 0, gcam->neg = 7 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 445 dt 25.600000 rms 0.497 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4210 tsec 12.0080 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 237.848 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 0.497103 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.494916) vs oldopt=(dt=32,rms=0.49506) #GCMRL# 447 dt 44.800000 rms 0.495 0.440% neg 0 invalid 762 tFOTS 17.8650 tGradient 3.4280 tsec 22.4510 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.49329) vs oldopt=(dt=32,rms=0.493575) #GCMRL# 448 dt 44.800000 rms 0.493 0.329% neg 0 invalid 762 tFOTS 17.8620 tGradient 3.6170 tsec 22.6330 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.493063) vs oldopt=(dt=32,rms=0.493073) #GCMRL# 449 dt 25.600000 rms 0.493 0.000% neg 0 invalid 762 tFOTS 17.8110 tGradient 3.4490 tsec 22.4560 #GCMRL# 450 dt 25.600000 rms 0.493 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4440 tsec 4.5980 #GCMRL# 451 dt 25.600000 rms 0.492 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4450 tsec 4.5980 #GCMRL# 452 dt 25.600000 rms 0.492 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4430 tsec 4.6010 #GCMRL# 453 dt 25.600000 rms 0.492 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4660 tsec 4.6610 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.490958) vs oldopt=(dt=128,rms=0.491017) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 454 dt 179.200000 rms 0.491 0.123% neg 0 invalid 762 tFOTS 17.7210 tGradient 3.4660 tsec 23.4980 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.490903) vs oldopt=(dt=8,rms=0.490912) 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 0.499396 #FOTS# QuadFit found better minimum quadopt=(dt=0.00084375,rms=0.499396) vs oldopt=(dt=0.000703125,rms=0.499396) #GCMRL# 456 dt 0.000844 rms 0.499 0.000% neg 0 invalid 762 tFOTS 16.7920 tGradient 3.1470 tsec 21.0850 #GCAMreg# pass 0 level1 2 level2 1 tsec 53.898 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 0.499396 #FOTS# QuadFit found better minimum quadopt=(dt=1.5,rms=0.49936) vs oldopt=(dt=0.72,rms=0.49937) #GCMRL# 458 dt 1.500000 rms 0.499 0.007% neg 0 invalid 762 tFOTS 17.9050 tGradient 3.1640 tsec 22.2350 #FOTS# QuadFit found better minimum quadopt=(dt=0.432,rms=0.499357) vs oldopt=(dt=0.72,rms=0.499358) #GCMRL# 459 dt 0.432000 rms 0.499 0.000% neg 0 invalid 762 tFOTS 17.8940 tGradient 3.1880 tsec 22.2730 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 0.516166 #GCAMreg# pass 0 level1 1 level2 1 tsec 29.379 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 0.516166 #FOTS# QuadFit found better minimum quadopt=(dt=0.192,rms=0.516134) vs oldopt=(dt=0.32,rms=0.516143) #GCMRL# 462 dt 0.192000 rms 0.516 0.006% neg 0 invalid 762 tFOTS 20.2980 tGradient 2.9880 tsec 24.4360 #FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.516133) vs oldopt=(dt=0.02,rms=0.516133) #GCMRL# 463 dt 0.028000 rms 0.516 0.000% neg 0 invalid 762 tFOTS 17.8290 tGradient 2.9740 tsec 21.9880 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 0.488963 #FOTS# QuadFit found better minimum quadopt=(dt=1.85111,rms=0.464702) vs oldopt=(dt=1.28,rms=0.467222) iter 0, gcam->neg = 662 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 465 dt 1.851109 rms 0.467 4.441% neg 0 invalid 762 tFOTS 17.7930 tGradient 2.2830 tsec 29.3280 #FOTS# QuadFit found better minimum quadopt=(dt=0.048,rms=0.467167) vs oldopt=(dt=0.08,rms=0.467193) #GCMRL# 466 dt 0.048000 rms 0.467 0.000% neg 0 invalid 762 tFOTS 17.7680 tGradient 2.3470 tsec 21.2980 #GCAMreg# pass 0 level1 0 level2 1 tsec 62.003 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 0.467167 #FOTS# QuadFit found better minimum quadopt=(dt=0.096,rms=0.466911) vs oldopt=(dt=0.08,rms=0.466916) #GCMRL# 468 dt 0.096000 rms 0.467 0.055% neg 0 invalid 762 tFOTS 18.0470 tGradient 2.3220 tsec 21.5180 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.46691) vs oldopt=(dt=0.005,rms=0.46691) #GCMRL# 469 dt 0.007000 rms 0.467 0.000% neg 0 invalid 762 tFOTS 17.7980 tGradient 2.3050 tsec 21.2930 GCAMregister done in 16.3029 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4300 tmin = 16.8847 Calls to gcamLabelEnergy 3632 tmin = 1.62137 Calls to gcamJacobianEnergy 4300 tmin = 15.4724 Calls to gcamSmoothnessEnergy 4300 tmin = 14.9291 Calls to gcamLogLikelihoodTerm 471 tmin = 4.08508 Calls to gcamLabelTerm 410 tmin = 8.29328 Calls to gcamJacobianTerm 471 tmin = 8.9939 Calls to gcamSmoothnessTerm 471 tmin = 2.64618 Calls to gcamComputeGradient 471 tmin = 43.3383 Calls to gcamComputeMetricProperties 5934 tmin = 17.2612 mri_ca_register took 2 hours, 9 minutes and 14 seconds. #VMPC# mri_ca_register VmPeak 2503740 FSRUNTIME@ mri_ca_register 2.1539 hours 1 threads @#@FSTIME 2022:09:05:13:41:07 mri_ca_register N 9 e 7754.11 S 4.74 U 7743.42 P 99% M 1721044 F 9 R 2135440 W 0 c 115146 w 10 I 1976 O 63448 L 1.22 1.45 1.53 @#@FSLOADPOST 2022:09:05:15:50:21 mri_ca_register N 9 1.62 1.29 1.21 #-------------------------------------- #@# SubCort Seg Mon Sep 5 15:50:21 UTC 2022 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/marcantf/software/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname mrphys-gpu1 machine x86_64 setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/marcantf/software/freesurfer/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 = 1 == reading 1 input volumes reading classifier array from /home/marcantf/software/freesurfer/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 27.18 Atlas used for the 3D morph was /home/marcantf/software/freesurfer/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 = 0.08888 (18) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (25609 voxels, overlap=0.853) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (25609 voxels, peak = 17), gca=17.3 gca peak = 0.20380 (13) mri peak = 0.09130 (14) Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (19919 voxels, overlap=0.707) Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (19919 voxels, peak = 12), gca=11.9 gca peak = 0.26283 (96) mri peak = 0.08721 (98) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (4553 voxels, overlap=0.951) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (4553 voxels, peak = 101), gca=101.3 gca peak = 0.15814 (97) mri peak = 0.07525 (100) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (3978 voxels, overlap=0.756) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (3978 voxels, peak = 102), gca=102.3 gca peak = 0.27624 (56) mri peak = 0.07305 (73) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (5590 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (5590 voxels, peak = 69), gca=68.6 gca peak = 0.28723 (59) mri peak = 0.06380 (75) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (4852 voxels, overlap=0.023) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (4852 voxels, peak = 72), gca=72.3 gca peak = 0.07623 (103) mri peak = 0.09016 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (292996 voxels, overlap=0.618) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (292996 voxels, peak = 107), gca=106.6 gca peak = 0.07837 (105) mri peak = 0.08198 (107) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (292822 voxels, overlap=0.620) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (292822 voxels, peak = 109), gca=108.7 gca peak = 0.10165 (58) mri peak = 0.03703 (72) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (242148 voxels, overlap=0.021) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (242148 voxels, peak = 73), gca=73.4 gca peak = 0.11113 (58) mri peak = 0.03248 (69) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (222858 voxels, overlap=0.098) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (222858 voxels, peak = 71), gca=71.1 gca peak = 0.27796 (67) mri peak = 0.09238 (82) Right_Caudate (50): linear fit = 1.27 x + 0.0 (6988 voxels, overlap=0.023) Right_Caudate (50): linear fit = 1.27 x + 0.0 (6988 voxels, peak = 85), gca=85.4 gca peak = 0.14473 (69) mri peak = 0.11366 (87) Left_Caudate (11): linear fit = 1.16 x + 0.0 (5964 voxels, overlap=0.022) Left_Caudate (11): linear fit = 1.16 x + 0.0 (5964 voxels, peak = 80), gca=80.4 gca peak = 0.14301 (56) mri peak = 0.03130 (66) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (46452 voxels, overlap=0.505) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (46452 voxels, peak = 64), gca=63.6 gca peak = 0.14610 (55) mri peak = 0.02800 (77) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (46423 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (46423 voxels, peak = 73), gca=73.4 gca peak = 0.16309 (85) mri peak = 0.04000 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (22287 voxels, overlap=0.989) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (22287 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.04947 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (11089 voxels, overlap=0.828) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (11089 voxels, peak = 94), gca=93.7 gca peak = 0.30461 (58) mri peak = 0.06582 (75) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (2123 voxels, overlap=0.073) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (2123 voxels, peak = 73), gca=72.8 gca peak = 0.32293 (57) mri peak = 0.06009 (77) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (1915 voxels, overlap=0.068) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (1915 voxels, peak = 74), gca=74.4 gca peak = 0.11083 (90) mri peak = 0.07470 (101) Left_Thalamus (10): linear fit = 1.13 x + 0.0 (22570 voxels, overlap=0.201) Left_Thalamus (10): linear fit = 1.13 x + 0.0 (22570 voxels, peak = 102), gca=102.2 gca peak = 0.11393 (83) mri peak = 0.07537 (98) Right_Thalamus (49): linear fit = 1.16 x + 0.0 (19004 voxels, overlap=0.059) Right_Thalamus (49): linear fit = 1.16 x + 0.0 (19004 voxels, peak = 97), gca=96.7 gca peak = 0.08575 (81) mri peak = 0.09488 (98) Left_Putamen (12): linear fit = 1.23 x + 0.0 (9422 voxels, overlap=0.014) Left_Putamen (12): linear fit = 1.23 x + 0.0 (9422 voxels, peak = 99), gca=99.2 gca peak = 0.08618 (78) mri peak = 0.07733 (94) Right_Putamen (51): linear fit = 1.23 x + 0.0 (9681 voxels, overlap=0.015) Right_Putamen (51): linear fit = 1.23 x + 0.0 (9681 voxels, peak = 96), gca=95.6 gca peak = 0.08005 (78) mri peak = 0.06386 (83) Brain_Stem (16): linear fit = 1.12 x + 0.0 (31500 voxels, overlap=0.492) Brain_Stem (16): linear fit = 1.12 x + 0.0 (31500 voxels, peak = 88), gca=87.8 gca peak = 0.12854 (88) mri peak = 0.05502 (95) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (7420 voxels, overlap=0.426) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (7420 voxels, peak = 97), gca=97.2 gca peak = 0.15703 (87) mri peak = 0.06410 (93) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (7997 voxels, overlap=0.606) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (7997 voxels, peak = 94), gca=93.5 gca peak = 0.17522 (25) mri peak = 0.08884 (26) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (473 voxels, overlap=1.009) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (473 voxels, peak = 24), gca=23.9 gca peak = 0.17113 (14) mri peak = 0.09222 (16) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (2248 voxels, overlap=0.854) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (2248 voxels, peak = 14), gca=14.5 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 1.25 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.94 x + 0.0 Left_Putamen too bright - rescaling by 0.976 (from 1.225) to 96.9 (was 99.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17103 (16) mri peak = 0.08888 (18) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (25609 voxels, overlap=0.944) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (25609 voxels, peak = 17), gca=16.6 gca peak = 0.23164 (12) mri peak = 0.09130 (14) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (19919 voxels, overlap=0.835) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (19919 voxels, peak = 12), gca=12.4 gca peak = 0.21434 (101) mri peak = 0.08721 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (4553 voxels, overlap=1.012) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (4553 voxels, peak = 102), gca=101.5 gca peak = 0.16452 (100) mri peak = 0.07525 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (3978 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (3978 voxels, peak = 100), gca=100.5 gca peak = 0.24482 (68) mri peak = 0.07305 (73) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (5590 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (5590 voxels, peak = 68), gca=68.0 gca peak = 0.31048 (69) mri peak = 0.06380 (75) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (4852 voxels, overlap=1.005) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (4852 voxels, peak = 69), gca=69.0 gca peak = 0.07642 (107) mri peak = 0.09016 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (292996 voxels, overlap=0.770) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (292996 voxels, peak = 107), gca=107.0 gca peak = 0.07610 (108) mri peak = 0.08198 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (292822 voxels, overlap=0.771) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (292822 voxels, peak = 108), gca=108.0 gca peak = 0.07739 (72) mri peak = 0.03703 (72) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (242148 voxels, overlap=0.860) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (242148 voxels, peak = 71), gca=70.9 gca peak = 0.09222 (71) mri peak = 0.03248 (69) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (222858 voxels, overlap=0.933) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (222858 voxels, peak = 73), gca=73.5 gca peak = 0.20424 (85) mri peak = 0.09238 (82) Right_Caudate (50): linear fit = 0.99 x + 0.0 (6988 voxels, overlap=0.998) Right_Caudate (50): linear fit = 0.99 x + 0.0 (6988 voxels, peak = 84), gca=83.7 gca peak = 0.11812 (81) mri peak = 0.11366 (87) Left_Caudate (11): linear fit = 1.00 x + 0.0 (5964 voxels, overlap=0.925) Left_Caudate (11): linear fit = 1.00 x + 0.0 (5964 voxels, peak = 81), gca=81.0 gca peak = 0.12353 (64) mri peak = 0.03130 (66) Left_Cerebellum_Cortex (8): linear fit = 1.05 x + 0.0 (46452 voxels, overlap=0.949) Left_Cerebellum_Cortex (8): linear fit = 1.05 x + 0.0 (46452 voxels, peak = 68), gca=67.5 gca peak = 0.11958 (74) mri peak = 0.02800 (77) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (46423 voxels, overlap=0.530) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (46423 voxels, peak = 73), gca=72.9 gca peak = 0.15314 (90) mri peak = 0.04000 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (22287 voxels, overlap=1.000) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (22287 voxels, peak = 90), gca=89.6 gca peak = 0.15181 (94) mri peak = 0.04947 (90) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (11089 voxels, overlap=1.000) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (11089 voxels, peak = 93), gca=92.6 gca peak = 0.28134 (73) mri peak = 0.06582 (75) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (2123 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (2123 voxels, peak = 76), gca=75.6 gca peak = 0.27118 (75) mri peak = 0.06009 (77) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (1915 voxels, overlap=1.025) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (1915 voxels, peak = 76), gca=76.1 gca peak = 0.10398 (100) mri peak = 0.07470 (101) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (22570 voxels, overlap=0.909) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (22570 voxels, peak = 100), gca=100.5 gca peak = 0.10461 (94) mri peak = 0.07537 (98) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (19004 voxels, overlap=0.928) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (19004 voxels, peak = 95), gca=95.4 gca peak = 0.08084 (90) mri peak = 0.09488 (98) Left_Putamen (12): linear fit = 1.04 x + 0.0 (9422 voxels, overlap=0.688) Left_Putamen (12): linear fit = 1.04 x + 0.0 (9422 voxels, peak = 94), gca=94.0 gca peak = 0.08143 (93) mri peak = 0.07733 (94) Right_Putamen (51): linear fit = 1.00 x + 0.0 (9681 voxels, overlap=0.761) Right_Putamen (51): linear fit = 1.00 x + 0.0 (9681 voxels, peak = 93), gca=93.5 gca peak = 0.07631 (88) mri peak = 0.06386 (83) Brain_Stem (16): linear fit = 0.99 x + 0.0 (31500 voxels, overlap=0.900) Brain_Stem (16): linear fit = 0.99 x + 0.0 (31500 voxels, peak = 87), gca=86.7 gca peak = 0.11096 (98) mri peak = 0.05502 (95) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (7420 voxels, overlap=0.826) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (7420 voxels, peak = 99), gca=99.5 gca peak = 0.14884 (93) mri peak = 0.06410 (93) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (7997 voxels, overlap=0.887) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (7997 voxels, peak = 95), gca=95.3 gca peak = 0.17535 (26) mri peak = 0.08884 (26) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (473 voxels, overlap=1.009) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (473 voxels, peak = 26), gca=25.6 gca peak = 0.18756 (15) mri peak = 0.09222 (16) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (2248 voxels, overlap=0.828) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (2248 voxels, peak = 15), gca=14.8 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.17362 (34) gca peak CSF = 0.22780 (34) gca peak Left_Accumbens_area = 0.53491 (73) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.23407 (28) gca peak Right_Accumbens_area = 0.35887 (82) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (31) gca peak WM_hypointensities = 0.11051 (79) gca peak non_WM_hypointensities = 0.14581 (42) gca peak Optic_Chiasm = 0.51651 (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 1.01 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 336171 voxels changed in iteration 0 of unlikely voxel relabeling 950 voxels changed in iteration 1 of unlikely voxel relabeling 18 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 269862 gm and wm labels changed (%19 to gray, %81 to white out of all changed labels) 1715 hippocampal voxels changed. 1 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 243920 changed. image ll: -2.361, PF=0.500 pass 2: 95540 changed. image ll: -2.356, PF=0.500 pass 3: 32249 changed. pass 4: 13807 changed. pass 5: 6926 changed. pass 6: 3912 changed. 304339 voxels changed in iteration 0 of unlikely voxel relabeling 1254 voxels changed in iteration 1 of unlikely voxel relabeling 206 voxels changed in iteration 2 of unlikely voxel relabeling 5 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 32903 voxels changed in iteration 0 of unlikely voxel relabeling 441 voxels changed in iteration 1 of unlikely voxel relabeling 111 voxels changed in iteration 2 of unlikely voxel relabeling 12 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 29571 voxels changed in iteration 0 of unlikely voxel relabeling 199 voxels changed in iteration 1 of unlikely voxel relabeling 16 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 28547 voxels changed in iteration 0 of unlikely voxel relabeling 98 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 6 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 12792 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 7 with volume 304 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 10 with volume 9930 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 631 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 9210.057441 mri_ca_label stimesec 11.006012 mri_ca_label ru_maxrss 3551916 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 5950231 mri_ca_label ru_majflt 7 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 2000 mri_ca_label ru_oublock 1880 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 10 mri_ca_label ru_nivcsw 100753 auto-labeling took 153 minutes and 45 seconds. @#@FSTIME 2022:09:05:15:50:21 mri_ca_label N 10 e 9225.36 S 11.19 U 9210.05 P 99% M 3551916 F 7 R 5950232 W 0 c 100755 w 11 I 2000 O 1880 L 1.62 1.29 1.21 @#@FSLOADPOST 2022:09:05:18:24:07 mri_ca_label N 10 1.11 1.19 1.21 #-------------------------------------- #@# CC Seg Mon Sep 5 18:24:07 UTC 2022 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/transforms/cc_up.lta P7T_020_001bc will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/transforms/cc_up.lta reading aseg from /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/aseg.auto_noCCseg.mgz reading norm from /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/norm.mgz MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 110399 voxels in left wm, 187008 in right wm, xrange [166, 180] searching rotation angles z=[-10 4], y=[-4 10] searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.2 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 global minimum found at slice 174.5, rotations (3.07, -2.93) final transformation (x=174.5, yr=3.069, zr=-2.930): 0.99726 0.05112 0.05346 -61.43900; -0.05104 0.99869 -0.00274 4.52192; -0.05353 -0.00000 0.99857 -24.42848; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 132] in xformed coordinates best xformed slice 128 min_x_fornix = 127 min_x_fornix = 140 min_x_fornix = 173 WARNING: min_x_fornix not set min_x_fornix = 124 cc center is found at 128 133 162 eigenvectors: 0.00197 -0.00681 0.99997; -0.01804 -0.99981 -0.00677; 0.99984 -0.01803 -0.00209; MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab writing aseg with callosum to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/aseg.auto.mgz... corpus callosum segmentation took 2.7 minutes #VMPC# mri_cc VmPeak 1011752 mri_cc done @#@FSTIME 2022:09:05:18:24:07 mri_cc N 7 e 162.35 S 1.11 U 160.84 P 99% M 789492 F 5 R 648029 W 0 c 8960 w 6 I 1064 O 1864 L 1.11 1.19 1.21 @#@FSLOADPOST 2022:09:05:18:26:49 mri_cc N 7 1.08 1.15 1.18 #-------------------------------------- #@# Merge ASeg Mon Sep 5 18:26:49 UTC 2022 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Sep 5 18:26:49 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_normalize -seed 1234 -mprage -noconform -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 not interpolating and embedding volume to be 256^3... 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 MRIcopyHeader(): source has ctab removing outliers in the aseg WM... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 611 control points removed MRIcopyHeader(): source has ctab Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 72 (72), valley at 35 (35) csf peak at 36, setting threshold to 60 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 72 (72), valley at 35 (35) csf peak at 36, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 8 minutes and 9 seconds. @#@FSTIME 2022:09:05:18:26:49 mri_normalize N 10 e 492.13 S 3.46 U 488.45 P 99% M 2788848 F 0 R 1631970 W 0 c 4594 w 1 I 0 O 9480 L 1.08 1.15 1.18 @#@FSLOADPOST 2022:09:05:18:35:01 mri_normalize N 10 1.15 1.18 1.18 #-------------------------------------------- #@# Mask BFS Mon Sep 5 18:35:01 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 5910257 voxels in mask (pct= 15.04) Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2022:09:05:18:35:01 mri_mask N 5 e 2.87 S 0.13 U 2.68 P 98% M 163804 F 4 R 39662 W 0 c 271 w 5 I 984 O 9344 L 1.15 1.18 1.18 @#@FSLOADPOST 2022:09:05:18:35:04 mri_mask N 5 1.22 1.19 1.18 #-------------------------------------------- #@# WM Segmentation Mon Sep 5 18:35:04 UTC 2022 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2022:09:05:18:35:04 AntsDenoiseImageFs N 4 e 143.60 S 0.36 U 143.06 P 99% M 813092 F 20 R 202107 W 0 c 2520 w 22 I 4216 O 9480 L 1.22 1.19 1.18 @#@FSLOADPOST 2022:09:05:18:37:28 AntsDenoiseImageFs N 4 1.12 1.17 1.17 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 0.6, wsize = 22 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 22 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 (102.0): 102.3 +- 5.7 [79.0 --> 125.0] CCS GM (76.0) : 74.8 +- 12.1 [30.0 --> 95.0] white_mean 102.334 white_sigma 5.74148 gray_mean 74.8229 gray_sigma 12.1317 setting bottom of white matter range wm_low to 87.0 setting top of gray matter range gray_hi to 99.1 wm_low 86.9546 wm_hi 125 gray_low 30 gray_hi 99.0864 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 86.9546 wm_hi 125 gray_low 30 gray_hi 99.0864 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 99.0864, wm_low = 86.9546 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=99.0864, wmlow=86.9546 509924 voxels processed (1.30%) 245575 voxels white (0.62%) 264349 voxels non-white (0.67%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=81.9546, gray_hi=99.0864, wsize=22 982565 voxels tested (2.50%) 174927 voxels changed (0.45%) 181429 multi-scale searches (0.46%) Recovering bright white MRIrecoverBrightWhite() wm_low 86.9546 wm_hi 125 slack 5.74148 pct_thresh 0.33 intensity_thresh 130.741 nvox_thresh 8.58 1709 voxels tested (0.00%) 922 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=81.9546, hithr=99.0864 smoothing input volume with sigma = 0.250 451545 voxels tested (1.15%) 65753 voxels changed (0.17%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 14106 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 9454 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 5478 filled MRIfindBrightNonWM(): 12523 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 9.9 minutes writing output to wm.seg.mgz... @#@FSTIME 2022:09:05:18:37:28 mri_segment N 5 e 593.09 S 1.81 U 590.51 P 99% M 301036 F 4 R 994980 W 0 c 22950 w 5 I 864 O 2704 L 1.12 1.17 1.17 @#@FSLOADPOST 2022:09:05:18:47:21 mri_segment N 5 1.17 1.17 1.18 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 1.02 minutes reading wm segmentation from wm.seg.mgz... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 0 voxels added to wm to prevent paths from MTL structures to cortex 14412 additional wm voxels added 0 additional wm voxels added SEG EDIT: 232168 voxels turned on, 51457 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2022:09:05:18:47:21 mri_edit_wm_with_aseg N 5 e 61.20 S 1.24 U 59.58 P 99% M 1061064 F 4 R 733341 W 0 c 2881 w 5 I 992 O 2608 L 1.17 1.17 1.18 @#@FSLOADPOST 2022:09:05:18:48:22 mri_edit_wm_with_aseg N 5 1.15 1.17 1.18 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 59 found - 59 modified | TOTAL: 59 pass 2 (xy+): 0 found - 59 modified | TOTAL: 59 pass 1 (xy-): 79 found - 79 modified | TOTAL: 138 pass 2 (xy-): 0 found - 79 modified | TOTAL: 138 pass 1 (yz+): 64 found - 64 modified | TOTAL: 202 pass 2 (yz+): 0 found - 64 modified | TOTAL: 202 pass 1 (yz-): 90 found - 90 modified | TOTAL: 292 pass 2 (yz-): 0 found - 90 modified | TOTAL: 292 pass 1 (xz+): 69 found - 69 modified | TOTAL: 361 pass 2 (xz+): 0 found - 69 modified | TOTAL: 361 pass 1 (xz-): 58 found - 58 modified | TOTAL: 419 pass 2 (xz-): 0 found - 58 modified | TOTAL: 419 Iteration Number : 1 pass 1 (+++): 90 found - 90 modified | TOTAL: 90 pass 2 (+++): 0 found - 90 modified | TOTAL: 90 pass 1 (+++): 76 found - 76 modified | TOTAL: 166 pass 2 (+++): 0 found - 76 modified | TOTAL: 166 pass 1 (+++): 126 found - 126 modified | TOTAL: 292 pass 2 (+++): 0 found - 126 modified | TOTAL: 292 pass 1 (+++): 167 found - 167 modified | TOTAL: 459 pass 2 (+++): 0 found - 167 modified | TOTAL: 459 Iteration Number : 1 pass 1 (++): 236 found - 236 modified | TOTAL: 236 pass 2 (++): 0 found - 236 modified | TOTAL: 236 pass 1 (+-): 209 found - 209 modified | TOTAL: 445 pass 2 (+-): 0 found - 209 modified | TOTAL: 445 pass 1 (--): 276 found - 276 modified | TOTAL: 721 pass 2 (--): 1 found - 277 modified | TOTAL: 722 pass 3 (--): 0 found - 277 modified | TOTAL: 722 pass 1 (-+): 230 found - 230 modified | TOTAL: 952 pass 2 (-+): 0 found - 230 modified | TOTAL: 952 Iteration Number : 2 pass 1 (xy+): 30 found - 30 modified | TOTAL: 30 pass 2 (xy+): 0 found - 30 modified | TOTAL: 30 pass 1 (xy-): 21 found - 21 modified | TOTAL: 51 pass 2 (xy-): 0 found - 21 modified | TOTAL: 51 pass 1 (yz+): 16 found - 16 modified | TOTAL: 67 pass 2 (yz+): 0 found - 16 modified | TOTAL: 67 pass 1 (yz-): 27 found - 27 modified | TOTAL: 94 pass 2 (yz-): 0 found - 27 modified | TOTAL: 94 pass 1 (xz+): 31 found - 31 modified | TOTAL: 125 pass 2 (xz+): 0 found - 31 modified | TOTAL: 125 pass 1 (xz-): 33 found - 33 modified | TOTAL: 158 pass 2 (xz-): 0 found - 33 modified | TOTAL: 158 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 8 found - 8 modified | TOTAL: 12 pass 2 (+++): 0 found - 8 modified | TOTAL: 12 pass 1 (+++): 8 found - 8 modified | TOTAL: 20 pass 2 (+++): 0 found - 8 modified | TOTAL: 20 pass 1 (+++): 10 found - 10 modified | TOTAL: 30 pass 2 (+++): 0 found - 10 modified | TOTAL: 30 Iteration Number : 2 pass 1 (++): 9 found - 9 modified | TOTAL: 9 pass 2 (++): 0 found - 9 modified | TOTAL: 9 pass 1 (+-): 16 found - 16 modified | TOTAL: 25 pass 2 (+-): 0 found - 16 modified | TOTAL: 25 pass 1 (--): 12 found - 12 modified | TOTAL: 37 pass 2 (--): 0 found - 12 modified | TOTAL: 37 pass 1 (-+): 15 found - 15 modified | TOTAL: 52 pass 2 (-+): 0 found - 15 modified | TOTAL: 52 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 5 found - 5 modified | TOTAL: 9 pass 2 (xy-): 0 found - 5 modified | TOTAL: 9 pass 1 (yz+): 1 found - 1 modified | TOTAL: 10 pass 2 (yz+): 0 found - 1 modified | TOTAL: 10 pass 1 (yz-): 4 found - 4 modified | TOTAL: 14 pass 2 (yz-): 0 found - 4 modified | TOTAL: 14 pass 1 (xz+): 2 found - 2 modified | TOTAL: 16 pass 2 (xz+): 0 found - 2 modified | TOTAL: 16 pass 1 (xz-): 0 found - 0 modified | TOTAL: 16 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 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 4 found - 4 modified | TOTAL: 8 pass 2 (--): 0 found - 4 modified | TOTAL: 8 pass 1 (-+): 0 found - 0 modified | TOTAL: 8 Iteration Number : 4 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 Iteration Number : 5 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 : 5 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 : 5 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 = 2096 (out of 2148794: 0.097543) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2022:09:05:18:48:22 mri_pretess N 4 e 8.93 S 0.10 U 8.19 P 92% M 124200 F 15 R 29790 W 0 c 855 w 18 I 3568 O 2608 L 1.15 1.17 1.18 @#@FSLOADPOST 2022:09:05:18:48:31 mri_pretess N 4 1.22 1.18 1.18 #-------------------------------------------- #@# Fill Mon Sep 5 18:48:31 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /home/marcantf/software/freesurfer/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 1.18564 0.01120 0.05388 -50.20270; -0.02660 1.10132 0.22977 -53.49084; -0.06695 -0.18585 1.00128 17.22388; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.18564 0.01120 0.05388 -50.20270; -0.02660 1.10132 0.22977 -53.49084; -0.06695 -0.18585 1.00128 17.22388; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Looking for area (min, max) = (972, 3889) area[0] = 457 (min = 972, max = 3889), aspect = 0.60 (min = 0.10, max = 0.75) need search nearby using seed (165, 189, 140), TAL = (3.0, -18.0, -11.4) talairach voxel to voxel transform 0.84072 -0.01558 -0.04166 42.09076; 0.00826 0.87400 -0.20101 50.62773; 0.05774 0.16118 0.95862 -4.99051; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (165, 189, 140) --> (3.0, -18.0, -11.4) done. filling took 2.8 minutes talairach cc position changed to (3.00, -18.00, -11.40) Erasing brainstem...done. seed_search_size = 16, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -18.00, -11.40) SRC: (146.81, 188.79, 167.48) search lh wm seed point around talairach space (-15.00, -18.00, -11.40), SRC: (197.25, 189.28, 170.94) 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 2022:09:05:18:48:31 mri_fill N 10 e 168.35 S 2.49 U 165.76 P 99% M 1987884 F 5 R 1124326 W 0 c 422 w 7 I 1280 O 736 L 1.22 1.18 1.18 @#@FSLOADPOST 2022:09:05:18:51:20 mri_fill N 10 1.24 1.19 1.18 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Mon Sep 5 18:51:20 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 25 found - 25 modified | TOTAL: 29 pass 2 (yz+): 0 found - 25 modified | TOTAL: 29 pass 1 (yz-): 24 found - 24 modified | TOTAL: 53 pass 2 (yz-): 0 found - 24 modified | TOTAL: 53 pass 1 (xz+): 3 found - 3 modified | TOTAL: 56 pass 2 (xz+): 0 found - 3 modified | TOTAL: 56 pass 1 (xz-): 5 found - 5 modified | TOTAL: 61 pass 2 (xz-): 0 found - 5 modified | TOTAL: 61 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 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 = 74 (out of 1086040: 0.006814) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2022:09:05:18:51:20 mri_pretess N 4 e 4.49 S 0.06 U 4.42 P 99% M 85264 F 0 R 20041 W 0 c 139 w 1 I 0 O 728 L 1.24 1.19 1.18 @#@FSLOADPOST 2022:09:05:18:51:24 mri_pretess N 4 1.30 1.21 1.19 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix.predec 7.2.0 7.2.0 slice 40: 3560 vertices, 3776 faces slice 50: 12850 vertices, 13216 faces slice 60: 25150 vertices, 25625 faces slice 70: 39374 vertices, 39874 faces slice 80: 55374 vertices, 55904 faces slice 90: 72898 vertices, 73543 faces slice 100: 90900 vertices, 91621 faces slice 110: 111549 vertices, 112264 faces slice 120: 131530 vertices, 132184 faces slice 130: 148775 vertices, 149458 faces slice 140: 168808 vertices, 169503 faces slice 150: 188329 vertices, 188999 faces slice 160: 207318 vertices, 208036 faces slice 170: 224960 vertices, 225667 faces slice 180: 243232 vertices, 243990 faces slice 190: 260464 vertices, 261195 faces slice 200: 278659 vertices, 279368 faces slice 210: 295712 vertices, 296428 faces slice 220: 310089 vertices, 310762 faces slice 230: 323532 vertices, 324208 faces slice 240: 336544 vertices, 337172 faces slice 250: 349565 vertices, 350174 faces slice 260: 360755 vertices, 361349 faces slice 270: 371695 vertices, 372265 faces slice 280: 381006 vertices, 381554 faces slice 290: 388320 vertices, 388798 faces slice 300: 392787 vertices, 393093 faces slice 310: 393154 vertices, 393390 faces slice 320: 393154 vertices, 393390 faces slice 330: 393154 vertices, 393390 faces slice 340: 393154 vertices, 393390 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix.predec using vox2ras matrix: -0.60000 0.00000 0.00000 101.99999; 0.00000 0.00000 0.60000 -101.99999; 0.00000 -0.60000 0.00000 101.99999; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2022:09:05:18:51:24 mri_tessellate N 3 e 2.79 S 0.07 U 2.68 P 98% M 84120 F 4 R 20309 W 0 c 6 w 5 I 1080 O 18440 L 1.30 1.21 1.19 @#@FSLOADPOST 2022:09:05:18:51:27 mri_tessellate N 3 1.27 1.20 1.19 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix.predec ../surf/lh.orig.nofix.predec counting number of connected components... 393154 voxel in cpt #1: X=-236 [v=393154,e=1180170,f=786780] located at (-27.646814, -7.728902, 12.481511) For the whole surface: X=-236 [v=393154,e=1180170,f=786780] One single component has been found nothing to do done @#@FSTIME 2022:09:05:18:51:27 mris_extract_main_component N 2 e 3.26 S 0.40 U 2.69 P 95% M 770476 F 14 R 205949 W 0 c 14 w 19 I 3240 O 27656 L 1.27 1.20 1.19 @#@FSLOADPOST 2022:09:05:18:51:31 mris_extract_main_component N 2 1.27 1.20 1.19 mris_remesh --desired-face-area 0.5 --input ../surf/lh.orig.nofix.predec --output ../surf/lh.orig.nofix iters = 5 target face area = 0.5 average source face area = 0.18 decimation level = 0.36 target vertices = 141535 Remesher::remeshBKV( 5 , 141535 ) vcount = 393154 vnum: 141535 area = 141620 avel: 0.682843 s0 = 0.644935 st: 1.07489 Targetn: 342830 points: 393154 Targetl: 0.761253 avg l: 0.682843 points: 393154 Maxndown:55356 Points: 337798 avg edge: 0.685388 Targetn: 292506 points: 337798 Targetl: 0.839663 avg l: 0.685388 points: 340090 Maxndown:52342 Points: 287748 avg edge: 0.721689 Targetn: 242182 points: 287748 Targetl: 0.918073 avg l: 0.721689 points: 287772 Maxndown:50149 Points: 237623 avg edge: 0.772538 Targetn: 191858 points: 237623 Targetl: 0.996484 avg l: 0.772538 points: 237629 Maxndown:50348 Points: 187281 avg edge: 0.847072 Targetn: 141535 points: 187281 Targetl: 1.07489 avg l: 0.847072 points: 187287 Maxndown:45752 Points: 141535 avg edge: 0.948652 Final Points: 141535 final avg edge: 0.948652 avg qual before : 0.866025 after: 0.942072 Removing intersections removing intersecting faces 000: 16 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 393154 nv = 141535 0.359999 Area 283542 0.37916 0.05579 0.001092 0.9563 Corner 850626 60.00000 10.55533 2.629818 173.2476 Edge 425313 0.94857 0.11846 0.026855 1.6710 Hinge 425313 30.62042 25.16686 0.000023 178.6447 mris_remesh done @#@FSTIME 2022:09:05:18:51:31 mris_remesh N 6 e 30.32 S 0.88 U 29.25 P 99% M 1174116 F 16 R 436545 W 0 c 1896 w 19 I 3584 O 9968 L 1.27 1.20 1.19 @#@FSLOADPOST 2022:09:05:18:52:01 mris_remesh N 6 1.31 1.22 1.19 #-------------------------------------------- #@# Tessellate rh Mon Sep 5 18:52:01 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 2 found - 2 modified | TOTAL: 6 pass 2 (xy-): 0 found - 2 modified | TOTAL: 6 pass 1 (yz+): 28 found - 28 modified | TOTAL: 34 pass 2 (yz+): 0 found - 28 modified | TOTAL: 34 pass 1 (yz-): 25 found - 25 modified | TOTAL: 59 pass 2 (yz-): 0 found - 25 modified | TOTAL: 59 pass 1 (xz+): 2 found - 2 modified | TOTAL: 61 pass 2 (xz+): 0 found - 2 modified | TOTAL: 61 pass 1 (xz-): 3 found - 3 modified | TOTAL: 64 pass 2 (xz-): 0 found - 3 modified | TOTAL: 64 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 67 (out of 1048682: 0.006389) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2022:09:05:18:52:01 mri_pretess N 4 e 4.05 S 0.06 U 3.98 P 99% M 85188 F 0 R 20039 W 0 c 62 w 1 I 0 O 728 L 1.31 1.22 1.19 @#@FSLOADPOST 2022:09:05:18:52:05 mri_pretess N 4 1.29 1.21 1.19 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix.predec 7.2.0 7.2.0 slice 40: 1699 vertices, 1840 faces slice 50: 8927 vertices, 9266 faces slice 60: 20598 vertices, 21054 faces slice 70: 34728 vertices, 35251 faces slice 80: 50998 vertices, 51600 faces slice 90: 70053 vertices, 70683 faces slice 100: 88037 vertices, 88785 faces slice 110: 107939 vertices, 108655 faces slice 120: 126727 vertices, 127351 faces slice 130: 146204 vertices, 146925 faces slice 140: 166732 vertices, 167511 faces slice 150: 186215 vertices, 186979 faces slice 160: 205063 vertices, 205799 faces slice 170: 224622 vertices, 225395 faces slice 180: 242227 vertices, 242910 faces slice 190: 259124 vertices, 259863 faces slice 200: 275390 vertices, 276098 faces slice 210: 290177 vertices, 290888 faces slice 220: 304892 vertices, 305603 faces slice 230: 318215 vertices, 318916 faces slice 240: 332116 vertices, 332821 faces slice 250: 343705 vertices, 344294 faces slice 260: 353972 vertices, 354595 faces slice 270: 363382 vertices, 363947 faces slice 280: 371979 vertices, 372503 faces slice 290: 378318 vertices, 378749 faces slice 300: 381098 vertices, 381402 faces slice 310: 381302 vertices, 381568 faces slice 320: 381302 vertices, 381568 faces slice 330: 381302 vertices, 381568 faces slice 340: 381302 vertices, 381568 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix.predec using vox2ras matrix: -0.60000 0.00000 0.00000 101.99999; 0.00000 0.00000 0.60000 -101.99999; 0.00000 -0.60000 0.00000 101.99999; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2022:09:05:18:52:05 mri_tessellate N 3 e 2.86 S 0.09 U 2.76 P 99% M 82968 F 0 R 20036 W 0 c 199 w 1 I 0 O 17888 L 1.29 1.21 1.19 @#@FSLOADPOST 2022:09:05:18:52:08 mri_tessellate N 3 1.26 1.21 1.19 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix.predec ../surf/rh.orig.nofix.predec counting number of connected components... 381302 voxel in cpt #1: X=-266 [v=381302,e=1144704,f=763136] located at (21.626825, -8.539768, 16.383051) For the whole surface: X=-266 [v=381302,e=1144704,f=763136] One single component has been found nothing to do done @#@FSTIME 2022:09:05:18:52:08 mris_extract_main_component N 2 e 3.33 S 0.37 U 2.94 P 99% M 747540 F 0 R 199817 W 0 c 142 w 4 I 0 O 26824 L 1.26 1.21 1.19 @#@FSLOADPOST 2022:09:05:18:52:11 mris_extract_main_component N 2 1.26 1.21 1.19 mris_remesh --desired-face-area 0.5 --input ../surf/rh.orig.nofix.predec --output ../surf/rh.orig.nofix iters = 5 target face area = 0.5 average source face area = 0.18 decimation level = 0.36 target vertices = 137269 Remesher::remeshBKV( 5 , 137269 ) vcount = 381302 vnum: 137269 area = 137364 avel: 0.682843 s0 = 0.644967 st: 1.07494 Targetn: 332495 points: 381302 Targetl: 0.761263 avg l: 0.682843 points: 381302 Maxndown:53687 Points: 327615 avg edge: 0.684837 Targetn: 283688 points: 327615 Targetl: 0.839683 avg l: 0.684837 points: 331308 Maxndown:52382 Points: 278926 avg edge: 0.721068 Targetn: 234882 points: 278926 Targetl: 0.918103 avg l: 0.721068 points: 278964 Maxndown:48490 Points: 230474 avg edge: 0.771691 Targetn: 186075 points: 230474 Targetl: 0.996523 avg l: 0.771691 points: 230478 Maxndown:48843 Points: 181635 avg edge: 0.84655 Targetn: 137269 points: 181635 Targetl: 1.07494 avg l: 0.84655 points: 181641 Maxndown:44372 Points: 137269 avg edge: 0.948268 Final Points: 137269 final avg edge: 0.948268 avg qual before : 0.866025 after: 0.94197 Removing intersections removing intersecting faces 000: 28 intersecting terminating search with 0 intersecting Remeshed surface quality stats nv0 = 381302 nv = 137269 0.360001 Area 275070 0.37882 0.05643 0.001023 0.9951 Corner 825210 60.00000 10.56888 3.585468 172.0741 Edge 412605 0.94813 0.11886 0.028722 1.7417 Hinge 412605 30.95822 25.29413 0.000000 179.9911 mris_remesh done @#@FSTIME 2022:09:05:18:52:12 mris_remesh N 6 e 26.87 S 0.86 U 25.98 P 99% M 1141364 F 0 R 422644 W 0 c 442 w 1 I 0 O 9672 L 1.26 1.21 1.19 @#@FSLOADPOST 2022:09:05:18:52:38 mris_remesh N 6 1.30 1.22 1.19 #-------------------------------------------- #@# Smooth1 lh Mon Sep 5 18:52:38 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts 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... @#@FSTIME 2022:09:05:18:52:38 mris_smooth N 5 e 3.65 S 0.18 U 3.40 P 97% M 221984 F 4 R 66681 W 0 c 35 w 5 I 648 O 9968 L 1.30 1.22 1.19 @#@FSLOADPOST 2022:09:05:18:52:42 mris_smooth N 5 1.30 1.22 1.19 #-------------------------------------------- #@# Smooth1 rh Mon Sep 5 18:52:42 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts 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... @#@FSTIME 2022:09:05:18:52:42 mris_smooth N 5 e 3.16 S 0.17 U 2.98 P 99% M 215620 F 0 R 64751 W 0 c 113 w 2 I 0 O 9672 L 1.30 1.22 1.19 @#@FSLOADPOST 2022:09:05:18:52:45 mris_smooth N 5 1.27 1.22 1.19 #-------------------------------------------- #@# Inflation1 lh Mon Sep 5 18:52:45 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_inflate -no-save-sulc -n 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix niterations = 100 Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.6 mm, total surface area = 71784 mm^2 resetting # of iterations to 167 for highres volume step 000: RMS=0.159 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.085 (target=0.015) step 020: RMS=0.078 (target=0.015) step 025: RMS=0.073 (target=0.015) step 030: RMS=0.068 (target=0.015) step 035: RMS=0.064 (target=0.015) step 040: RMS=0.062 (target=0.015) step 045: RMS=0.060 (target=0.015) step 050: RMS=0.059 (target=0.015) step 055: RMS=0.058 (target=0.015) step 060: RMS=0.057 (target=0.015) step 065: RMS=0.056 (target=0.015) step 070: RMS=0.056 (target=0.015) step 075: RMS=0.055 (target=0.015) step 080: RMS=0.055 (target=0.015) step 085: RMS=0.055 (target=0.015) step 090: RMS=0.055 (target=0.015) step 095: RMS=0.054 (target=0.015) step 100: RMS=0.054 (target=0.015) step 105: RMS=0.054 (target=0.015) step 110: RMS=0.054 (target=0.015) step 115: RMS=0.054 (target=0.015) step 120: RMS=0.054 (target=0.015) step 125: RMS=0.053 (target=0.015) step 130: RMS=0.053 (target=0.015) step 135: RMS=0.053 (target=0.015) step 140: RMS=0.053 (target=0.015) step 145: RMS=0.053 (target=0.015) step 150: RMS=0.053 (target=0.015) step 155: RMS=0.053 (target=0.015) step 160: RMS=0.053 (target=0.015) step 165: RMS=0.053 (target=0.015) step 170: RMS=0.053 (target=0.015) step 175: RMS=0.053 (target=0.015) step 180: RMS=0.053 (target=0.015) step 185: RMS=0.053 (target=0.015) step 190: RMS=0.053 (target=0.015) step 195: RMS=0.053 (target=0.015) step 200: RMS=0.053 (target=0.015) step 205: RMS=0.053 (target=0.015) step 210: RMS=0.053 (target=0.015) step 215: RMS=0.053 (target=0.015) step 220: RMS=0.053 (target=0.015) step 225: RMS=0.053 (target=0.015) step 230: RMS=0.052 (target=0.015) step 235: RMS=0.052 (target=0.015) step 240: RMS=0.053 (target=0.015) step 245: RMS=0.052 (target=0.015) step 250: RMS=0.052 (target=0.015) step 255: RMS=0.052 (target=0.015) step 260: RMS=0.052 (target=0.015) step 265: RMS=0.052 (target=0.015) step 270: RMS=0.052 (target=0.015) step 275: RMS=0.052 (target=0.015) step 280: RMS=0.052 (target=0.015) step 285: RMS=0.052 (target=0.015) step 290: RMS=0.052 (target=0.015) step 295: RMS=0.052 (target=0.015) step 300: RMS=0.052 (target=0.015) step 305: RMS=0.052 (target=0.015) step 310: RMS=0.052 (target=0.015) step 315: RMS=0.052 (target=0.015) step 320: RMS=0.052 (target=0.015) step 325: RMS=0.052 (target=0.015) step 330: RMS=0.052 (target=0.015) step 335: RMS=0.052 (target=0.015) step 340: RMS=0.052 (target=0.015) step 345: RMS=0.052 (target=0.015) step 350: RMS=0.052 (target=0.015) step 355: RMS=0.052 (target=0.015) step 360: RMS=0.052 (target=0.015) step 365: RMS=0.052 (target=0.015) step 370: RMS=0.052 (target=0.015) step 375: RMS=0.052 (target=0.015) step 380: RMS=0.052 (target=0.015) step 385: RMS=0.052 (target=0.015) step 390: RMS=0.052 (target=0.015) step 395: RMS=0.052 (target=0.015) step 400: RMS=0.052 (target=0.015) step 405: RMS=0.052 (target=0.015) step 410: RMS=0.052 (target=0.015) step 415: RMS=0.052 (target=0.015) step 420: RMS=0.052 (target=0.015) step 425: RMS=0.052 (target=0.015) step 430: RMS=0.052 (target=0.015) step 435: RMS=0.052 (target=0.015) step 440: RMS=0.052 (target=0.015) step 445: RMS=0.052 (target=0.015) step 450: RMS=0.052 (target=0.015) step 455: RMS=0.052 (target=0.015) step 460: RMS=0.052 (target=0.015) step 465: RMS=0.052 (target=0.015) step 470: RMS=0.052 (target=0.015) step 475: RMS=0.052 (target=0.015) step 480: RMS=0.052 (target=0.015) step 485: RMS=0.052 (target=0.015) step 490: RMS=0.052 (target=0.015) step 495: RMS=0.052 (target=0.015) step 500: RMS=0.052 (target=0.015) step 505: RMS=0.052 (target=0.015) step 510: RMS=0.052 (target=0.015) step 515: RMS=0.052 (target=0.015) step 520: RMS=0.052 (target=0.015) step 525: RMS=0.052 (target=0.015) step 530: RMS=0.052 (target=0.015) step 535: RMS=0.052 (target=0.015) step 540: RMS=0.052 (target=0.015) step 545: RMS=0.052 (target=0.015) step 550: RMS=0.052 (target=0.015) step 555: RMS=0.052 (target=0.015) step 560: RMS=0.052 (target=0.015) step 565: RMS=0.052 (target=0.015) step 570: RMS=0.052 (target=0.015) step 575: RMS=0.052 (target=0.015) step 580: RMS=0.052 (target=0.015) step 585: RMS=0.052 (target=0.015) step 590: RMS=0.052 (target=0.015) step 595: RMS=0.052 (target=0.015) step 600: RMS=0.052 (target=0.015) step 605: RMS=0.052 (target=0.015) step 610: RMS=0.052 (target=0.015) step 615: RMS=0.052 (target=0.015) step 620: RMS=0.052 (target=0.015) step 625: RMS=0.052 (target=0.015) step 630: RMS=0.052 (target=0.015) step 635: RMS=0.052 (target=0.015) step 640: RMS=0.052 (target=0.015) step 645: RMS=0.052 (target=0.015) step 650: RMS=0.052 (target=0.015) step 655: RMS=0.052 (target=0.015) step 660: RMS=0.052 (target=0.015) step 665: RMS=0.052 (target=0.015) step 670: RMS=0.052 (target=0.015) step 675: RMS=0.052 (target=0.015) step 680: RMS=0.052 (target=0.015) step 685: RMS=0.052 (target=0.015) step 690: RMS=0.052 (target=0.015) step 695: RMS=0.052 (target=0.015) step 700: RMS=0.053 (target=0.015) step 705: RMS=0.052 (target=0.015) step 710: RMS=0.052 (target=0.015) step 715: RMS=0.052 (target=0.015) step 720: RMS=0.052 (target=0.015) step 725: RMS=0.052 (target=0.015) step 730: RMS=0.052 (target=0.015) step 735: RMS=0.052 (target=0.015) step 740: RMS=0.053 (target=0.015) step 745: RMS=0.052 (target=0.015) step 750: RMS=0.052 (target=0.015) step 755: RMS=0.053 (target=0.015) step 760: RMS=0.052 (target=0.015) step 765: RMS=0.053 (target=0.015) step 770: RMS=0.052 (target=0.015) step 775: RMS=0.052 (target=0.015) step 780: RMS=0.052 (target=0.015) step 785: RMS=0.052 (target=0.015) step 790: RMS=0.053 (target=0.015) step 795: RMS=0.053 (target=0.015) step 800: RMS=0.052 (target=0.015) step 805: RMS=0.052 (target=0.015) step 810: RMS=0.052 (target=0.015) step 815: RMS=0.052 (target=0.015) step 820: RMS=0.052 (target=0.015) step 825: RMS=0.052 (target=0.015) step 830: RMS=0.052 (target=0.015) step 835: RMS=0.052 (target=0.015) step 840: RMS=0.054 (target=0.015) step 845: RMS=0.056 (target=0.015) step 850: RMS=0.056 (target=0.015) step 855: RMS=0.056 (target=0.015) step 860: RMS=0.056 (target=0.015) step 865: RMS=0.057 (target=0.015) step 870: RMS=0.056 (target=0.015) step 875: RMS=0.056 (target=0.015) step 880: RMS=0.057 (target=0.015) step 885: RMS=0.057 (target=0.015) step 890: RMS=0.056 (target=0.015) step 895: RMS=0.057 (target=0.015) step 900: RMS=0.056 (target=0.015) step 905: RMS=0.057 (target=0.015) step 910: RMS=0.057 (target=0.015) step 915: RMS=0.056 (target=0.015) step 920: RMS=0.057 (target=0.015) step 925: RMS=0.057 (target=0.015) step 930: RMS=0.057 (target=0.015) step 935: RMS=0.057 (target=0.015) step 940: RMS=0.056 (target=0.015) step 945: RMS=0.057 (target=0.015) step 950: RMS=0.057 (target=0.015) step 955: RMS=0.057 (target=0.015) step 960: RMS=0.057 (target=0.015) step 965: RMS=0.057 (target=0.015) step 970: RMS=0.057 (target=0.015) step 975: RMS=0.057 (target=0.015) step 980: RMS=0.057 (target=0.015) step 985: RMS=0.057 (target=0.015) step 990: RMS=0.057 (target=0.015) step 995: RMS=0.057 (target=0.015) step 1000: RMS=0.057 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 6.0 minutes inflation complete. Not saving sulc mris_inflate utimesec 344.705998 mris_inflate stimesec 17.844005 mris_inflate ru_maxrss 222348 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 8975605 mris_inflate ru_majflt 18 mris_inflate ru_nswap 0 mris_inflate ru_inblock 3736 mris_inflate ru_oublock 9968 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 19 mris_inflate ru_nivcsw 3814 @#@FSTIME 2022:09:05:18:52:45 mris_inflate N 5 e 362.85 S 17.85 U 344.70 P 99% M 222348 F 18 R 8975608 W 0 c 3816 w 20 I 3736 O 9968 L 1.27 1.22 1.19 @#@FSLOADPOST 2022:09:05:18:58:48 mris_inflate N 5 1.37 1.28 1.21 #-------------------------------------------- #@# Inflation1 rh Mon Sep 5 18:58:48 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_inflate -no-save-sulc -n 100 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix niterations = 100 Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.2 mm, total surface area = 68771 mm^2 resetting # of iterations to 167 for highres volume step 000: RMS=0.164 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.100 (target=0.015) step 015: RMS=0.089 (target=0.015) step 020: RMS=0.081 (target=0.015) step 025: RMS=0.076 (target=0.015) step 030: RMS=0.072 (target=0.015) step 035: RMS=0.068 (target=0.015) step 040: RMS=0.066 (target=0.015) step 045: RMS=0.063 (target=0.015) step 050: RMS=0.062 (target=0.015) step 055: RMS=0.061 (target=0.015) step 060: RMS=0.060 (target=0.015) step 065: RMS=0.060 (target=0.015) step 070: RMS=0.060 (target=0.015) step 075: RMS=0.060 (target=0.015) step 080: RMS=0.059 (target=0.015) step 085: RMS=0.059 (target=0.015) step 090: RMS=0.059 (target=0.015) step 095: RMS=0.058 (target=0.015) step 100: RMS=0.058 (target=0.015) step 105: RMS=0.058 (target=0.015) step 110: RMS=0.058 (target=0.015) step 115: RMS=0.058 (target=0.015) step 120: RMS=0.058 (target=0.015) step 125: RMS=0.058 (target=0.015) step 130: RMS=0.058 (target=0.015) step 135: RMS=0.058 (target=0.015) step 140: RMS=0.058 (target=0.015) step 145: RMS=0.058 (target=0.015) step 150: RMS=0.058 (target=0.015) step 155: RMS=0.058 (target=0.015) step 160: RMS=0.058 (target=0.015) step 165: RMS=0.058 (target=0.015) step 170: RMS=0.057 (target=0.015) step 175: RMS=0.058 (target=0.015) step 180: RMS=0.058 (target=0.015) step 185: RMS=0.058 (target=0.015) step 190: RMS=0.058 (target=0.015) step 195: RMS=0.058 (target=0.015) step 200: RMS=0.058 (target=0.015) step 205: RMS=0.058 (target=0.015) step 210: RMS=0.058 (target=0.015) step 215: RMS=0.058 (target=0.015) step 220: RMS=0.058 (target=0.015) step 225: RMS=0.058 (target=0.015) step 230: RMS=0.058 (target=0.015) step 235: RMS=0.058 (target=0.015) step 240: RMS=0.058 (target=0.015) step 245: RMS=0.058 (target=0.015) step 250: RMS=0.058 (target=0.015) step 255: RMS=0.058 (target=0.015) step 260: RMS=0.058 (target=0.015) step 265: RMS=0.058 (target=0.015) step 270: RMS=0.058 (target=0.015) step 275: RMS=0.058 (target=0.015) step 280: RMS=0.058 (target=0.015) step 285: RMS=0.058 (target=0.015) step 290: RMS=0.058 (target=0.015) step 295: RMS=0.058 (target=0.015) step 300: RMS=0.058 (target=0.015) step 305: RMS=0.058 (target=0.015) step 310: RMS=0.058 (target=0.015) step 315: RMS=0.058 (target=0.015) step 320: RMS=0.058 (target=0.015) step 325: RMS=0.058 (target=0.015) step 330: RMS=0.058 (target=0.015) step 335: RMS=0.058 (target=0.015) step 340: RMS=0.058 (target=0.015) step 345: RMS=0.058 (target=0.015) step 350: RMS=0.058 (target=0.015) step 355: RMS=0.058 (target=0.015) step 360: RMS=0.058 (target=0.015) step 365: RMS=0.058 (target=0.015) step 370: RMS=0.058 (target=0.015) step 375: RMS=0.058 (target=0.015) step 380: RMS=0.058 (target=0.015) step 385: RMS=0.058 (target=0.015) step 390: RMS=0.058 (target=0.015) step 395: RMS=0.058 (target=0.015) step 400: RMS=0.058 (target=0.015) step 405: RMS=0.058 (target=0.015) step 410: RMS=0.058 (target=0.015) step 415: RMS=0.058 (target=0.015) step 420: RMS=0.058 (target=0.015) step 425: RMS=0.058 (target=0.015) step 430: RMS=0.058 (target=0.015) step 435: RMS=0.058 (target=0.015) step 440: RMS=0.058 (target=0.015) step 445: RMS=0.059 (target=0.015) step 450: RMS=0.058 (target=0.015) step 455: RMS=0.059 (target=0.015) step 460: RMS=0.058 (target=0.015) step 465: RMS=0.058 (target=0.015) step 470: RMS=0.058 (target=0.015) step 475: RMS=0.058 (target=0.015) step 480: RMS=0.058 (target=0.015) step 485: RMS=0.058 (target=0.015) step 490: RMS=0.058 (target=0.015) step 495: RMS=0.058 (target=0.015) step 500: RMS=0.058 (target=0.015) step 505: RMS=0.059 (target=0.015) step 510: RMS=0.059 (target=0.015) step 515: RMS=0.059 (target=0.015) step 520: RMS=0.059 (target=0.015) step 525: RMS=0.059 (target=0.015) step 530: RMS=0.059 (target=0.015) step 535: RMS=0.059 (target=0.015) step 540: RMS=0.059 (target=0.015) step 545: RMS=0.059 (target=0.015) step 550: RMS=0.059 (target=0.015) step 555: RMS=0.059 (target=0.015) step 560: RMS=0.059 (target=0.015) step 565: RMS=0.059 (target=0.015) step 570: RMS=0.059 (target=0.015) step 575: RMS=0.059 (target=0.015) step 580: RMS=0.059 (target=0.015) step 585: RMS=0.059 (target=0.015) step 590: RMS=0.059 (target=0.015) step 595: RMS=0.059 (target=0.015) step 600: RMS=0.059 (target=0.015) step 605: RMS=0.059 (target=0.015) step 610: RMS=0.059 (target=0.015) step 615: RMS=0.059 (target=0.015) step 620: RMS=0.059 (target=0.015) step 625: RMS=0.059 (target=0.015) step 630: RMS=0.059 (target=0.015) step 635: RMS=0.059 (target=0.015) step 640: RMS=0.059 (target=0.015) step 645: RMS=0.059 (target=0.015) step 650: RMS=0.059 (target=0.015) step 655: RMS=0.059 (target=0.015) step 660: RMS=0.059 (target=0.015) step 665: RMS=0.059 (target=0.015) step 670: RMS=0.059 (target=0.015) step 675: RMS=0.060 (target=0.015) step 680: RMS=0.060 (target=0.015) step 685: RMS=0.060 (target=0.015) step 690: RMS=0.060 (target=0.015) step 695: RMS=0.060 (target=0.015) step 700: RMS=0.060 (target=0.015) step 705: RMS=0.060 (target=0.015) step 710: RMS=0.060 (target=0.015) step 715: RMS=0.060 (target=0.015) step 720: RMS=0.060 (target=0.015) step 725: RMS=0.060 (target=0.015) step 730: RMS=0.060 (target=0.015) step 735: RMS=0.060 (target=0.015) step 740: RMS=0.060 (target=0.015) step 745: RMS=0.060 (target=0.015) step 750: RMS=0.060 (target=0.015) step 755: RMS=0.060 (target=0.015) step 760: RMS=0.061 (target=0.015) step 765: RMS=0.061 (target=0.015) step 770: RMS=0.060 (target=0.015) step 775: RMS=0.060 (target=0.015) step 780: RMS=0.061 (target=0.015) step 785: RMS=0.060 (target=0.015) step 790: RMS=0.060 (target=0.015) step 795: RMS=0.061 (target=0.015) step 800: RMS=0.060 (target=0.015) step 805: RMS=0.060 (target=0.015) step 810: RMS=0.061 (target=0.015) step 815: RMS=0.061 (target=0.015) step 820: RMS=0.060 (target=0.015) step 825: RMS=0.061 (target=0.015) step 830: RMS=0.060 (target=0.015) step 835: RMS=0.061 (target=0.015) step 840: RMS=0.062 (target=0.015) step 845: RMS=0.066 (target=0.015) step 850: RMS=0.067 (target=0.015) step 855: RMS=0.067 (target=0.015) step 860: RMS=0.067 (target=0.015) step 865: RMS=0.068 (target=0.015) step 870: RMS=0.067 (target=0.015) step 875: RMS=0.068 (target=0.015) step 880: RMS=0.068 (target=0.015) step 885: RMS=0.068 (target=0.015) step 890: RMS=0.067 (target=0.015) step 895: RMS=0.068 (target=0.015) step 900: RMS=0.068 (target=0.015) step 905: RMS=0.068 (target=0.015) step 910: RMS=0.068 (target=0.015) step 915: RMS=0.068 (target=0.015) step 920: RMS=0.067 (target=0.015) step 925: RMS=0.067 (target=0.015) step 930: RMS=0.068 (target=0.015) step 935: RMS=0.068 (target=0.015) step 940: RMS=0.067 (target=0.015) step 945: RMS=0.068 (target=0.015) step 950: RMS=0.068 (target=0.015) step 955: RMS=0.068 (target=0.015) step 960: RMS=0.068 (target=0.015) step 965: RMS=0.068 (target=0.015) step 970: RMS=0.068 (target=0.015) step 975: RMS=0.068 (target=0.015) step 980: RMS=0.068 (target=0.015) step 985: RMS=0.068 (target=0.015) step 990: RMS=0.068 (target=0.015) step 995: RMS=0.068 (target=0.015) step 1000: RMS=0.068 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 5.8 minutes inflation complete. Not saving sulc mris_inflate utimesec 332.972303 mris_inflate stimesec 16.622244 mris_inflate ru_maxrss 216216 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 8482083 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9672 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 1426 @#@FSTIME 2022:09:05:18:58:48 mris_inflate N 5 e 349.67 S 16.63 U 332.97 P 99% M 216216 F 0 R 8482085 W 0 c 1428 w 1 I 0 O 9672 L 1.37 1.28 1.21 @#@FSLOADPOST 2022:09:05:19:04:38 mris_inflate N 5 1.13 1.21 1.19 #-------------------------------------------- #@# QSphere lh Mon Sep 5 19:04:38 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts 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: 7.2.0 available threads: 1 scaling brain by 0.352... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.51 (0.00-->9.31) (max @ vno 80086 --> 81402) face area 0.03 +- 0.03 (-0.30-->0.66) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=171.994, avgs=0 005/300: dt: 0.9000, rms radial error=171.738, avgs=0 010/300: dt: 0.9000, rms radial error=171.191, avgs=0 015/300: dt: 0.9000, rms radial error=170.471, avgs=0 020/300: dt: 0.9000, rms radial error=169.652, avgs=0 025/300: dt: 0.9000, rms radial error=168.776, avgs=0 030/300: dt: 0.9000, rms radial error=167.869, avgs=0 035/300: dt: 0.9000, rms radial error=166.946, avgs=0 040/300: dt: 0.9000, rms radial error=166.015, avgs=0 045/300: dt: 0.9000, rms radial error=165.082, avgs=0 050/300: dt: 0.9000, rms radial error=164.149, avgs=0 055/300: dt: 0.9000, rms radial error=163.220, avgs=0 060/300: dt: 0.9000, rms radial error=162.294, avgs=0 065/300: dt: 0.9000, rms radial error=161.373, avgs=0 070/300: dt: 0.9000, rms radial error=160.457, avgs=0 075/300: dt: 0.9000, rms radial error=159.545, avgs=0 080/300: dt: 0.9000, rms radial error=158.639, avgs=0 085/300: dt: 0.9000, rms radial error=157.740, avgs=0 090/300: dt: 0.9000, rms radial error=156.845, avgs=0 095/300: dt: 0.9000, rms radial error=155.956, avgs=0 100/300: dt: 0.9000, rms radial error=155.072, avgs=0 105/300: dt: 0.9000, rms radial error=154.193, avgs=0 110/300: dt: 0.9000, rms radial error=153.319, avgs=0 115/300: dt: 0.9000, rms radial error=152.449, avgs=0 120/300: dt: 0.9000, rms radial error=151.585, avgs=0 125/300: dt: 0.9000, rms radial error=150.726, avgs=0 130/300: dt: 0.9000, rms radial error=149.871, avgs=0 135/300: dt: 0.9000, rms radial error=149.022, avgs=0 140/300: dt: 0.9000, rms radial error=148.177, avgs=0 145/300: dt: 0.9000, rms radial error=147.337, avgs=0 150/300: dt: 0.9000, rms radial error=146.502, avgs=0 155/300: dt: 0.9000, rms radial error=145.671, avgs=0 160/300: dt: 0.9000, rms radial error=144.846, avgs=0 165/300: dt: 0.9000, rms radial error=144.025, avgs=0 170/300: dt: 0.9000, rms radial error=143.209, avgs=0 175/300: dt: 0.9000, rms radial error=142.397, avgs=0 180/300: dt: 0.9000, rms radial error=141.590, avgs=0 185/300: dt: 0.9000, rms radial error=140.787, avgs=0 190/300: dt: 0.9000, rms radial error=139.990, avgs=0 195/300: dt: 0.9000, rms radial error=139.196, avgs=0 200/300: dt: 0.9000, rms radial error=138.407, avgs=0 205/300: dt: 0.9000, rms radial error=137.623, avgs=0 210/300: dt: 0.9000, rms radial error=136.843, avgs=0 215/300: dt: 0.9000, rms radial error=136.068, avgs=0 220/300: dt: 0.9000, rms radial error=135.297, avgs=0 225/300: dt: 0.9000, rms radial error=134.530, avgs=0 230/300: dt: 0.9000, rms radial error=133.768, avgs=0 235/300: dt: 0.9000, rms radial error=133.010, avgs=0 240/300: dt: 0.9000, rms radial error=132.257, avgs=0 245/300: dt: 0.9000, rms radial error=131.507, avgs=0 250/300: dt: 0.9000, rms radial error=130.762, avgs=0 255/300: dt: 0.9000, rms radial error=130.022, avgs=0 260/300: dt: 0.9000, rms radial error=129.285, avgs=0 265/300: dt: 0.9000, rms radial error=128.553, avgs=0 270/300: dt: 0.9000, rms radial error=127.825, avgs=0 275/300: dt: 0.9000, rms radial error=127.101, avgs=0 280/300: dt: 0.9000, rms radial error=126.381, avgs=0 285/300: dt: 0.9000, rms radial error=125.665, avgs=0 290/300: dt: 0.9000, rms radial error=124.953, avgs=0 295/300: dt: 0.9000, rms radial error=124.246, avgs=0 300/300: dt: 0.9000, rms radial error=123.542, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15911.72 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00026 epoch 2 (K=40.0), pass 1, starting sse = 2423.44 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 = 226.38 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/13 = 0.00160 epoch 4 (K=640.0), pass 1, starting sse = 25.22 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/21 = 0.00353 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0452 hours FSRUNTIME@ mris_sphere 0.0452 hours 1 threads #VMPC# mris_sphere VmPeak 507328 mris_sphere done @#@FSTIME 2022:09:05:19:04:38 mris_sphere N 9 e 162.57 S 7.05 U 155.39 P 99% M 227716 F 5 R 3553060 W 0 c 1719 w 7 I 1792 O 9968 L 1.13 1.21 1.19 @#@FSLOADPOST 2022:09:05:19:07:21 mris_sphere N 9 1.08 1.16 1.17 #-------------------------------------------- #@# QSphere rh Mon Sep 5 19:07:21 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts 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: 7.2.0 available threads: 1 scaling brain by 0.362... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.51 (0.00-->8.08) (max @ vno 98681 --> 99267) face area 0.03 +- 0.04 (-0.26-->1.11) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=171.532, avgs=0 005/300: dt: 0.9000, rms radial error=171.278, avgs=0 010/300: dt: 0.9000, rms radial error=170.734, avgs=0 015/300: dt: 0.9000, rms radial error=170.019, avgs=0 020/300: dt: 0.9000, rms radial error=169.206, avgs=0 025/300: dt: 0.9000, rms radial error=168.335, avgs=0 030/300: dt: 0.9000, rms radial error=167.434, avgs=0 035/300: dt: 0.9000, rms radial error=166.515, avgs=0 040/300: dt: 0.9000, rms radial error=165.589, avgs=0 045/300: dt: 0.9000, rms radial error=164.660, avgs=0 050/300: dt: 0.9000, rms radial error=163.732, avgs=0 055/300: dt: 0.9000, rms radial error=162.807, avgs=0 060/300: dt: 0.9000, rms radial error=161.885, avgs=0 065/300: dt: 0.9000, rms radial error=160.968, avgs=0 070/300: dt: 0.9000, rms radial error=160.055, avgs=0 075/300: dt: 0.9000, rms radial error=159.146, avgs=0 080/300: dt: 0.9000, rms radial error=158.243, avgs=0 085/300: dt: 0.9000, rms radial error=157.345, avgs=0 090/300: dt: 0.9000, rms radial error=156.452, avgs=0 095/300: dt: 0.9000, rms radial error=155.563, avgs=0 100/300: dt: 0.9000, rms radial error=154.680, avgs=0 105/300: dt: 0.9000, rms radial error=153.802, avgs=0 110/300: dt: 0.9000, rms radial error=152.929, avgs=0 115/300: dt: 0.9000, rms radial error=152.060, avgs=0 120/300: dt: 0.9000, rms radial error=151.197, avgs=0 125/300: dt: 0.9000, rms radial error=150.339, avgs=0 130/300: dt: 0.9000, rms radial error=149.485, avgs=0 135/300: dt: 0.9000, rms radial error=148.637, avgs=0 140/300: dt: 0.9000, rms radial error=147.793, avgs=0 145/300: dt: 0.9000, rms radial error=146.955, avgs=0 150/300: dt: 0.9000, rms radial error=146.121, avgs=0 155/300: dt: 0.9000, rms radial error=145.291, avgs=0 160/300: dt: 0.9000, rms radial error=144.467, avgs=0 165/300: dt: 0.9000, rms radial error=143.647, avgs=0 170/300: dt: 0.9000, rms radial error=142.832, avgs=0 175/300: dt: 0.9000, rms radial error=142.021, avgs=0 180/300: dt: 0.9000, rms radial error=141.215, avgs=0 185/300: dt: 0.9000, rms radial error=140.414, avgs=0 190/300: dt: 0.9000, rms radial error=139.617, avgs=0 195/300: dt: 0.9000, rms radial error=138.825, avgs=0 200/300: dt: 0.9000, rms radial error=138.037, avgs=0 205/300: dt: 0.9000, rms radial error=137.254, avgs=0 210/300: dt: 0.9000, rms radial error=136.475, avgs=0 215/300: dt: 0.9000, rms radial error=135.701, avgs=0 220/300: dt: 0.9000, rms radial error=134.931, avgs=0 225/300: dt: 0.9000, rms radial error=134.166, avgs=0 230/300: dt: 0.9000, rms radial error=133.405, avgs=0 235/300: dt: 0.9000, rms radial error=132.648, avgs=0 240/300: dt: 0.9000, rms radial error=131.895, avgs=0 245/300: dt: 0.9000, rms radial error=131.147, avgs=0 250/300: dt: 0.9000, rms radial error=130.403, avgs=0 255/300: dt: 0.9000, rms radial error=129.663, avgs=0 260/300: dt: 0.9000, rms radial error=128.928, avgs=0 265/300: dt: 0.9000, rms radial error=128.196, avgs=0 270/300: dt: 0.9000, rms radial error=127.469, avgs=0 275/300: dt: 0.9000, rms radial error=126.746, avgs=0 280/300: dt: 0.9000, rms radial error=126.027, avgs=0 285/300: dt: 0.9000, rms radial error=125.312, avgs=0 290/300: dt: 0.9000, rms radial error=124.601, avgs=0 295/300: dt: 0.9000, rms radial error=123.895, avgs=0 300/300: dt: 0.9000, rms radial error=123.192, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15327.02 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00022 epoch 2 (K=40.0), pass 1, starting sse = 2294.96 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00044 epoch 3 (K=160.0), pass 1, starting sse = 210.96 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/14 = 0.00672 epoch 4 (K=640.0), pass 1, starting sse = 20.73 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/17 = 0.00440 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0427 hours FSRUNTIME@ mris_sphere 0.0427 hours 1 threads #VMPC# mris_sphere VmPeak 500912 mris_sphere done @#@FSTIME 2022:09:05:19:07:21 mris_sphere N 9 e 153.65 S 6.54 U 147.04 P 99% M 221164 F 0 R 3270850 W 0 c 1792 w 1 I 0 O 9672 L 1.08 1.16 1.17 @#@FSLOADPOST 2022:09:05:19:09:55 mris_sphere N 9 1.43 1.23 1.20 #@# Fix Topology lh Mon Sep 5 19:09:55 UTC 2022 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 P7T_020_001bc 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' 7.2.0 7.2.0 before topology correction, eno=-236 (nv=141535, nf=283542, ne=425313, g=119) 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... 10217 ambiguous faces found in tessellation segmenting defects... 92 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 18 into 19 -merging segment 32 into 26 -merging segment 58 into 51 -merging segment 57 into 51 -merging segment 48 into 53 -merging segment 77 into 71 -merging segment 74 into 72 85 defects to be corrected 0 vertices coincident reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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: -9.5938 (-4.7969) -vertex loglikelihood: -6.7941 (-3.3971) -normal dot loglikelihood: -3.5417 (-3.5417) -quad curv loglikelihood: -5.5669 (-2.7835) Total Loglikelihood : -25.4966 CORRECTING DEFECT 0 (vertices=35, convex hull=86, v0=640) After retessellation of defect 0 (v0=640), euler #=-87 (135191,402909,267631) : difference with theory (-82) = 5 CORRECTING DEFECT 1 (vertices=21, convex hull=48, v0=3153) After retessellation of defect 1 (v0=3153), euler #=-86 (135197,402944,267661) : difference with theory (-81) = 5 CORRECTING DEFECT 2 (vertices=56, convex hull=63, v0=3608) After retessellation of defect 2 (v0=3608), euler #=-85 (135208,403003,267710) : difference with theory (-80) = 5 CORRECTING DEFECT 3 (vertices=22, convex hull=57, v0=3719) After retessellation of defect 3 (v0=3719), euler #=-84 (135213,403041,267744) : difference with theory (-79) = 5 CORRECTING DEFECT 4 (vertices=48, convex hull=72, v0=6875) After retessellation of defect 4 (v0=6875), euler #=-83 (135224,403101,267794) : difference with theory (-78) = 5 CORRECTING DEFECT 5 (vertices=14, convex hull=35, v0=10212) After retessellation of defect 5 (v0=10212), euler #=-82 (135227,403123,267814) : difference with theory (-77) = 5 CORRECTING DEFECT 6 (vertices=35, convex hull=48, v0=14727) After retessellation of defect 6 (v0=14727), euler #=-81 (135234,403162,267847) : difference with theory (-76) = 5 CORRECTING DEFECT 7 (vertices=51, convex hull=42, v0=16625) After retessellation of defect 7 (v0=16625), euler #=-80 (135237,403186,267869) : difference with theory (-75) = 5 CORRECTING DEFECT 8 (vertices=40, convex hull=68, v0=25050) After retessellation of defect 8 (v0=25050), euler #=-79 (135246,403240,267915) : difference with theory (-74) = 5 CORRECTING DEFECT 9 (vertices=31, convex hull=41, v0=31228) After retessellation of defect 9 (v0=31228), euler #=-79 (135251,403276,267946) : difference with theory (-73) = 6 CORRECTING DEFECT 10 (vertices=35, convex hull=29, v0=31307) After retessellation of defect 10 (v0=31307), euler #=-78 (135253,403293,267962) : difference with theory (-72) = 6 CORRECTING DEFECT 11 (vertices=9, convex hull=25, v0=32633) After retessellation of defect 11 (v0=32633), euler #=-77 (135254,403303,267972) : difference with theory (-71) = 6 CORRECTING DEFECT 12 (vertices=55, convex hull=52, v0=34219) After retessellation of defect 12 (v0=34219), euler #=-76 (135266,403358,268016) : difference with theory (-70) = 6 CORRECTING DEFECT 13 (vertices=44, convex hull=61, v0=36981) After retessellation of defect 13 (v0=36981), euler #=-75 (135285,403441,268081) : difference with theory (-69) = 6 CORRECTING DEFECT 14 (vertices=13, convex hull=32, v0=38451) After retessellation of defect 14 (v0=38451), euler #=-74 (135286,403452,268092) : difference with theory (-68) = 6 CORRECTING DEFECT 15 (vertices=24, convex hull=55, v0=39661) After retessellation of defect 15 (v0=39661), euler #=-73 (135294,403496,268129) : difference with theory (-67) = 6 CORRECTING DEFECT 16 (vertices=1246, convex hull=1058, v0=42548) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview After retessellation of defect 16 (v0=42548), euler #=-72 (135555,404799,269172) : difference with theory (-66) = 6 CORRECTING DEFECT 17 (vertices=31, convex hull=23, v0=43704) After retessellation of defect 17 (v0=43704), euler #=-71 (135558,404814,269185) : difference with theory (-65) = 6 CORRECTING DEFECT 18 (vertices=160, convex hull=163, v0=47809) After retessellation of defect 18 (v0=47809), euler #=-69 (135587,404975,269319) : difference with theory (-64) = 5 CORRECTING DEFECT 19 (vertices=19, convex hull=30, v0=54115) After retessellation of defect 19 (v0=54115), euler #=-68 (135590,404996,269338) : difference with theory (-63) = 5 CORRECTING DEFECT 20 (vertices=6, convex hull=18, v0=55248) After retessellation of defect 20 (v0=55248), euler #=-67 (135590,405000,269343) : difference with theory (-62) = 5 CORRECTING DEFECT 21 (vertices=91, convex hull=75, v0=57454) After retessellation of defect 21 (v0=57454), euler #=-66 (135619,405121,269436) : difference with theory (-61) = 5 CORRECTING DEFECT 22 (vertices=215, convex hull=150, v0=57483) After retessellation of defect 22 (v0=57483), euler #=-65 (135632,405229,269532) : difference with theory (-60) = 5 CORRECTING DEFECT 23 (vertices=90, convex hull=55, v0=59256) After retessellation of defect 23 (v0=59256), euler #=-64 (135647,405298,269587) : difference with theory (-59) = 5 CORRECTING DEFECT 24 (vertices=13, convex hull=41, v0=61934) After retessellation of defect 24 (v0=61934), euler #=-63 (135650,405320,269607) : difference with theory (-58) = 5 CORRECTING DEFECT 25 (vertices=261, convex hull=353, v0=63199) After retessellation of defect 25 (v0=63199), euler #=-61 (135673,405562,269828) : difference with theory (-57) = 4 CORRECTING DEFECT 26 (vertices=26, convex hull=45, v0=63241) After retessellation of defect 26 (v0=63241), euler #=-60 (135682,405609,269867) : difference with theory (-56) = 4 CORRECTING DEFECT 27 (vertices=10, convex hull=50, v0=63296) After retessellation of defect 27 (v0=63296), euler #=-59 (135684,405635,269892) : difference with theory (-55) = 4 CORRECTING DEFECT 28 (vertices=8, convex hull=30, v0=63927) After retessellation of defect 28 (v0=63927), euler #=-58 (135685,405649,269906) : difference with theory (-54) = 4 CORRECTING DEFECT 29 (vertices=6, convex hull=36, v0=66063) After retessellation of defect 29 (v0=66063), euler #=-57 (135686,405667,269924) : difference with theory (-53) = 4 CORRECTING DEFECT 30 (vertices=133, convex hull=97, v0=67510) After retessellation of defect 30 (v0=67510), euler #=-56 (135724,405826,270046) : difference with theory (-52) = 4 CORRECTING DEFECT 31 (vertices=15, convex hull=18, v0=69319) After retessellation of defect 31 (v0=69319), euler #=-55 (135724,405831,270052) : difference with theory (-51) = 4 CORRECTING DEFECT 32 (vertices=11, convex hull=23, v0=71356) After retessellation of defect 32 (v0=71356), euler #=-54 (135725,405838,270059) : difference with theory (-50) = 4 CORRECTING DEFECT 33 (vertices=5, convex hull=31, v0=72182) After retessellation of defect 33 (v0=72182), euler #=-53 (135727,405853,270073) : difference with theory (-49) = 4 CORRECTING DEFECT 34 (vertices=11, convex hull=37, v0=73608) After retessellation of defect 34 (v0=73608), euler #=-52 (135728,405869,270089) : difference with theory (-48) = 4 CORRECTING DEFECT 35 (vertices=101, convex hull=72, v0=74204) After retessellation of defect 35 (v0=74204), euler #=-51 (135751,405962,270160) : difference with theory (-47) = 4 CORRECTING DEFECT 36 (vertices=10, convex hull=16, v0=74943) After retessellation of defect 36 (v0=74943), euler #=-50 (135754,405975,270171) : difference with theory (-46) = 4 CORRECTING DEFECT 37 (vertices=40, convex hull=25, v0=75627) After retessellation of defect 37 (v0=75627), euler #=-49 (135756,405990,270185) : difference with theory (-45) = 4 CORRECTING DEFECT 38 (vertices=5, convex hull=10, v0=78772) After retessellation of defect 38 (v0=78772), euler #=-48 (135757,405994,270189) : difference with theory (-44) = 4 CORRECTING DEFECT 39 (vertices=86, convex hull=56, v0=81281) After retessellation of defect 39 (v0=81281), euler #=-47 (135768,406046,270231) : difference with theory (-43) = 4 CORRECTING DEFECT 40 (vertices=12, convex hull=24, v0=81670) After retessellation of defect 40 (v0=81670), euler #=-46 (135770,406059,270243) : difference with theory (-42) = 4 CORRECTING DEFECT 41 (vertices=14, convex hull=34, v0=83301) After retessellation of defect 41 (v0=83301), euler #=-45 (135771,406072,270256) : difference with theory (-41) = 4 CORRECTING DEFECT 42 (vertices=10, convex hull=20, v0=83946) After retessellation of defect 42 (v0=83946), euler #=-44 (135772,406079,270263) : difference with theory (-40) = 4 CORRECTING DEFECT 43 (vertices=60, convex hull=68, v0=85373) After retessellation of defect 43 (v0=85373), euler #=-43 (135790,406162,270329) : difference with theory (-39) = 4 CORRECTING DEFECT 44 (vertices=54, convex hull=25, v0=85769) After retessellation of defect 44 (v0=85769), euler #=-42 (135795,406183,270346) : difference with theory (-38) = 4 CORRECTING DEFECT 45 (vertices=22, convex hull=20, v0=85899) After retessellation of defect 45 (v0=85899), euler #=-41 (135796,406190,270353) : difference with theory (-37) = 4 CORRECTING DEFECT 46 (vertices=15, convex hull=41, v0=89803) After retessellation of defect 46 (v0=89803), euler #=-40 (135804,406228,270384) : difference with theory (-36) = 4 CORRECTING DEFECT 47 (vertices=13, convex hull=22, v0=90294) After retessellation of defect 47 (v0=90294), euler #=-39 (135806,406243,270398) : difference with theory (-35) = 4 CORRECTING DEFECT 48 (vertices=815, convex hull=381, v0=91083) After retessellation of defect 48 (v0=91083), euler #=-36 (135921,406798,270841) : difference with theory (-34) = 2 CORRECTING DEFECT 49 (vertices=10, convex hull=38, v0=91089) After retessellation of defect 49 (v0=91089), euler #=-35 (135924,406817,270858) : difference with theory (-33) = 2 CORRECTING DEFECT 50 (vertices=120, convex hull=63, v0=91693) After retessellation of defect 50 (v0=91693), euler #=-33 (135933,406870,270904) : difference with theory (-32) = 1 CORRECTING DEFECT 51 (vertices=18, convex hull=25, v0=94052) After retessellation of defect 51 (v0=94052), euler #=-32 (135933,406879,270914) : difference with theory (-31) = 1 CORRECTING DEFECT 52 (vertices=138, convex hull=72, v0=94726) After retessellation of defect 52 (v0=94726), euler #=-32 (135943,406941,270966) : difference with theory (-30) = 2 CORRECTING DEFECT 53 (vertices=10, convex hull=32, v0=96234) After retessellation of defect 53 (v0=96234), euler #=-31 (135945,406956,270980) : difference with theory (-29) = 2 CORRECTING DEFECT 54 (vertices=80, convex hull=89, v0=99344) After retessellation of defect 54 (v0=99344), euler #=-30 (135953,407019,271036) : difference with theory (-28) = 2 CORRECTING DEFECT 55 (vertices=69, convex hull=46, v0=99425) After retessellation of defect 55 (v0=99425), euler #=-29 (135965,407073,271079) : difference with theory (-27) = 2 CORRECTING DEFECT 56 (vertices=10, convex hull=28, v0=100146) After retessellation of defect 56 (v0=100146), euler #=-28 (135968,407091,271095) : difference with theory (-26) = 2 CORRECTING DEFECT 57 (vertices=155, convex hull=105, v0=100702) After retessellation of defect 57 (v0=100702), euler #=-27 (136003,407245,271215) : difference with theory (-25) = 2 CORRECTING DEFECT 58 (vertices=118, convex hull=102, v0=100934) After retessellation of defect 58 (v0=100934), euler #=-26 (136012,407319,271281) : difference with theory (-24) = 2 CORRECTING DEFECT 59 (vertices=7, convex hull=27, v0=106286) After retessellation of defect 59 (v0=106286), euler #=-25 (136015,407334,271294) : difference with theory (-23) = 2 CORRECTING DEFECT 60 (vertices=94, convex hull=66, v0=107328) After retessellation of defect 60 (v0=107328), euler #=-24 (136039,407430,271367) : difference with theory (-22) = 2 CORRECTING DEFECT 61 (vertices=54, convex hull=38, v0=107900) After retessellation of defect 61 (v0=107900), euler #=-23 (136047,407468,271398) : difference with theory (-21) = 2 CORRECTING DEFECT 62 (vertices=8, convex hull=33, v0=110723) After retessellation of defect 62 (v0=110723), euler #=-22 (136047,407476,271407) : difference with theory (-20) = 2 CORRECTING DEFECT 63 (vertices=32, convex hull=42, v0=114568) After retessellation of defect 63 (v0=114568), euler #=-21 (136052,407505,271432) : difference with theory (-19) = 2 CORRECTING DEFECT 64 (vertices=9, convex hull=7, v0=115104) After retessellation of defect 64 (v0=115104), euler #=-20 (136052,407505,271433) : difference with theory (-18) = 2 CORRECTING DEFECT 65 (vertices=123, convex hull=119, v0=115474) After retessellation of defect 65 (v0=115474), euler #=-19 (136064,407592,271509) : difference with theory (-17) = 2 CORRECTING DEFECT 66 (vertices=270, convex hull=228, v0=116584) After retessellation of defect 66 (v0=116584), euler #=-17 (136104,407818,271697) : difference with theory (-16) = 1 CORRECTING DEFECT 67 (vertices=33, convex hull=69, v0=116981) After retessellation of defect 67 (v0=116981), euler #=-15 (136115,407881,271751) : difference with theory (-15) = 0 CORRECTING DEFECT 68 (vertices=52, convex hull=95, v0=118193) After retessellation of defect 68 (v0=118193), euler #=-14 (136126,407951,271811) : difference with theory (-14) = 0 CORRECTING DEFECT 69 (vertices=28, convex hull=66, v0=121163) After retessellation of defect 69 (v0=121163), euler #=-13 (136134,408000,271853) : difference with theory (-13) = 0 CORRECTING DEFECT 70 (vertices=189, convex hull=159, v0=122796) After retessellation of defect 70 (v0=122796), euler #=-12 (136161,408161,271988) : difference with theory (-12) = 0 CORRECTING DEFECT 71 (vertices=20, convex hull=54, v0=123818) After retessellation of defect 71 (v0=123818), euler #=-11 (136169,408205,272025) : difference with theory (-11) = 0 CORRECTING DEFECT 72 (vertices=52, convex hull=83, v0=127982) After retessellation of defect 72 (v0=127982), euler #=-10 (136187,408294,272097) : difference with theory (-10) = 0 CORRECTING DEFECT 73 (vertices=16, convex hull=55, v0=130660) After retessellation of defect 73 (v0=130660), euler #=-9 (136191,408327,272127) : difference with theory (-9) = 0 CORRECTING DEFECT 74 (vertices=16, convex hull=56, v0=132765) After retessellation of defect 74 (v0=132765), euler #=-8 (136198,408368,272162) : difference with theory (-8) = 0 CORRECTING DEFECT 75 (vertices=31, convex hull=71, v0=134940) After retessellation of defect 75 (v0=134940), euler #=-7 (136206,408418,272205) : difference with theory (-7) = 0 CORRECTING DEFECT 76 (vertices=167, convex hull=93, v0=135735) After retessellation of defect 76 (v0=135735), euler #=-6 (136231,408540,272303) : difference with theory (-6) = 0 CORRECTING DEFECT 77 (vertices=34, convex hull=31, v0=136010) After retessellation of defect 77 (v0=136010), euler #=-5 (136234,408559,272320) : difference with theory (-5) = 0 CORRECTING DEFECT 78 (vertices=51, convex hull=53, v0=137322) After retessellation of defect 78 (v0=137322), euler #=-4 (136240,408597,272353) : difference with theory (-4) = 0 CORRECTING DEFECT 79 (vertices=17, convex hull=42, v0=138385) After retessellation of defect 79 (v0=138385), euler #=-3 (136246,408630,272381) : difference with theory (-3) = 0 CORRECTING DEFECT 80 (vertices=17, convex hull=48, v0=138967) After retessellation of defect 80 (v0=138967), euler #=-2 (136253,408669,272414) : difference with theory (-2) = 0 CORRECTING DEFECT 81 (vertices=23, convex hull=18, v0=139701) After retessellation of defect 81 (v0=139701), euler #=-1 (136254,408677,272422) : difference with theory (-1) = 0 CORRECTING DEFECT 82 (vertices=35, convex hull=51, v0=139817) After retessellation of defect 82 (v0=139817), euler #=0 (136261,408719,272458) : difference with theory (0) = 0 CORRECTING DEFECT 83 (vertices=80, convex hull=92, v0=140802) After retessellation of defect 83 (v0=140802), euler #=1 (136284,408828,272545) : difference with theory (1) = 0 CORRECTING DEFECT 84 (vertices=18, convex hull=48, v0=140859) After retessellation of defect 84 (v0=140859), euler #=2 (136290,408864,272576) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.86 +- 0.23 (0.06-->14.99) (max @ vno 78573 --> 81690) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.86 +- 0.23 (0.06-->14.99) (max @ vno 78573 --> 81690) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 337 mutations (37.5%), 561 crossovers (62.5%), 538 vertices were eliminated building final representation... 5245 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=136290, nf=272576, ne=408864, g=0) writing corrected surface to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 248 intersecting 001: 74 intersecting 002: 8 intersecting terminating search with 0 intersecting topology fixing took 6.8 minutes FSRUNTIME@ mris_fix_topology lh 0.1135 hours 1 threads #VMPC# mris_fix_topology VmPeak 1063684 @#@FSTIME 2022:09:05:19:09:55 mris_fix_topology N 14 e 408.79 S 0.74 U 407.81 P 99% M 1018756 F 7 R 291223 W 0 c 2744 w 9 I 1696 O 12920 L 1.43 1.23 1.20 @#@FSLOADPOST 2022:09:05:19:16:43 mris_fix_topology N 14 1.19 1.23 1.20 #@# Fix Topology rh Mon Sep 5 19:16:43 UTC 2022 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 P7T_020_001bc 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' 7.2.0 7.2.0 before topology correction, eno=-266 (nv=137269, nf=275070, ne=412605, g=134) 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... 12167 ambiguous faces found in tessellation segmenting defects... 95 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 57 into 51 -merging segment 70 into 66 93 defects to be corrected 0 vertices coincident reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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: -9.7023 (-4.8512) -vertex loglikelihood: -6.8738 (-3.4369) -normal dot loglikelihood: -3.4282 (-3.4282) -quad curv loglikelihood: -5.5994 (-2.7997) Total Loglikelihood : -25.6036 CORRECTING DEFECT 0 (vertices=28, convex hull=66, v0=710) After retessellation of defect 0 (v0=710), euler #=-88 (130067,387720,257565) : difference with theory (-90) = -2 CORRECTING DEFECT 1 (vertices=77, convex hull=108, v0=1820) After retessellation of defect 1 (v0=1820), euler #=-87 (130085,387818,257646) : difference with theory (-89) = -2 CORRECTING DEFECT 2 (vertices=37, convex hull=68, v0=3068) After retessellation of defect 2 (v0=3068), euler #=-86 (130094,387874,257694) : difference with theory (-88) = -2 CORRECTING DEFECT 3 (vertices=12, convex hull=41, v0=7153) After retessellation of defect 3 (v0=7153), euler #=-85 (130099,387903,257719) : difference with theory (-87) = -2 CORRECTING DEFECT 4 (vertices=523, convex hull=216, v0=8950) After retessellation of defect 4 (v0=8950), euler #=-85 (130161,388204,257958) : difference with theory (-86) = -1 CORRECTING DEFECT 5 (vertices=61, convex hull=85, v0=12422) After retessellation of defect 5 (v0=12422), euler #=-84 (130178,388291,258029) : difference with theory (-85) = -1 CORRECTING DEFECT 6 (vertices=20, convex hull=47, v0=13573) After retessellation of defect 6 (v0=13573), euler #=-83 (130183,388325,258059) : difference with theory (-84) = -1 CORRECTING DEFECT 7 (vertices=26, convex hull=26, v0=17316) After retessellation of defect 7 (v0=17316), euler #=-82 (130184,388336,258070) : difference with theory (-83) = -1 CORRECTING DEFECT 8 (vertices=40, convex hull=31, v0=19149) After retessellation of defect 8 (v0=19149), euler #=-81 (130188,388360,258091) : difference with theory (-82) = -1 CORRECTING DEFECT 9 (vertices=15, convex hull=46, v0=20217) After retessellation of defect 9 (v0=20217), euler #=-80 (130193,388389,258116) : difference with theory (-81) = -1 CORRECTING DEFECT 10 (vertices=163, convex hull=215, v0=24743) After retessellation of defect 10 (v0=24743), euler #=-79 (130245,388639,258315) : difference with theory (-80) = -1 CORRECTING DEFECT 11 (vertices=9, convex hull=29, v0=25921) After retessellation of defect 11 (v0=25921), euler #=-78 (130245,388648,258325) : difference with theory (-79) = -1 CORRECTING DEFECT 12 (vertices=165, convex hull=33, v0=26663) After retessellation of defect 12 (v0=26663), euler #=-77 (130252,388680,258351) : difference with theory (-78) = -1 CORRECTING DEFECT 13 (vertices=13, convex hull=44, v0=28909) After retessellation of defect 13 (v0=28909), euler #=-76 (130255,388704,258373) : difference with theory (-77) = -1 CORRECTING DEFECT 14 (vertices=20, convex hull=52, v0=30741) After retessellation of defect 14 (v0=30741), euler #=-75 (130260,388738,258403) : difference with theory (-76) = -1 CORRECTING DEFECT 15 (vertices=13, convex hull=42, v0=32755) After retessellation of defect 15 (v0=32755), euler #=-74 (130264,388764,258426) : difference with theory (-75) = -1 CORRECTING DEFECT 16 (vertices=52, convex hull=79, v0=34113) After retessellation of defect 16 (v0=34113), euler #=-73 (130276,388835,258486) : difference with theory (-74) = -1 CORRECTING DEFECT 17 (vertices=29, convex hull=20, v0=43151) After retessellation of defect 17 (v0=43151), euler #=-72 (130281,388858,258505) : difference with theory (-73) = -1 CORRECTING DEFECT 18 (vertices=18, convex hull=43, v0=43873) After retessellation of defect 18 (v0=43873), euler #=-71 (130287,388890,258532) : difference with theory (-72) = -1 CORRECTING DEFECT 19 (vertices=14, convex hull=37, v0=48312) After retessellation of defect 19 (v0=48312), euler #=-70 (130292,388918,258556) : difference with theory (-71) = -1 CORRECTING DEFECT 20 (vertices=72, convex hull=93, v0=50188) After retessellation of defect 20 (v0=50188), euler #=-69 (130307,389007,258631) : difference with theory (-70) = -1 CORRECTING DEFECT 21 (vertices=79, convex hull=103, v0=51075) After retessellation of defect 21 (v0=51075), euler #=-68 (130327,389109,258714) : difference with theory (-69) = -1 CORRECTING DEFECT 22 (vertices=29, convex hull=68, v0=51083) After retessellation of defect 22 (v0=51083), euler #=-67 (130335,389162,258760) : difference with theory (-68) = -1 CORRECTING DEFECT 23 (vertices=6, convex hull=23, v0=51833) After retessellation of defect 23 (v0=51833), euler #=-66 (130335,389169,258768) : difference with theory (-67) = -1 CORRECTING DEFECT 24 (vertices=15, convex hull=34, v0=53843) After retessellation of defect 24 (v0=53843), euler #=-65 (130340,389194,258789) : difference with theory (-66) = -1 CORRECTING DEFECT 25 (vertices=13, convex hull=32, v0=54720) After retessellation of defect 25 (v0=54720), euler #=-64 (130343,389216,258809) : difference with theory (-65) = -1 CORRECTING DEFECT 26 (vertices=43, convex hull=49, v0=55006) After retessellation of defect 26 (v0=55006), euler #=-63 (130348,389249,258838) : difference with theory (-64) = -1 CORRECTING DEFECT 27 (vertices=10, convex hull=32, v0=56148) After retessellation of defect 27 (v0=56148), euler #=-62 (130350,389265,258853) : difference with theory (-63) = -1 CORRECTING DEFECT 28 (vertices=135, convex hull=124, v0=56179) After retessellation of defect 28 (v0=56179), euler #=-61 (130387,389431,258983) : difference with theory (-62) = -1 CORRECTING DEFECT 29 (vertices=19, convex hull=54, v0=56416) After retessellation of defect 29 (v0=56416), euler #=-60 (130394,389475,259021) : difference with theory (-61) = -1 CORRECTING DEFECT 30 (vertices=48, convex hull=77, v0=58942) After retessellation of defect 30 (v0=58942), euler #=-59 (130409,389551,259083) : difference with theory (-60) = -1 CORRECTING DEFECT 31 (vertices=26, convex hull=58, v0=60231) After retessellation of defect 31 (v0=60231), euler #=-58 (130416,389596,259122) : difference with theory (-59) = -1 CORRECTING DEFECT 32 (vertices=19, convex hull=30, v0=60703) After retessellation of defect 32 (v0=60703), euler #=-57 (130418,389621,259146) : difference with theory (-58) = -1 CORRECTING DEFECT 33 (vertices=34, convex hull=30, v0=61973) After retessellation of defect 33 (v0=61973), euler #=-56 (130423,389645,259166) : difference with theory (-57) = -1 CORRECTING DEFECT 34 (vertices=26, convex hull=26, v0=62643) After retessellation of defect 34 (v0=62643), euler #=-55 (130425,389658,259178) : difference with theory (-56) = -1 CORRECTING DEFECT 35 (vertices=11, convex hull=15, v0=62915) After retessellation of defect 35 (v0=62915), euler #=-54 (130425,389663,259184) : difference with theory (-55) = -1 CORRECTING DEFECT 36 (vertices=24, convex hull=47, v0=65358) After retessellation of defect 36 (v0=65358), euler #=-53 (130431,389698,259214) : difference with theory (-54) = -1 CORRECTING DEFECT 37 (vertices=22, convex hull=47, v0=66065) After retessellation of defect 37 (v0=66065), euler #=-52 (130441,389743,259250) : difference with theory (-53) = -1 CORRECTING DEFECT 38 (vertices=42, convex hull=33, v0=68313) After retessellation of defect 38 (v0=68313), euler #=-51 (130445,389763,259267) : difference with theory (-52) = -1 CORRECTING DEFECT 39 (vertices=35, convex hull=51, v0=69006) After retessellation of defect 39 (v0=69006), euler #=-50 (130459,389825,259316) : difference with theory (-51) = -1 CORRECTING DEFECT 40 (vertices=979, convex hull=450, v0=70476) After retessellation of defect 40 (v0=70476), euler #=-49 (130580,390404,259775) : difference with theory (-50) = -1 CORRECTING DEFECT 41 (vertices=50, convex hull=40, v0=70624) After retessellation of defect 41 (v0=70624), euler #=-48 (130585,390431,259798) : difference with theory (-49) = -1 CORRECTING DEFECT 42 (vertices=32, convex hull=45, v0=73381) After retessellation of defect 42 (v0=73381), euler #=-47 (130598,390486,259841) : difference with theory (-48) = -1 CORRECTING DEFECT 43 (vertices=208, convex hull=130, v0=74258) After retessellation of defect 43 (v0=74258), euler #=-46 (130653,390719,260020) : difference with theory (-47) = -1 CORRECTING DEFECT 44 (vertices=5, convex hull=14, v0=75255) After retessellation of defect 44 (v0=75255), euler #=-45 (130653,390722,260024) : difference with theory (-46) = -1 CORRECTING DEFECT 45 (vertices=8, convex hull=24, v0=76644) After retessellation of defect 45 (v0=76644), euler #=-44 (130654,390732,260034) : difference with theory (-45) = -1 CORRECTING DEFECT 46 (vertices=15, convex hull=53, v0=77750) After retessellation of defect 46 (v0=77750), euler #=-43 (130660,390770,260067) : difference with theory (-44) = -1 CORRECTING DEFECT 47 (vertices=43, convex hull=25, v0=78331) After retessellation of defect 47 (v0=78331), euler #=-42 (130664,390789,260083) : difference with theory (-43) = -1 CORRECTING DEFECT 48 (vertices=22, convex hull=61, v0=80074) After retessellation of defect 48 (v0=80074), euler #=-41 (130671,390835,260123) : difference with theory (-42) = -1 CORRECTING DEFECT 49 (vertices=36, convex hull=29, v0=86193) After retessellation of defect 49 (v0=86193), euler #=-40 (130676,390859,260143) : difference with theory (-41) = -1 CORRECTING DEFECT 50 (vertices=21, convex hull=57, v0=86982) After retessellation of defect 50 (v0=86982), euler #=-39 (130682,390900,260179) : difference with theory (-40) = -1 CORRECTING DEFECT 51 (vertices=860, convex hull=421, v0=87520) After retessellation of defect 51 (v0=87520), euler #=-40 (130745,391321,260536) : difference with theory (-39) = 1 CORRECTING DEFECT 52 (vertices=16, convex hull=20, v0=87648) After retessellation of defect 52 (v0=87648), euler #=-39 (130747,391330,260544) : difference with theory (-38) = 1 CORRECTING DEFECT 53 (vertices=18, convex hull=31, v0=88071) After retessellation of defect 53 (v0=88071), euler #=-38 (130754,391361,260569) : difference with theory (-37) = 1 CORRECTING DEFECT 54 (vertices=28, convex hull=41, v0=88889) After retessellation of defect 54 (v0=88889), euler #=-37 (130756,391381,260588) : difference with theory (-36) = 1 CORRECTING DEFECT 55 (vertices=7, convex hull=11, v0=89278) After retessellation of defect 55 (v0=89278), euler #=-36 (130757,391387,260594) : difference with theory (-35) = 1 CORRECTING DEFECT 56 (vertices=119, convex hull=46, v0=89388) After retessellation of defect 56 (v0=89388), euler #=-35 (130767,391438,260636) : difference with theory (-34) = 1 CORRECTING DEFECT 57 (vertices=13, convex hull=13, v0=93703) After retessellation of defect 57 (v0=93703), euler #=-34 (130768,391445,260643) : difference with theory (-33) = 1 CORRECTING DEFECT 58 (vertices=765, convex hull=43, v0=95406) After retessellation of defect 58 (v0=95406), euler #=-33 (130776,391482,260673) : difference with theory (-32) = 1 CORRECTING DEFECT 59 (vertices=180, convex hull=99, v0=96953) After retessellation of defect 59 (v0=96953), euler #=-32 (130792,391574,260750) : difference with theory (-31) = 1 CORRECTING DEFECT 60 (vertices=119, convex hull=108, v0=97599) After retessellation of defect 60 (v0=97599), euler #=-31 (130824,391715,260860) : difference with theory (-30) = 1 CORRECTING DEFECT 61 (vertices=28, convex hull=34, v0=98068) After retessellation of defect 61 (v0=98068), euler #=-30 (130831,391747,260886) : difference with theory (-29) = 1 CORRECTING DEFECT 62 (vertices=47, convex hull=46, v0=98750) After retessellation of defect 62 (v0=98750), euler #=-29 (130841,391793,260923) : difference with theory (-28) = 1 CORRECTING DEFECT 63 (vertices=77, convex hull=98, v0=98883) After retessellation of defect 63 (v0=98883), euler #=-28 (130865,391907,261014) : difference with theory (-27) = 1 CORRECTING DEFECT 64 (vertices=49, convex hull=35, v0=99239) After retessellation of defect 64 (v0=99239), euler #=-27 (130869,391931,261035) : difference with theory (-26) = 1 CORRECTING DEFECT 65 (vertices=124, convex hull=166, v0=99304) After retessellation of defect 65 (v0=99304), euler #=-25 (130906,392124,261193) : difference with theory (-25) = 0 CORRECTING DEFECT 66 (vertices=10, convex hull=30, v0=101764) After retessellation of defect 66 (v0=101764), euler #=-24 (130908,392142,261210) : difference with theory (-24) = 0 CORRECTING DEFECT 67 (vertices=101, convex hull=121, v0=101966) After retessellation of defect 67 (v0=101966), euler #=-23 (130948,392314,261343) : difference with theory (-23) = 0 CORRECTING DEFECT 68 (vertices=30, convex hull=43, v0=102321) After retessellation of defect 68 (v0=102321), euler #=-22 (130953,392345,261370) : difference with theory (-22) = 0 CORRECTING DEFECT 69 (vertices=49, convex hull=24, v0=104113) After retessellation of defect 69 (v0=104113), euler #=-21 (130957,392366,261388) : difference with theory (-21) = 0 CORRECTING DEFECT 70 (vertices=38, convex hull=40, v0=104413) After retessellation of defect 70 (v0=104413), euler #=-20 (130965,392400,261415) : difference with theory (-20) = 0 CORRECTING DEFECT 71 (vertices=17, convex hull=24, v0=106166) After retessellation of defect 71 (v0=106166), euler #=-19 (130967,392412,261426) : difference with theory (-19) = 0 CORRECTING DEFECT 72 (vertices=9, convex hull=21, v0=106952) After retessellation of defect 72 (v0=106952), euler #=-18 (130969,392424,261437) : difference with theory (-18) = 0 CORRECTING DEFECT 73 (vertices=157, convex hull=88, v0=107642) After retessellation of defect 73 (v0=107642), euler #=-17 (131001,392560,261542) : difference with theory (-17) = 0 CORRECTING DEFECT 74 (vertices=13, convex hull=18, v0=108495) After retessellation of defect 74 (v0=108495), euler #=-16 (131003,392572,261553) : difference with theory (-16) = 0 CORRECTING DEFECT 75 (vertices=96, convex hull=49, v0=110348) After retessellation of defect 75 (v0=110348), euler #=-15 (131013,392625,261597) : difference with theory (-15) = 0 CORRECTING DEFECT 76 (vertices=13, convex hull=44, v0=111038) After retessellation of defect 76 (v0=111038), euler #=-14 (131017,392653,261622) : difference with theory (-14) = 0 CORRECTING DEFECT 77 (vertices=162, convex hull=190, v0=111324) After retessellation of defect 77 (v0=111324), euler #=-13 (131070,392899,261816) : difference with theory (-13) = 0 CORRECTING DEFECT 78 (vertices=25, convex hull=28, v0=112487) After retessellation of defect 78 (v0=112487), euler #=-12 (131073,392919,261834) : difference with theory (-12) = 0 CORRECTING DEFECT 79 (vertices=42, convex hull=45, v0=112546) After retessellation of defect 79 (v0=112546), euler #=-11 (131078,392951,261862) : difference with theory (-11) = 0 CORRECTING DEFECT 80 (vertices=84, convex hull=110, v0=112606) After retessellation of defect 80 (v0=112606), euler #=-10 (131099,393064,261955) : difference with theory (-10) = 0 CORRECTING DEFECT 81 (vertices=40, convex hull=38, v0=116823) After retessellation of defect 81 (v0=116823), euler #=-9 (131106,393100,261985) : difference with theory (-9) = 0 CORRECTING DEFECT 82 (vertices=84, convex hull=95, v0=117555) After retessellation of defect 82 (v0=117555), euler #=-8 (131118,393182,262056) : difference with theory (-8) = 0 CORRECTING DEFECT 83 (vertices=37, convex hull=41, v0=118271) After retessellation of defect 83 (v0=118271), euler #=-7 (131121,393210,262082) : difference with theory (-7) = 0 CORRECTING DEFECT 84 (vertices=46, convex hull=25, v0=119738) After retessellation of defect 84 (v0=119738), euler #=-6 (131126,393231,262099) : difference with theory (-6) = 0 CORRECTING DEFECT 85 (vertices=20, convex hull=49, v0=120929) After retessellation of defect 85 (v0=120929), euler #=-5 (131133,393271,262133) : difference with theory (-5) = 0 CORRECTING DEFECT 86 (vertices=19, convex hull=43, v0=120933) After retessellation of defect 86 (v0=120933), euler #=-4 (131137,393297,262156) : difference with theory (-4) = 0 CORRECTING DEFECT 87 (vertices=45, convex hull=61, v0=127860) After retessellation of defect 87 (v0=127860), euler #=-3 (131145,393343,262195) : difference with theory (-3) = 0 CORRECTING DEFECT 88 (vertices=11, convex hull=40, v0=129218) After retessellation of defect 88 (v0=129218), euler #=-2 (131148,393365,262215) : difference with theory (-2) = 0 CORRECTING DEFECT 89 (vertices=15, convex hull=26, v0=129697) After retessellation of defect 89 (v0=129697), euler #=-1 (131149,393380,262230) : difference with theory (-1) = 0 CORRECTING DEFECT 90 (vertices=82, convex hull=77, v0=131808) After retessellation of defect 90 (v0=131808), euler #=0 (131158,393440,262282) : difference with theory (0) = 0 CORRECTING DEFECT 91 (vertices=19, convex hull=44, v0=133683) After retessellation of defect 91 (v0=133683), euler #=1 (131161,393464,262304) : difference with theory (1) = 0 CORRECTING DEFECT 92 (vertices=23, convex hull=44, v0=136687) After retessellation of defect 92 (v0=136687), euler #=2 (131166,393492,262328) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.86 +- 0.23 (0.03-->11.47) (max @ vno 71576 --> 74042) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.86 +- 0.23 (0.03-->11.47) (max @ vno 71576 --> 74042) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 362 mutations (37.6%), 601 crossovers (62.4%), 314 vertices were eliminated building final representation... 6103 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=131166, nf=262328, ne=393492, g=0) writing corrected surface to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 241 intersecting 001: 48 intersecting 002: 9 intersecting 003: 2 intersecting step 1 with no progress (num=2, old_num=2) 004: 2 intersecting step 2 with no progress (num=2, old_num=2) 005: 2 intersecting step 3 with no progress (num=2, old_num=2) 006: 2 intersecting step 4 with no progress (num=2, old_num=2) 007: 2 intersecting step 5 with no progress (num=2, old_num=2) 008: 2 intersecting step 6 with no progress (num=2, old_num=2) 009: 2 intersecting step 7 with no progress (num=2, old_num=2) 010: 2 intersecting step 8 with no progress (num=2, old_num=2) 011: 2 intersecting step 9 with no progress (num=2, old_num=2) 012: 2 intersecting step 10 with no progress (num=2, old_num=2) 013: 2 intersecting step 11 with no progress (num=2, old_num=2) 014: 2 intersecting step 12 with no progress (num=2, old_num=2) 015: 2 intersecting step 13 with no progress (num=2, old_num=2) 016: 2 intersecting step 14 with no progress (num=2, old_num=2) 017: 2 intersecting step 15 with no progress (num=2, old_num=2) 018: 2 intersecting step 16 with no progress (num=2, old_num=2) terminating search with 2 intersecting topology fixing took 5.0 minutes FSRUNTIME@ mris_fix_topology rh 0.0836 hours 1 threads #VMPC# mris_fix_topology VmPeak 1059568 @#@FSTIME 2022:09:05:19:16:43 mris_fix_topology N 14 e 300.92 S 0.65 U 300.22 P 99% M 1014592 F 0 R 297132 W 0 c 1023 w 2 I 0 O 12464 L 1.19 1.23 1.20 @#@FSLOADPOST 2022:09:05:19:21:44 mris_fix_topology N 14 1.18 1.26 1.22 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 136290 - 408864 + 272576 = 2 --> 0 holes F =2V-4: 272576 = 272580-4 (0) 2E=3F: 817728 = 817728 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 131166 - 393492 + 262328 = 2 --> 0 holes F =2V-4: 262328 = 262332-4 (0) 2E=3F: 786984 = 786984 (0) total defect index = 0 Mon Sep 5 19:21:46 UTC 2022 setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts /home/marcantf/software/freesurfer/bin/defect2seg --s P7T_020_001bc freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b defect2seg 7.2.0 Linux mrphys-gpu1 4.15.0-180-generic #189-Ubuntu SMP Wed May 18 14:13:57 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux pid 5403 mri_label2vol --defects /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.orig.nofix /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.defect_labels /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz 1000 0 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/surface.defects.mgz mris_defects_pointset -s /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.orig.nofix -d /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.defect_labels -o /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.defects.pointset Reading in surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.orig.nofix Reading in defect segmentation /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.defect_labels #VMPC# mris_defects_pointset 197344 mris_defects_pointset done mri_label2vol --defects /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.orig.nofix /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.defect_labels /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/surface.defects.mgz 2000 1 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Converting defects to volume: offset=2000, merge=1 MRIcopyHeader(): source has ctab Writing to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/surface.defects.mgz mris_defects_pointset -s /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.orig.nofix -d /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.defect_labels -o /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.defects.pointset Reading in surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.orig.nofix Reading in defect segmentation /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.defect_labels #VMPC# mris_defects_pointset 192708 mris_defects_pointset done Started at Mon Sep 5 19:21:46 UTC 2022 Ended at Mon Sep 5 19:21:55 UTC 2022 Defect2seg-Run-Time-Sec 9 Defect2seg-Run-Time-Min 0.18 Defect2seg-Run-Time-Hours 0.00 tkmeditfv P7T_020_001bc brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2022:09:05:19:21:46 defect2seg N 2 e 9.16 S 0.63 U 8.35 P 98% M 359916 F 24 R 276417 W 0 c 271 w 186 I 5600 O 896 L 1.18 1.26 1.22 @#@FSLOADPOST 2022:09:05:19:21:55 defect2seg N 2 1.23 1.27 1.23 mris_remesh --remesh --iters 3 --input /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.orig.premesh --output /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.688501 remeshing to edge length 0.688501 with 3 iterations avg qual before : 0.931779 after: 0.970339 Removing intersections Remeshed surface quality stats nv0 = 136290 nv = 146407 1.07423 Area 292810 0.28342 0.03194 0.075121 0.4485 Corner 878430 60.00000 8.91750 16.527747 144.9979 Edge 439215 0.81697 0.08093 0.446121 1.2258 Hinge 439215 9.51757 10.95009 0.000004 177.8544 mris_remesh done @#@FSTIME 2022:09:05:19:21:55 mris_remesh N 7 e 35.95 S 0.54 U 35.33 P 99% M 742076 F 0 R 271488 W 0 c 2154 w 1 I 0 O 10296 L 1.23 1.27 1.23 @#@FSLOADPOST 2022:09:05:19:22:31 mris_remesh N 7 1.24 1.27 1.23 mris_remesh --remesh --iters 3 --input /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.orig.premesh --output /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.687442 remeshing to edge length 0.687442 with 3 iterations avg qual before : 0.930918 after: 0.970371 Removing intersections Remeshed surface quality stats nv0 = 131166 nv = 140498 1.07115 Area 280992 0.28261 0.03188 0.066168 0.4854 Corner 842976 60.00000 8.91800 14.813065 148.7770 Edge 421488 0.81579 0.08073 0.434877 1.2518 Hinge 421488 9.65736 11.14631 0.000047 144.6082 mris_remesh done @#@FSTIME 2022:09:05:19:22:31 mris_remesh N 7 e 35.54 S 0.42 U 35.09 P 99% M 714300 F 0 R 253703 W 0 c 615 w 1 I 0 O 9880 L 1.24 1.27 1.23 @#@FSLOADPOST 2022:09:05:19:23:07 mris_remesh N 7 1.13 1.24 1.22 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2022:09:05:19:23:07 mris_remove_intersection N 2 e 3.03 S 0.21 U 2.67 P 95% M 334996 F 16 R 88806 W 0 c 103 w 19 I 3296 O 10304 L 1.13 1.24 1.22 @#@FSLOADPOST 2022:09:05:19:23:10 mris_remove_intersection N 2 1.12 1.24 1.22 rm -f ../surf/lh.inflated /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2022:09:05:19:23:10 mris_remove_intersection N 2 e 2.86 S 0.20 U 2.65 P 99% M 321876 F 0 R 85310 W 0 c 62 w 2 I 0 O 9888 L 1.12 1.24 1.22 @#@FSLOADPOST 2022:09:05:19:23:13 mris_remove_intersection N 2 1.12 1.24 1.22 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Mon Sep 5 19:23:13 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.2.0 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 802519 voxels (2.04%) border gray 838371 voxels (2.13%) 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=76207, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (101.0): 101.1 +- 6.8 [70.0 --> 110.0] CCS GM (80.0) : 78.8 +- 11.2 [30.0 --> 110.0] white_mean = 101.133 +/- 6.81447, gray_mean = 78.7552 +/- 11.2172 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=244 nbins=245 intensity peaks found at WM=110+-2.6, GM=71+-8.7 white_mode = 110, gray_mode = 71 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70.000000) setting MAX_BORDER_WHITE to 116.8 (was 105.000000) setting MIN_BORDER_WHITE to 71.0 (was 85.000000) setting MAX_CSF to 48.6 (was 40.000000) setting MAX_GRAY to 103.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 59.8 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40.000000) When placing the white surface white_border_hi = 116.814; white_border_low = 71; white_outside_low = 59.7828; white_inside_hi = 120; white_outside_hi = 116.814; When placing the pial surface pial_border_hi = 59.7828; pial_border_low = 37.3485; pial_outside_low = 10; pial_inside_hi = 103.186; pial_outside_hi = 54.1742; #VMPC# mris_autodet_gwstats VmPeak 348844 mris_autodet_gwstats done @#@FSTIME 2022:09:05:19:23:13 mris_autodet_gwstats N 8 e 8.70 S 0.20 U 8.27 P 97% M 315720 F 16 R 97255 W 0 c 731 w 18 I 3800 O 8 L 1.12 1.24 1.22 @#@FSLOADPOST 2022:09:05:19:23:22 mris_autodet_gwstats N 8 1.32 1.28 1.23 #-------------------------------------------- #@# AutoDetGWStats rh Mon Sep 5 19:23:22 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.2.0 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 802519 voxels (2.04%) border gray 838371 voxels (2.13%) 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=76207, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (101.0): 101.1 +- 6.8 [70.0 --> 110.0] CCS GM (80.0) : 78.8 +- 11.2 [30.0 --> 110.0] white_mean = 101.133 +/- 6.81447, gray_mean = 78.7552 +/- 11.2172 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=244 nbins=245 intensity peaks found at WM=110+-2.6, GM=69+-11.3 white_mode = 110, gray_mode = 69 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 57.8 (was 70.000000) setting MAX_BORDER_WHITE to 116.8 (was 105.000000) setting MIN_BORDER_WHITE to 69.0 (was 85.000000) setting MAX_CSF to 46.6 (was 40.000000) setting MAX_GRAY to 103.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 57.8 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 35.3 (was 40.000000) When placing the white surface white_border_hi = 116.814; white_border_low = 69; white_outside_low = 57.7828; white_inside_hi = 120; white_outside_hi = 116.814; When placing the pial surface pial_border_hi = 57.7828; pial_border_low = 35.3485; pial_outside_low = 10; pial_inside_hi = 103.186; pial_outside_hi = 52.1742; #VMPC# mris_autodet_gwstats VmPeak 343104 mris_autodet_gwstats done @#@FSTIME 2022:09:05:19:23:22 mris_autodet_gwstats N 8 e 8.42 S 0.21 U 8.18 P 99% M 310216 F 0 R 95113 W 0 c 569 w 1 I 0 O 8 L 1.32 1.28 1.23 @#@FSLOADPOST 2022:09:05:19:23:30 mris_autodet_gwstats N 8 1.27 1.27 1.23 #-------------------------------------------- #@# WhitePreAparc lh Mon Sep 5 19:23:30 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.2.0 7.2.0 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --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 with 5 iterations Area 292810 0.24853 0.06109 0.000752 0.5771 Corner 878430 60.00000 10.12116 5.267589 154.9544 Edge 439215 0.76180 0.11534 0.032860 1.2787 Hinge 439215 6.55675 6.97815 0.000008 155.5383 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=76207, wmmin=5, clip=110 MRIfindBrightNonWM(): 15306 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 MRIcopyHeader(): source has ctab removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6728, nmarked2=87, nripped=6728 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 73204: xyz = (-38.5811,3.15693,40.11) oxyz = (-38.5811,3.15693,40.11) wxzy = (-38.5811,3.15693,40.11) pxyz = (0,0,0) CBVO Creating mask 146407 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=6728 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6728, nmarked2=87, nripped=6728 Ripping WMSA 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 = 116.8144760; border_low = 71.0000000; outside_low = 59.7828250; outside_hi = 116.8144760; sigma = 2; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=2 had to be increased for 469 vertices, nripped=6728 mean border=86.2, 131 (131) missing vertices, mean dist 0.1 [0.6 (%40.4)->0.6 (%59.6))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2187 min Finding expansion regions mean absolute distance = 0.59 +- 0.72 5417 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=mrphy, 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=3330373.5, rms=10.667 001: dt: 0.5000, sse=1654058.1, rms=7.346 (31.135%) 002: dt: 0.5000, sse=1146095.8, rms=5.965 (18.800%) 003: dt: 0.5000, sse=916319.0, rms=5.225 (12.407%) 004: dt: 0.5000, sse=832259.2, rms=4.892 (6.374%) 005: dt: 0.5000, sse=756672.0, rms=4.637 (5.203%) 006: dt: 0.5000, sse=736718.0, rms=4.556 (1.751%) 007: dt: 0.5000, sse=718249.1, rms=4.450 (2.326%) rms = 4.4260/4.4501, sse=709410.7/718249.1, time step reduction 1 of 3 to 0.250 0 0 1 008: dt: 0.5000, sse=709410.8, rms=4.426 (0.541%) 009: dt: 0.2500, sse=399481.8, rms=2.860 (35.386%) 010: dt: 0.2500, sse=331829.2, rms=2.455 (14.170%) 011: dt: 0.2500, sse=322352.8, rms=2.379 (3.097%) 012: dt: 0.2500, sse=309703.4, rms=2.283 (4.000%) rms = 2.2733/2.2834, sse=308822.9/309703.4, time step reduction 2 of 3 to 0.125 0 0 1 013: dt: 0.2500, sse=308822.9, rms=2.273 (0.446%) 014: dt: 0.1250, sse=263807.7, rms=1.868 (17.833%) 015: dt: 0.1250, sse=258011.7, rms=1.798 (3.725%) rms = 1.7783/1.7983, sse=258237.2/258011.7, time step reduction 3 of 3 to 0.062 0 1 1 016: dt: 0.1250, sse=258237.2, rms=1.778 (1.114%) maximum number of reductions reached, breaking from loop positioning took 1.7 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=6728 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 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 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 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6957, nmarked2=93, nripped=6957 Ripping WMSA 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 = 116.8144760; border_low = 71.0000000; outside_low = 59.7828250; outside_hi = 116.8144760; sigma = 1; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=1 had to be increased for 595 vertices, nripped=6957 mean border=90.1, 368 (62) missing vertices, mean dist -0.2 [0.3 (%78.7)->0.3 (%21.3))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1455 min Finding expansion regions mean absolute distance = 0.31 +- 0.43 4845 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=mrphy, 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=994705.0, rms=5.304 017: dt: 0.5000, sse=702249.7, rms=4.180 (21.188%) rms = 4.2787/4.1800, sse=743773.0/702249.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=439085.6, rms=2.873 (31.261%) 019: dt: 0.2500, sse=356101.1, rms=2.234 (22.263%) 020: dt: 0.2500, sse=322105.3, rms=1.953 (12.580%) 021: dt: 0.2500, sse=318735.4, rms=1.885 (3.471%) 022: dt: 0.2500, sse=310729.0, rms=1.814 (3.762%) rms = 1.8222/1.8139, sse=306807.0/310729.0, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step 023: dt: 0.1250, sse=292690.2, rms=1.667 (8.112%) 024: dt: 0.1250, sse=273174.8, rms=1.437 (13.789%) rms = 1.3871/1.4370, sse=268417.0/273174.8, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=268416.9, rms=1.387 (3.469%) maximum number of reductions reached, breaking from loop positioning took 1.1 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=6957 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 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 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 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 #FML# MRISripMidline(): nmarked=7023, nmarked2=93, nripped=7023 Ripping WMSA 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 = 116.8144760; border_low = 71.0000000; outside_low = 59.7828250; outside_hi = 116.8144760; sigma = 0.5; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 745 vertices, nripped=7023 mean border=91.0, 411 (47) missing vertices, mean dist -0.0 [0.2 (%60.5)->0.2 (%39.5))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0759 min Finding expansion regions mean absolute distance = 0.19 +- 0.30 3822 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=mrphy, 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=325708.4, rms=2.009 rms = 2.9891/2.0089, sse=492033.4/325708.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=279423.8, rms=1.513 (24.688%) rms = 1.4417/1.5129, sse=281216.9/279423.8, time step reduction 2 of 3 to 0.125 0 1 0 027: dt: 0.2500, sse=281216.9, rms=1.442 (4.706%) 028: dt: 0.1250, sse=265758.1, rms=1.319 (8.540%) rms = 1.2721/1.3186, sse=262382.0/265758.1, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=262382.0, rms=1.272 (3.528%) 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=7023 removing 2 vertices from ripped group in thread:0 removing 1 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 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 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 #FML# MRISripMidline(): nmarked=7065, nmarked2=94, nripped=7065 Ripping WMSA 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 = 116.8144760; border_low = 71.0000000; outside_low = 59.7828250; outside_hi = 116.8144760; sigma = 0.25; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 668 vertices, nripped=7065 mean border=91.3, 517 (22) missing vertices, mean dist -0.0 [0.2 (%52.9)->0.2 (%47.1))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0477 min Finding expansion regions mean absolute distance = 0.18 +- 0.27 3901 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=mrphy, 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=276224.9, rms=1.452 rms = 2.1148/1.4522, sse=376228.4/276224.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=253750.2, rms=1.098 (24.405%) rms = 1.1066/1.0978, sse=261813.3/253750.2, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 1.0661/1.0978, sse=251207.4/253750.2, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=251207.4, rms=1.066 (2.891%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 4.23 minutes #VMPC# mris_place_surfaces VmPeak 2321144 mris_place_surface done @#@FSTIME 2022:09:05:19:23:30 mris_place_surface N 18 e 267.22 S 1.20 U 265.81 P 99% M 2049348 F 10 R 602746 W 0 c 3029 w 11 I 2120 O 10304 L 1.27 1.27 1.23 @#@FSLOADPOST 2022:09:05:19:27:57 mris_place_surface N 18 1.19 1.28 1.25 #-------------------------------------------- #@# WhitePreAparc rh Mon Sep 5 19:27:57 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.2.0 7.2.0 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --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 with 5 iterations Area 280992 0.24693 0.06126 0.000487 0.5623 Corner 842976 60.00000 10.23414 1.837793 162.5166 Edge 421488 0.75938 0.11615 0.020464 1.3525 Hinge 421488 6.66253 7.09318 0.000023 164.2873 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=76207, wmmin=5, clip=110 MRIfindBrightNonWM(): 15306 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 MRIcopyHeader(): source has ctab 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=7310, nmarked2=56, nripped=7310 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 70249: xyz = (36.6255,0.967741,11.082) oxyz = (36.6255,0.967741,11.082) wxzy = (36.6255,0.967741,11.082) pxyz = (0,0,0) CBVO Creating mask 140498 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=7310 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=7310, nmarked2=56, nripped=7310 Ripping WMSA 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 = 116.8144760; border_low = 69.0000000; outside_low = 57.7828250; outside_hi = 116.8144760; sigma = 2; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=2 had to be increased for 428 vertices, nripped=7310 mean border=85.4, 57 (57) missing vertices, mean dist 0.2 [0.5 (%39.5)->0.6 (%60.5))] %61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2111 min Finding expansion regions mean absolute distance = 0.59 +- 0.69 4561 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=mrphy, 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=3586633.0, rms=11.365 001: dt: 0.5000, sse=1829103.5, rms=7.958 (29.978%) 002: dt: 0.5000, sse=1270590.8, rms=6.495 (18.388%) 003: dt: 0.5000, sse=999547.9, rms=5.638 (13.188%) 004: dt: 0.5000, sse=898819.9, rms=5.277 (6.405%) 005: dt: 0.5000, sse=833516.5, rms=4.974 (5.753%) 006: dt: 0.5000, sse=805994.2, rms=4.913 (1.227%) 007: dt: 0.5000, sse=762902.1, rms=4.750 (3.302%) rms = 4.7505/4.7503, sse=764647.8/762902.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 008: dt: 0.2500, sse=460626.3, rms=3.376 (28.930%) 009: dt: 0.2500, sse=375606.9, rms=2.841 (15.853%) 010: dt: 0.2500, sse=359936.8, rms=2.716 (4.391%) 011: dt: 0.2500, sse=348984.8, rms=2.651 (2.397%) rms = 2.6166/2.6510, sse=343652.1/348984.8, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=343652.1, rms=2.617 (1.298%) 013: dt: 0.1250, sse=278071.2, rms=2.067 (21.006%) 014: dt: 0.1250, sse=265040.5, rms=1.959 (5.209%) rms = 1.9318/1.9593, sse=262835.1/265040.5, time step reduction 3 of 3 to 0.062 0 0 1 015: dt: 0.1250, sse=262835.1, rms=1.932 (1.404%) maximum number of reductions reached, breaking from loop positioning took 1.7 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=7310 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 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 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=7592, nmarked2=60, nripped=7592 Ripping WMSA 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 = 116.8144760; border_low = 69.0000000; outside_low = 57.7828250; outside_hi = 116.8144760; sigma = 1; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=1 had to be increased for 503 vertices, nripped=7592 mean border=89.2, 258 (4) missing vertices, mean dist -0.2 [0.3 (%78.6)->0.3 (%21.4))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1385 min Finding expansion regions mean absolute distance = 0.30 +- 0.43 4496 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=mrphy, 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=954660.4, rms=5.312 016: dt: 0.5000, sse=751127.3, rms=4.489 (15.499%) rms = 4.5183/4.4891, sse=760101.6/751127.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=458563.5, rms=3.065 (31.730%) 018: dt: 0.2500, sse=368973.4, rms=2.437 (20.470%) 019: dt: 0.2500, sse=333747.3, rms=2.163 (11.253%) rms = 2.1260/2.1631, sse=330316.1/333747.3, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=330316.1, rms=2.126 (1.712%) 021: dt: 0.1250, sse=274834.5, rms=1.616 (23.981%) 022: dt: 0.1250, sse=266366.0, rms=1.508 (6.682%) rms = 1.4907/1.5082, sse=266579.3/266366.0, time step reduction 3 of 3 to 0.062 0 1 1 023: dt: 0.1250, sse=266579.3, rms=1.491 (1.164%) maximum number of reductions reached, breaking from loop positioning took 0.9 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=7592 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 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 3 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7680, nmarked2=59, nripped=7680 Ripping WMSA 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 = 116.8144760; border_low = 69.0000000; outside_low = 57.7828250; outside_hi = 116.8144760; sigma = 0.5; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 602 vertices, nripped=7680 mean border=90.2, 319 (0) missing vertices, mean dist -0.0 [0.2 (%61.0)->0.2 (%39.0))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0731 min Finding expansion regions mean absolute distance = 0.19 +- 0.30 3849 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=mrphy, 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=325945.4, rms=2.121 rms = 3.2663/2.1211, sse=505643.2/325945.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=276214.0, rms=1.603 (24.424%) rms = 1.5399/1.6030, sse=279173.7/276214.0, time step reduction 2 of 3 to 0.125 0 1 0 025: dt: 0.2500, sse=279173.7, rms=1.540 (3.938%) 026: dt: 0.1250, sse=271387.6, rms=1.417 (7.950%) rms = 1.3785/1.4175, sse=260837.1/271387.6, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=260837.1, rms=1.379 (2.750%) 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=7680 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 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7700, nmarked2=59, nripped=7700 Ripping WMSA 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 = 116.8144760; border_low = 69.0000000; outside_low = 57.7828250; outside_hi = 116.8144760; sigma = 0.25; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 540 vertices, nripped=7700 mean border=90.5, 431 (0) missing vertices, mean dist -0.0 [0.2 (%52.9)->0.2 (%47.1))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0456 min Finding expansion regions mean absolute distance = 0.18 +- 0.27 3964 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=mrphy, 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=274223.8, rms=1.547 rms = 2.2692/1.5469, sse=376233.5/274223.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=249754.7, rms=1.179 (23.812%) rms = 1.1417/1.1786, sse=252087.3/249754.7, time step reduction 2 of 3 to 0.125 0 1 1 029: dt: 0.2500, sse=252087.3, rms=1.142 (3.133%) 030: dt: 0.1250, sse=239151.6, rms=1.072 (6.140%) rms = 1.0332/1.0716, sse=236979.9/239151.6, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=236979.9, rms=1.033 (3.579%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 3.98 minutes #VMPC# mris_place_surfaces VmPeak 2253600 mris_place_surface done @#@FSTIME 2022:09:05:19:27:57 mris_place_surface N 18 e 250.98 S 1.12 U 249.82 P 99% M 1982008 F 0 R 584874 W 0 c 374 w 1 I 0 O 9888 L 1.19 1.28 1.25 @#@FSLOADPOST 2022:09:05:19:32:08 mris_place_surface N 18 1.34 1.28 1.26 #-------------------------------------------- #@# CortexLabel lh Mon Sep 5 19:32:08 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 MRIcopyHeader(): source has ctab 16 non-cortical segments detected only using segment with 8107 vertices erasing segment 0 (vno[0] = 22775) erasing segment 2 (vno[0] = 49261) erasing segment 3 (vno[0] = 71590) erasing segment 4 (vno[0] = 74435) erasing segment 5 (vno[0] = 76148) erasing segment 6 (vno[0] = 79286) erasing segment 7 (vno[0] = 85519) erasing segment 8 (vno[0] = 89363) erasing segment 9 (vno[0] = 92955) erasing segment 10 (vno[0] = 94528) erasing segment 11 (vno[0] = 96264) erasing segment 12 (vno[0] = 98312) erasing segment 13 (vno[0] = 102508) erasing segment 14 (vno[0] = 125976) erasing segment 15 (vno[0] = 138304) @#@FSTIME 2022:09:05:19:32:08 mri_label2label N 5 e 17.88 S 0.46 U 17.30 P 99% M 567032 F 6 R 158600 W 0 c 1261 w 8 I 1392 O 12040 L 1.34 1.28 1.26 @#@FSLOADPOST 2022:09:05:19:32:26 mri_label2label N 5 1.46 1.31 1.27 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Mon Sep 5 19:32:26 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 MRIcopyHeader(): source has ctab 19 non-cortical segments detected only using segment with 6700 vertices erasing segment 0 (vno[0] = 22775) erasing segment 2 (vno[0] = 49261) erasing segment 3 (vno[0] = 53521) erasing segment 4 (vno[0] = 57087) erasing segment 5 (vno[0] = 63247) erasing segment 6 (vno[0] = 71590) erasing segment 7 (vno[0] = 74435) erasing segment 8 (vno[0] = 76148) erasing segment 9 (vno[0] = 79286) erasing segment 10 (vno[0] = 85519) erasing segment 11 (vno[0] = 89363) erasing segment 12 (vno[0] = 92955) erasing segment 13 (vno[0] = 94528) erasing segment 14 (vno[0] = 96264) erasing segment 15 (vno[0] = 98312) erasing segment 16 (vno[0] = 102508) erasing segment 17 (vno[0] = 125976) erasing segment 18 (vno[0] = 137691) @#@FSTIME 2022:09:05:19:32:26 mri_label2label N 5 e 17.32 S 0.41 U 16.86 P 99% M 582516 F 0 R 162480 W 0 c 850 w 1 I 0 O 12168 L 1.46 1.31 1.27 @#@FSLOADPOST 2022:09:05:19:32:44 mri_label2label N 5 1.43 1.31 1.27 #-------------------------------------------- #@# CortexLabel rh Mon Sep 5 19:32:44 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 MRIcopyHeader(): source has ctab 17 non-cortical segments detected only using segment with 8367 vertices erasing segment 0 (vno[0] = 13462) erasing segment 1 (vno[0] = 33437) erasing segment 2 (vno[0] = 35912) erasing segment 4 (vno[0] = 64627) erasing segment 5 (vno[0] = 69108) erasing segment 6 (vno[0] = 77543) erasing segment 7 (vno[0] = 79035) erasing segment 8 (vno[0] = 79983) erasing segment 9 (vno[0] = 83304) erasing segment 10 (vno[0] = 84001) erasing segment 11 (vno[0] = 84603) erasing segment 12 (vno[0] = 87079) erasing segment 13 (vno[0] = 91508) erasing segment 14 (vno[0] = 96719) erasing segment 15 (vno[0] = 99372) erasing segment 16 (vno[0] = 134286) @#@FSTIME 2022:09:05:19:32:44 mri_label2label N 5 e 17.39 S 0.30 U 17.06 P 99% M 561788 F 0 R 156587 W 0 c 773 w 1 I 0 O 11200 L 1.43 1.31 1.27 @#@FSLOADPOST 2022:09:05:19:33:01 mri_label2label N 5 1.38 1.31 1.27 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Mon Sep 5 19:33:01 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 MRIcopyHeader(): source has ctab 18 non-cortical segments detected only using segment with 6917 vertices erasing segment 0 (vno[0] = 13462) erasing segment 1 (vno[0] = 33437) erasing segment 2 (vno[0] = 35912) erasing segment 4 (vno[0] = 52579) erasing segment 5 (vno[0] = 58586) erasing segment 6 (vno[0] = 64627) erasing segment 7 (vno[0] = 69108) erasing segment 8 (vno[0] = 77543) erasing segment 9 (vno[0] = 79035) erasing segment 10 (vno[0] = 79983) erasing segment 11 (vno[0] = 84001) erasing segment 12 (vno[0] = 84137) erasing segment 13 (vno[0] = 87079) erasing segment 14 (vno[0] = 91508) erasing segment 15 (vno[0] = 96719) erasing segment 16 (vno[0] = 99372) erasing segment 17 (vno[0] = 134286) @#@FSTIME 2022:09:05:19:33:01 mri_label2label N 5 e 17.19 S 0.36 U 16.79 P 99% M 566856 F 0 R 157843 W 0 c 842 w 1 I 0 O 11320 L 1.38 1.31 1.27 @#@FSLOADPOST 2022:09:05:19:33:19 mri_label2label N 5 1.37 1.31 1.27 #-------------------------------------------- #@# Smooth2 lh Mon Sep 5 19:33:19 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts 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... @#@FSTIME 2022:09:05:19:33:19 mris_smooth N 7 e 3.55 S 0.12 U 3.42 P 99% M 224764 F 0 R 67845 W 0 c 172 w 1 I 0 O 10304 L 1.37 1.31 1.27 @#@FSLOADPOST 2022:09:05:19:33:22 mris_smooth N 7 1.34 1.30 1.27 #-------------------------------------------- #@# Smooth2 rh Mon Sep 5 19:33:22 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts 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... @#@FSTIME 2022:09:05:19:33:22 mris_smooth N 7 e 3.58 S 0.13 U 3.44 P 99% M 215896 F 0 R 65129 W 0 c 64 w 1 I 0 O 9888 L 1.34 1.30 1.27 @#@FSLOADPOST 2022:09:05:19:33:26 mris_smooth N 7 1.31 1.30 1.27 #-------------------------------------------- #@# Inflation2 lh Mon Sep 5 19:33:26 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_inflate -n 100 ../surf/lh.smoothwm ../surf/lh.inflated niterations = 100 Reading ../surf/lh.smoothwm avg radius = 46.7 mm, total surface area = 82221 mm^2 resetting # of iterations to 167 for highres volume step 000: RMS=0.175 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) step 065: RMS=0.020 (target=0.015) step 070: RMS=0.019 (target=0.015) step 075: RMS=0.018 (target=0.015) step 080: RMS=0.018 (target=0.015) step 085: RMS=0.017 (target=0.015) step 090: RMS=0.017 (target=0.015) step 095: RMS=0.017 (target=0.015) step 100: RMS=0.017 (target=0.015) step 105: RMS=0.016 (target=0.015) step 110: RMS=0.016 (target=0.015) step 115: RMS=0.016 (target=0.015) step 120: RMS=0.016 (target=0.015) step 125: RMS=0.016 (target=0.015) step 130: RMS=0.016 (target=0.015) step 135: RMS=0.015 (target=0.015) step 140: RMS=0.015 (target=0.015) step 145: RMS=0.015 (target=0.015) step 150: RMS=0.015 (target=0.015) step 155: RMS=0.015 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 1.3 minutes mris_inflate utimesec 73.030637 mris_inflate stimesec 2.899495 mris_inflate ru_maxrss 225164 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 1446565 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11448 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 1090 @#@FSTIME 2022:09:05:19:33:26 mris_inflate N 4 e 76.00 S 2.90 U 73.03 P 99% M 225164 F 0 R 1446568 W 0 c 1092 w 1 I 0 O 11448 L 1.31 1.30 1.27 @#@FSLOADPOST 2022:09:05:19:34:42 mris_inflate N 4 1.26 1.28 1.26 #-------------------------------------------- #@# Inflation2 rh Mon Sep 5 19:34:42 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_inflate -n 100 ../surf/rh.smoothwm ../surf/rh.inflated niterations = 100 Reading ../surf/rh.smoothwm avg radius = 45.8 mm, total surface area = 79671 mm^2 resetting # of iterations to 167 for highres volume step 000: RMS=0.179 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.021 (target=0.015) step 065: RMS=0.020 (target=0.015) step 070: RMS=0.019 (target=0.015) step 075: RMS=0.019 (target=0.015) step 080: RMS=0.018 (target=0.015) step 085: RMS=0.017 (target=0.015) step 090: RMS=0.017 (target=0.015) step 095: RMS=0.017 (target=0.015) step 100: RMS=0.017 (target=0.015) step 105: RMS=0.016 (target=0.015) step 110: RMS=0.016 (target=0.015) step 115: RMS=0.016 (target=0.015) step 120: RMS=0.016 (target=0.015) step 125: RMS=0.016 (target=0.015) step 130: RMS=0.016 (target=0.015) step 135: RMS=0.016 (target=0.015) step 140: RMS=0.016 (target=0.015) step 145: RMS=0.016 (target=0.015) step 150: RMS=0.015 (target=0.015) step 155: RMS=0.015 (target=0.015) step 160: RMS=0.015 (target=0.015) step 165: RMS=0.015 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 1.3 minutes mris_inflate utimesec 80.117679 mris_inflate stimesec 0.163989 mris_inflate ru_maxrss 217248 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 58167 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10992 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 2264 @#@FSTIME 2022:09:05:19:34:42 mris_inflate N 4 e 80.42 S 0.17 U 80.12 P 99% M 217456 F 0 R 58169 W 0 c 2266 w 1 I 0 O 10992 L 1.26 1.28 1.26 @#@FSLOADPOST 2022:09:05:19:36:03 mris_inflate N 4 1.12 1.23 1.25 #-------------------------------------------- #@# Curv .H and .K lh Mon Sep 5 19:36:03 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 2.891*4pi (36.324) --> -2 handles ICI = 176.5, FI = 1878.5, variation=29571.638 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. @#@FSTIME 2022:09:05:19:36:03 mris_curvature N 4 e 2.09 S 0.11 U 1.91 P 96% M 167136 F 3 R 45813 W 0 c 28 w 4 I 616 O 2288 L 1.12 1.23 1.25 @#@FSLOADPOST 2022:09:05:19:36:05 mris_curvature N 4 1.11 1.23 1.25 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 223 vertices thresholded to be in k1 ~ [-0.15 0.09], k2 ~ [-0.09 0.07] total integrated curvature = 0.837*4pi (10.514) --> 0 handles ICI = 1.1, FI = 3.6, variation=70.384 145 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 170 vertices thresholded to be in [-0.10 0.04] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.013 done. @#@FSTIME 2022:09:05:19:36:05 mris_curvature N 12 e 52.34 S 0.24 U 52.02 P 99% M 396376 F 0 R 103151 W 0 c 2598 w 1 I 0 O 2288 L 1.11 1.23 1.25 @#@FSLOADPOST 2022:09:05:19:36:57 mris_curvature N 12 1.26 1.24 1.25 #-------------------------------------------- #@# Curv .H and .K rh Mon Sep 5 19:36:57 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 28.235*4pi (354.807) --> -27 handles ICI = 190.1, FI = 1896.0, variation=29794.766 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. @#@FSTIME 2022:09:05:19:36:57 mris_curvature N 4 e 2.16 S 0.17 U 1.97 P 99% M 160640 F 0 R 43988 W 0 c 269 w 1 I 0 O 2208 L 1.26 1.24 1.25 @#@FSLOADPOST 2022:09:05:19:36:59 mris_curvature N 4 1.32 1.26 1.26 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 190 vertices thresholded to be in k1 ~ [-0.82 0.22], k2 ~ [-0.19 0.22] total integrated curvature = 0.739*4pi (9.282) --> 0 handles ICI = 1.0, FI = 3.4, variation=65.617 186 vertices thresholded to be in [-0.07 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 142 vertices thresholded to be in [-0.34 0.03] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.016 done. @#@FSTIME 2022:09:05:19:36:59 mris_curvature N 12 e 50.12 S 0.31 U 49.78 P 99% M 380676 F 0 R 99025 W 0 c 728 w 1 I 0 O 2208 L 1.32 1.26 1.26 @#@FSLOADPOST 2022:09:05:19:37:50 mris_curvature N 12 1.35 1.28 1.26 #-------------------------------------------- #@# Sphere lh Mon Sep 5 19:37:50 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.2.0 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.285... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=mrphy, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %38.37 pass 1: epoch 2 of 3 starting distance error %20.88 unfolding complete - removing small folds... starting distance error %20.70 removing remaining folds... final distance error %20.74 MRISunfold() return, current seed 1234 -01: dt=0.0000, 56 negative triangles VmPeak 580940 128: dt=0.9900, 56 negative triangles 129: dt=0.9900, 19 negative triangles 130: dt=0.9900, 15 negative triangles 131: dt=0.9900, 13 negative triangles 132: dt=0.9900, 12 negative triangles 133: dt=0.9900, 10 negative triangles 134: dt=0.9900, 7 negative triangles 135: dt=0.9900, 7 negative triangles 136: dt=0.9900, 4 negative triangles 137: dt=0.9900, 5 negative triangles 138: dt=0.9900, 6 negative triangles 139: dt=0.9900, 3 negative triangles 140: dt=0.9900, 5 negative triangles 141: dt=0.9900, 5 negative triangles 142: dt=0.9900, 4 negative triangles 143: dt=0.9900, 2 negative triangles 144: dt=0.9900, 5 negative triangles 145: dt=0.9900, 1 negative triangles 146: dt=0.9900, 2 negative triangles 147: dt=0.9900, 4 negative triangles 148: dt=0.9900, 1 negative triangles 149: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1427 hours FSRUNTIME@ mris_sphere 0.1427 hours 1 threads #VMPC# mris_sphere VmPeak 580940 mris_sphere done @#@FSTIME 2022:09:05:19:37:50 mris_sphere N 4 e 513.68 S 20.39 U 492.82 P 99% M 301192 F 0 R 10795724 W 0 c 11365 w 1 I 0 O 10304 L 1.35 1.28 1.26 @#@FSLOADPOST 2022:09:05:19:46:23 mris_sphere N 4 1.12 1.15 1.20 #-------------------------------------------- #@# Sphere rh Mon Sep 5 19:46:23 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.2.0 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.293... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=mrphy, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %36.97 pass 1: epoch 2 of 3 starting distance error %21.14 unfolding complete - removing small folds... starting distance error %21.00 removing remaining folds... final distance error %21.04 MRISunfold() return, current seed 1234 -01: dt=0.0000, 34 negative triangles VmPeak 569136 122: dt=0.9900, 34 negative triangles 123: dt=0.9900, 23 negative triangles 124: dt=0.9900, 14 negative triangles 125: dt=0.9900, 12 negative triangles 126: dt=0.9900, 10 negative triangles 127: dt=0.9900, 8 negative triangles 128: dt=0.9900, 8 negative triangles 129: dt=0.9900, 9 negative triangles 130: dt=0.9900, 9 negative triangles 131: dt=0.9900, 4 negative triangles 132: dt=0.9900, 7 negative triangles 133: dt=0.9900, 7 negative triangles 134: dt=0.9900, 7 negative triangles 135: dt=0.9900, 5 negative triangles 136: dt=0.9900, 6 negative triangles 137: dt=0.9900, 4 negative triangles 138: dt=0.9900, 4 negative triangles 139: dt=0.9900, 4 negative triangles 140: dt=0.9900, 5 negative triangles 141: dt=0.9405, 4 negative triangles 142: dt=0.9405, 4 negative triangles 143: dt=0.9405, 3 negative triangles 144: dt=0.9405, 3 negative triangles 145: dt=0.9405, 4 negative triangles 146: dt=0.9405, 2 negative triangles 147: dt=0.9405, 1 negative triangles 148: dt=0.9405, 3 negative triangles 149: dt=0.9405, 3 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1354 hours FSRUNTIME@ mris_sphere 0.1354 hours 1 threads #VMPC# mris_sphere VmPeak 569136 mris_sphere done @#@FSTIME 2022:09:05:19:46:23 mris_sphere N 4 e 487.38 S 19.76 U 467.34 P 99% M 289184 F 0 R 9892237 W 0 c 6053 w 1 I 0 O 9888 L 1.12 1.15 1.20 @#@FSLOADPOST 2022:09:05:19:54:31 mris_sphere N 4 1.25 1.13 1.16 #-------------------------------------------- #@# Surf Reg lh Mon Sep 5 19:54:31 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_register -curv ../surf/lh.sphere /home/marcantf/software/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts cmdline mris_register -curv ../surf/lh.sphere /home/marcantf/software/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.2.0 7.2.0 reading surface from ../surf/lh.sphere... reading template parameterization from /home/marcantf/software/freesurfer/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=mrphy, 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=mrphy, 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=mrphy, 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 = 6.801 curvature mean = 0.025, std = 0.809 curvature mean = 0.011, std = 0.901 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (3.00, -10.50, 8.00) sse = 274772.6, elapsed since starting=0.4427 min MRISrigidBodyAlignGlobal() done 0.44 min curvature mean = -0.006, std = 0.852 curvature mean = 0.005, std = 0.960 curvature mean = -0.010, std = 0.863 curvature mean = 0.002, std = 0.984 curvature mean = -0.011, std = 0.866 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.024, std = 0.309 curvature mean = 0.041, std = 0.245 curvature mean = 0.061, std = 0.326 curvature mean = 0.033, std = 0.302 curvature mean = 0.036, std = 0.505 curvature mean = 0.032, std = 0.328 curvature mean = 0.020, std = 0.649 curvature mean = 0.032, std = 0.340 curvature mean = 0.006, std = 0.766 MRISregister() return, current seed 0 -01: dt=0.0000, 84 negative triangles VmPeak 559252 116: dt=0.9900, 84 negative triangles expanding nbhd size to 1 117: dt=0.9900, 84 negative triangles 118: dt=0.9900, 75 negative triangles 119: dt=0.9900, 69 negative triangles 120: dt=0.9900, 67 negative triangles 121: dt=0.9900, 64 negative triangles 122: dt=0.9900, 60 negative triangles 123: dt=0.9900, 64 negative triangles 124: dt=0.9900, 60 negative triangles 125: dt=0.9900, 59 negative triangles 126: dt=0.9900, 53 negative triangles 127: dt=0.9900, 54 negative triangles 128: dt=0.9900, 47 negative triangles 129: dt=0.9900, 48 negative triangles 130: dt=0.9900, 47 negative triangles 131: dt=0.9900, 45 negative triangles 132: dt=0.9900, 45 negative triangles 133: dt=0.9900, 43 negative triangles 134: dt=0.9900, 43 negative triangles 135: dt=0.9900, 44 negative triangles 136: dt=0.9900, 42 negative triangles 137: dt=0.9900, 40 negative triangles 138: dt=0.9900, 43 negative triangles 139: dt=0.9900, 43 negative triangles 140: dt=0.9900, 36 negative triangles 141: dt=0.9900, 35 negative triangles 142: dt=0.9900, 34 negative triangles 143: dt=0.9900, 34 negative triangles 144: dt=0.9900, 29 negative triangles 145: dt=0.9900, 26 negative triangles 146: dt=0.9900, 29 negative triangles 147: dt=0.9900, 25 negative triangles 148: dt=0.9900, 30 negative triangles 149: dt=0.9900, 28 negative triangles 150: dt=0.9900, 25 negative triangles 151: dt=0.9900, 22 negative triangles 152: dt=0.9900, 25 negative triangles 153: dt=0.9900, 24 negative triangles 154: dt=0.9900, 22 negative triangles 155: dt=0.9900, 19 negative triangles 156: dt=0.9900, 17 negative triangles 157: dt=0.9900, 16 negative triangles 158: dt=0.9900, 18 negative triangles 159: dt=0.9900, 15 negative triangles 160: dt=0.9900, 11 negative triangles 161: dt=0.9900, 9 negative triangles 162: dt=0.9900, 8 negative triangles 163: dt=0.9900, 10 negative triangles 164: dt=0.9900, 10 negative triangles 165: dt=0.9900, 7 negative triangles 166: dt=0.9900, 9 negative triangles 167: dt=0.9900, 5 negative triangles 168: dt=0.9900, 4 negative triangles 169: dt=0.9900, 4 negative triangles 170: dt=0.9900, 4 negative triangles 171: dt=0.9900, 3 negative triangles 172: dt=0.9900, 3 negative triangles 173: dt=0.9900, 2 negative triangles 174: dt=0.9900, 2 negative triangles 175: dt=0.9900, 1 negative triangles 176: dt=0.9900, 1 negative triangles 177: dt=0.9900, 4 negative triangles 178: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.16 hours #VMPC# mris_register VmPeak 559252 FSRUNTIME@ mris_register 0.1626 hours 1 threads @#@FSTIME 2022:09:05:19:54:31 mris_register N 4 e 585.52 S 18.83 U 565.37 P 99% M 279992 F 9 R 9540168 W 0 c 9018 w 22 I 7656 O 10304 L 1.25 1.13 1.16 @#@FSLOADPOST 2022:09:05:20:04:16 mris_register N 4 1.22 1.17 1.15 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Mon Sep 5 20:04:16 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_register -curv ../surf/rh.sphere /home/marcantf/software/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts cmdline mris_register -curv ../surf/rh.sphere /home/marcantf/software/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.2.0 7.2.0 reading surface from ../surf/rh.sphere... reading template parameterization from /home/marcantf/software/freesurfer/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=mrphy, 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=mrphy, 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=mrphy, 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 = 6.924 curvature mean = 0.047, std = 0.814 curvature mean = 0.008, std = 0.907 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (1.50, -8.00, 13.00) sse = 303637.3, elapsed since starting=0.4338 min MRISrigidBodyAlignGlobal() done 0.43 min curvature mean = 0.026, std = 0.844 curvature mean = 0.004, std = 0.963 curvature mean = 0.023, std = 0.854 curvature mean = 0.002, std = 0.985 curvature mean = 0.022, std = 0.857 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.023, std = 0.317 curvature mean = 0.043, std = 0.236 curvature mean = 0.056, std = 0.324 curvature mean = 0.034, std = 0.293 curvature mean = 0.033, std = 0.504 curvature mean = 0.034, std = 0.319 curvature mean = 0.018, std = 0.647 curvature mean = 0.034, std = 0.331 curvature mean = 0.005, std = 0.762 MRISregister() return, current seed 0 -01: dt=0.0000, 24 negative triangles VmPeak 549076 116: dt=0.9900, 24 negative triangles 117: dt=0.9900, 23 negative triangles 118: dt=0.9900, 21 negative triangles 119: dt=0.9900, 21 negative triangles 120: dt=0.9900, 28 negative triangles 121: dt=0.9900, 21 negative triangles 122: dt=0.9900, 19 negative triangles 123: dt=0.9900, 22 negative triangles 124: dt=0.9900, 21 negative triangles 125: dt=0.9900, 19 negative triangles 126: dt=0.9900, 13 negative triangles 127: dt=0.9900, 13 negative triangles 128: dt=0.9900, 8 negative triangles 129: dt=0.9900, 6 negative triangles 130: dt=0.9900, 5 negative triangles 131: dt=0.9900, 2 negative triangles 132: dt=0.9900, 2 negative triangles 133: dt=0.9900, 3 negative triangles 134: dt=0.9900, 3 negative triangles 135: dt=0.9900, 3 negative triangles 136: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.16 hours #VMPC# mris_register VmPeak 549076 FSRUNTIME@ mris_register 0.1563 hours 1 threads @#@FSTIME 2022:09:05:20:04:17 mris_register N 4 e 562.66 S 16.60 U 545.80 P 99% M 269868 F 0 R 8772834 W 0 c 3692 w 14 I 5584 O 9888 L 1.22 1.17 1.15 @#@FSLOADPOST 2022:09:05:20:13:39 mris_register N 4 1.17 1.16 1.16 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Mon Sep 5 20:13:39 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts 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 @#@FSTIME 2022:09:05:20:13:39 mris_jacobian N 3 e 1.39 S 0.19 U 1.16 P 97% M 224240 F 3 R 67774 W 0 c 72 w 4 I 640 O 1144 L 1.17 1.16 1.16 @#@FSLOADPOST 2022:09:05:20:13:41 mris_jacobian N 3 1.17 1.16 1.16 #-------------------------------------------- #@# Jacobian white rh Mon Sep 5 20:13:41 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts 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 @#@FSTIME 2022:09:05:20:13:41 mris_jacobian N 3 e 1.27 S 0.12 U 1.15 P 99% M 215700 F 0 R 65073 W 0 c 3 w 1 I 0 O 1104 L 1.17 1.16 1.16 @#@FSLOADPOST 2022:09:05:20:13:42 mris_jacobian N 3 1.15 1.16 1.16 #-------------------------------------------- #@# AvgCurv lh Mon Sep 5 20:13:42 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mrisp_paint -a 5 /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2022:09:05:20:13:42 mrisp_paint N 5 e 1.08 S 0.09 U 0.96 P 96% M 172076 F 5 R 47062 W 0 c 17 w 6 I 1096 O 1144 L 1.15 1.16 1.16 @#@FSLOADPOST 2022:09:05:20:13:43 mrisp_paint N 5 1.15 1.16 1.16 #-------------------------------------------- #@# AvgCurv rh Mon Sep 5 20:13:43 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mrisp_paint -a 5 /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2022:09:05:20:13:43 mrisp_paint N 5 e 1.03 S 0.12 U 0.89 P 98% M 165576 F 0 R 45242 W 0 c 80 w 1 I 0 O 1104 L 1.15 1.16 1.16 @#@FSLOADPOST 2022:09:05:20:13:44 mrisp_paint N 5 1.15 1.16 1.16 #----------------------------------------- #@# Cortical Parc lh Mon Sep 5 20:13:44 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 P7T_020_001bc lh ../surf/lh.sphere.reg /home/marcantf/software/freesurfer/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 7.2.0 7.2.0 reading atlas from /home/marcantf/software/freesurfer/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... MRIcopyHeader(): source has ctab 1736 labels changed using aseg relabeling using gibbs priors... 000: 3200 changed, 146407 examined... 001: 764 changed, 13628 examined... 002: 198 changed, 4305 examined... 003: 62 changed, 1216 examined... 004: 25 changed, 385 examined... 005: 12 changed, 128 examined... 006: 8 changed, 73 examined... 007: 6 changed, 41 examined... 008: 0 changed, 30 examined... 292 labels changed using aseg 000: 111 total segments, 69 labels (293 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, 7 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/lh.aparc.annot... classification took 0 minutes and 14 seconds. @#@FSTIME 2022:09:05:20:13:44 mris_ca_label N 11 e 14.30 S 0.83 U 12.97 P 96% M 1340480 F 6 R 473854 W 0 c 379 w 168 I 64168 O 2296 L 1.15 1.16 1.16 @#@FSLOADPOST 2022:09:05:20:13:59 mris_ca_label N 11 1.12 1.15 1.16 #----------------------------------------- #@# Cortical Parc rh Mon Sep 5 20:13:59 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 P7T_020_001bc rh ../surf/rh.sphere.reg /home/marcantf/software/freesurfer/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 7.2.0 7.2.0 reading atlas from /home/marcantf/software/freesurfer/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... MRIcopyHeader(): source has ctab 1559 labels changed using aseg relabeling using gibbs priors... 000: 2913 changed, 140498 examined... 001: 696 changed, 12669 examined... 002: 164 changed, 3937 examined... 003: 53 changed, 1004 examined... 004: 18 changed, 324 examined... 005: 8 changed, 120 examined... 006: 3 changed, 52 examined... 007: 1 changed, 19 examined... 008: 0 changed, 7 examined... 258 labels changed using aseg 000: 107 total segments, 70 labels (300 vertices) changed 001: 39 total segments, 2 labels (5 vertices) changed 002: 37 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... 921 vertices marked for relabeling... 921 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 12 seconds. @#@FSTIME 2022:09:05:20:13:59 mris_ca_label N 11 e 12.33 S 0.82 U 11.11 P 96% M 1289004 F 0 R 446433 W 0 c 71 w 117 I 36352 O 2200 L 1.12 1.15 1.16 @#@FSLOADPOST 2022:09:05:20:14:11 mris_ca_label N 11 1.09 1.14 1.16 #-------------------------------------------- #@# WhiteSurfs lh Mon Sep 5 20:14:11 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --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 7.2.0 7.2.0 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --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 292810 0.31244 0.12143 0.000469 1.4634 Corner 878430 60.00000 16.50845 0.125624 179.5754 Edge 439215 0.86425 0.21219 0.018844 3.2355 Hinge 439215 12.49389 14.56789 0.000012 179.9971 Reading in aparc ../label/lh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=76207, wmmin=5, clip=110 MRIfindBrightNonWM(): 15306 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 Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf Ripping BG MRIcopyHeader(): source has ctab MRISripBasalGanglia(): -2 2 0.5 ripped 476 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 73204: xyz = (-38.594,3.16217,40.1428) oxyz = (-38.594,3.16217,40.1428) wxzy = (-38.594,3.16217,40.1428) pxyz = (0,0,0) CBVO Creating mask 146407 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 116.8144760; border_low = 71.0000000; outside_low = 59.7828250; outside_hi = 116.8144760; sigma = 2; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=2 had to be increased for 438 vertices, nripped=8804 mean border=85.6, 227 (227) missing vertices, mean dist 0.2 [0.9 (%15.7)->0.4 (%84.3))] %54 local maxima, %40 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1994 min Finding expansion regions mean absolute distance = 0.49 +- 0.67 4148 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=mrphy, 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=1549336.0, rms=6.967 001: dt: 0.5000, sse=703364.6, rms=4.252 (38.963%) 002: dt: 0.5000, sse=627165.9, rms=3.914 (7.949%) rms = 4.1306/3.9145, sse=668014.9/627165.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 003: dt: 0.2500, sse=390897.2, rms=2.621 (33.045%) 004: dt: 0.2500, sse=328322.8, rms=2.154 (17.831%) 005: dt: 0.2500, sse=303218.2, rms=1.920 (10.863%) 006: dt: 0.2500, sse=298317.0, rms=1.867 (2.739%) rms = 1.8227/1.8671, sse=295198.2/298317.0, time step reduction 2 of 3 to 0.125 0 0 1 007: dt: 0.2500, sse=295198.2, rms=1.823 (2.374%) 008: dt: 0.1250, sse=274564.9, rms=1.608 (11.770%) rms = 1.5658/1.6082, sse=272450.4/274564.9, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=272450.4, rms=1.566 (2.636%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 116.8144760; border_low = 71.0000000; outside_low = 59.7828250; outside_hi = 116.8144760; sigma = 1; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=1 had to be increased for 460 vertices, nripped=8804 mean border=90.0, 254 (115) missing vertices, mean dist -0.2 [0.3 (%81.4)->0.2 (%18.6))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1416 min Finding expansion regions mean absolute distance = 0.32 +- 0.42 3924 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=mrphy, 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=1037882.4, rms=5.485 010: dt: 0.5000, sse=664167.0, rms=4.029 (26.548%) rms = 4.1642/4.0286, sse=691075.8/664167.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 011: dt: 0.2500, sse=417324.0, rms=2.715 (32.606%) 012: dt: 0.2500, sse=328705.5, rms=2.041 (24.826%) 013: dt: 0.2500, sse=304572.9, rms=1.764 (13.560%) rms = 1.7204/1.7642, sse=302251.8/304572.9, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=302251.8, rms=1.720 (2.484%) 015: dt: 0.1250, sse=275410.4, rms=1.337 (22.290%) 016: dt: 0.1250, sse=271661.0, rms=1.251 (6.428%) rms = 1.2448/1.2510, sse=262462.2/271661.0, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=262462.2, rms=1.245 (0.497%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 116.8144760; border_low = 71.0000000; outside_low = 59.7828250; outside_hi = 116.8144760; sigma = 0.5; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 607 vertices, nripped=8804 mean border=90.9, 326 (86) missing vertices, mean dist -0.0 [0.2 (%61.0)->0.2 (%39.0))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0755 min Finding expansion regions mean absolute distance = 0.18 +- 0.29 3481 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=mrphy, 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=316583.8, rms=1.914 rms = 2.9239/1.9138, sse=479742.7/316583.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=272082.0, rms=1.396 (27.052%) rms = 1.3077/1.3961, sse=276220.3/272082.0, time step reduction 2 of 3 to 0.125 0 1 0 019: dt: 0.2500, sse=276220.3, rms=1.308 (6.331%) 020: dt: 0.1250, sse=263724.5, rms=1.208 (7.625%) rms = 1.1710/1.2080, sse=252987.0/263724.5, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=252987.0, rms=1.171 (3.063%) 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 = 116.8144760; border_low = 71.0000000; outside_low = 59.7828250; outside_hi = 116.8144760; sigma = 0.25; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 584 vertices, nripped=8804 mean border=91.2, 460 (81) missing vertices, mean dist -0.0 [0.2 (%52.9)->0.2 (%47.1))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0484 min Finding expansion regions mean absolute distance = 0.18 +- 0.26 3695 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=mrphy, 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=266449.4, rms=1.365 rms = 2.0244/1.3648, sse=343154.9/266449.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 022: dt: 0.2500, sse=244472.7, rms=1.013 (25.763%) rms = 1.0152/1.0132, sse=248673.8/244472.7, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.9819/1.0132, sse=242720.9/244472.7, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=242720.9, rms=0.982 (3.091%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 3.32 minutes #VMPC# mris_place_surfaces VmPeak 2195472 mris_place_surface done @#@FSTIME 2022:09:05:20:14:11 mris_place_surface N 25 e 212.42 S 1.20 U 211.15 P 99% M 1924344 F 3 R 587993 W 0 c 665 w 4 I 384 O 10304 L 1.09 1.14 1.16 @#@FSLOADPOST 2022:09:05:20:17:44 mris_place_surface N 25 1.31 1.19 1.17 #-------------------------------------------- #@# WhiteSurfs rh Mon Sep 5 20:17:44 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --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 7.2.0 7.2.0 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --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 280992 0.31811 0.11748 0.000487 1.6316 Corner 842976 60.00000 15.14757 0.485075 178.3071 Edge 421488 0.87010 0.20328 0.020464 3.3195 Hinge 421488 12.61965 14.31865 0.000023 179.9583 Reading in aparc ../label/rh.aparc.annot Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=76207, wmmin=5, clip=110 MRIfindBrightNonWM(): 15306 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 Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf Ripping BG MRIcopyHeader(): source has ctab MRISripBasalGanglia(): -2 2 0.5 ripped 665 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 70249: xyz = (36.4262,0.604503,10.4087) oxyz = (36.4262,0.604503,10.4087) wxzy = (36.4262,0.604503,10.4087) pxyz = (0,0,0) CBVO Creating mask 140498 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 116.8144760; border_low = 69.0000000; outside_low = 57.7828250; outside_hi = 116.8144760; sigma = 2; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=2 had to be increased for 353 vertices, nripped=9268 mean border=84.7, 176 (176) missing vertices, mean dist 0.2 [0.9 (%15.7)->0.4 (%84.3))] %55 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1974 min Finding expansion regions mean absolute distance = 0.48 +- 0.67 3684 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=mrphy, 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=1571314.9, rms=7.217 001: dt: 0.5000, sse=767557.1, rms=4.671 (35.283%) 002: dt: 0.5000, sse=676615.4, rms=4.236 (9.295%) rms = 4.5393/4.2364, sse=745867.5/676615.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 003: dt: 0.2500, sse=416629.2, rms=2.883 (31.952%) 004: dt: 0.2500, sse=360119.1, rms=2.448 (15.078%) 005: dt: 0.2500, sse=328752.1, rms=2.229 (8.938%) rms = 2.2136/2.2293, sse=328092.8/328752.1, time step reduction 2 of 3 to 0.125 0 0 1 006: dt: 0.2500, sse=328092.8, rms=2.214 (0.705%) 007: dt: 0.1250, sse=296835.7, rms=1.906 (13.878%) 008: dt: 0.1250, sse=290679.8, rms=1.841 (3.410%) rms = 1.8233/1.8414, sse=289420.4/290679.8, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=289420.4, rms=1.823 (0.980%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 116.8144760; border_low = 69.0000000; outside_low = 57.7828250; outside_hi = 116.8144760; sigma = 1; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=1 had to be increased for 399 vertices, nripped=9268 mean border=89.0, 214 (70) missing vertices, mean dist -0.2 [0.3 (%81.1)->0.3 (%18.9))] %76 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1371 min Finding expansion regions mean absolute distance = 0.31 +- 0.42 3724 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=mrphy, 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=1015060.5, rms=5.551 010: dt: 0.5000, sse=716876.8, rms=4.374 (21.210%) rms = 4.4157/4.3737, sse=729803.1/716876.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 011: dt: 0.2500, sse=442426.5, rms=2.951 (32.533%) 012: dt: 0.2500, sse=349404.0, rms=2.281 (22.692%) 013: dt: 0.2500, sse=329573.9, rms=2.011 (11.860%) rms = 1.9856/2.0107, sse=317275.2/329573.9, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=317275.2, rms=1.986 (1.249%) 015: dt: 0.1250, sse=267273.8, rms=1.466 (26.169%) 016: dt: 0.1250, sse=266498.1, rms=1.370 (6.568%) rms = 1.3565/1.3697, sse=263319.5/266498.1, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=263319.5, rms=1.356 (0.963%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 116.8144760; border_low = 69.0000000; outside_low = 57.7828250; outside_hi = 116.8144760; sigma = 0.5; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 482 vertices, nripped=9268 mean border=90.0, 331 (47) missing vertices, mean dist -0.1 [0.2 (%61.6)->0.2 (%38.4))] %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0736 min Finding expansion regions mean absolute distance = 0.19 +- 0.30 3608 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=mrphy, 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=322176.1, rms=2.049 rms = 3.2496/2.0486, sse=499441.5/322176.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=270189.0, rms=1.499 (26.829%) 019: dt: 0.2500, sse=268941.5, rms=1.420 (5.293%) rms = 1.5297/1.4196, sse=269096.3/268941.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 020: dt: 0.1250, sse=257608.1, rms=1.348 (5.028%) 021: dt: 0.1250, sse=252934.7, rms=1.275 (5.412%) rms = 1.2594/1.2753, sse=249622.2/252934.7, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=249622.2, rms=1.259 (1.245%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 116.8144760; border_low = 69.0000000; outside_low = 57.7828250; outside_hi = 116.8144760; sigma = 0.25; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 511 vertices, nripped=9268 mean border=90.4, 456 (38) missing vertices, mean dist -0.0 [0.2 (%53.1)->0.2 (%46.9))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0460 min Finding expansion regions mean absolute distance = 0.18 +- 0.26 3672 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=mrphy, 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=263330.2, rms=1.451 rms = 2.2219/1.4509, sse=351814.4/263330.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=238628.9, rms=1.075 (25.936%) rms = 1.0737/1.0746, sse=241068.8/238628.9, time step reduction 2 of 3 to 0.125 0 1 1 024: dt: 0.2500, sse=241068.8, rms=1.074 (0.086%) 025: dt: 0.1250, sse=234539.8, rms=0.986 (8.176%) rms = 0.9463/0.9859, sse=232109.4/234539.8, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=232109.4, rms=0.946 (4.010%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 3.43 minutes #VMPC# mris_place_surfaces VmPeak 2186412 mris_place_surface done @#@FSTIME 2022:09:05:20:17:44 mris_place_surface N 25 e 218.53 S 1.22 U 217.28 P 99% M 1915212 F 0 R 583963 W 0 c 352 w 1 I 0 O 9888 L 1.31 1.19 1.17 @#@FSLOADPOST 2022:09:05:20:21:22 mris_place_surface N 25 1.41 1.26 1.20 #-------------------------------------------- #@# T1PialSurf lh Mon Sep 5 20:21:22 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --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 7.2.0 7.2.0 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --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 292810 0.31517 0.13050 0.000416 1.6865 Corner 878430 60.00000 17.50275 0.217622 179.4864 Edge 439215 0.86908 0.22400 0.017751 3.1854 Hinge 439215 12.57842 14.68110 0.000003 179.7927 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=76207, wmmin=5, clip=110 MRIfindBrightNonWM(): 15306 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 70.267 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 INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRIcopyHeader(): source has ctab MRISripSegs(): -2 2 0.5 ripped 0 vertex 73204: xyz = (-38.5997,3.14863,40.1837) oxyz = (-38.5997,3.14863,40.1837) wxzy = (-38.5997,3.14863,40.1837) pxyz = (-38.5997,3.14863,40.1837) CBVO Creating mask 146407 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 103.1855240; border_hi = 59.7828250; border_low = 37.3484800; outside_low = 10.0000000; outside_hi = 54.1742400; sigma = 2; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=2 had to be increased for 441 vertices, nripped=6898 mean border=55.2, 245 (245) missing vertices, mean dist 1.5 [0.0 (%0.0)->2.1 (%100.0))] %20 local maxima, %47 large gradients and %29 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1621 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=mrphy, 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=37734740.0, rms=36.711 001: dt: 0.5000, sse=25536696.0, rms=30.162 (17.840%) 002: dt: 0.5000, sse=17954370.0, rms=25.248 (16.292%) 003: dt: 0.5000, sse=13694276.0, rms=22.009 (12.826%) 004: dt: 0.5000, sse=11174367.0, rms=19.845 (9.832%) 005: dt: 0.5000, sse=9390312.0, rms=18.157 (8.506%) 006: dt: 0.5000, sse=7780149.5, rms=16.486 (9.205%) 007: dt: 0.5000, sse=6313139.0, rms=14.800 (10.228%) 008: dt: 0.5000, sse=4903029.5, rms=12.974 (12.339%) 009: dt: 0.5000, sse=3740609.2, rms=11.247 (13.309%) 010: dt: 0.5000, sse=2834916.8, rms=9.690 (13.844%) 011: dt: 0.5000, sse=2321787.0, rms=8.684 (10.386%) 012: dt: 0.5000, sse=2043127.0, rms=8.084 (6.908%) 013: dt: 0.5000, sse=1954655.2, rms=7.882 (2.496%) 014: dt: 0.5000, sse=1885875.8, rms=7.721 (2.047%) rms = 7.7010/7.7206, sse=1878325.9/1885875.7, time step reduction 1 of 3 to 0.250 0 0 1 015: dt: 0.5000, sse=1878325.9, rms=7.701 (0.253%) 016: dt: 0.2500, sse=1198587.9, rms=5.890 (23.513%) 017: dt: 0.2500, sse=1119089.0, rms=5.642 (4.211%) rms = 5.7983/5.6423, sse=1169458.9/1119089.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 018: dt: 0.1250, sse=967964.1, rms=5.136 (8.971%) 019: dt: 0.1250, sse=775059.1, rms=4.405 (14.230%) 020: dt: 0.1250, sse=731950.8, rms=4.225 (4.101%) 021: dt: 0.1250, sse=718846.3, rms=4.168 (1.349%) rms = 4.1407/4.1676, sse=712783.3/718846.3, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=712783.2, rms=4.141 (0.646%) maximum number of reductions reached, breaking from loop positioning took 2.2 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 103.1855240; border_hi = 59.7828250; border_low = 37.3484800; outside_low = 10.0000000; outside_hi = 54.1742400; sigma = 1; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=1 had to be increased for 4787 vertices, nripped=6898 mean border=52.3, 1986 (32) missing vertices, mean dist 0.1 [0.1 (%40.3)->0.3 (%59.7))] %44 local maxima, %23 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0450 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=mrphy, 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=1194151.9, rms=5.722 rms = 8.3702/5.7220, sse=2234640.0/1194151.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=966560.2, rms=4.955 (13.407%) rms = 5.1754/4.9549, sse=1029026.1/966560.2, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 024: dt: 0.1250, sse=918078.2, rms=4.775 (3.624%) 025: dt: 0.1250, sse=845362.3, rms=4.492 (5.936%) 026: dt: 0.1250, sse=822077.6, rms=4.397 (2.118%) 027: dt: 0.1250, sse=802255.1, rms=4.315 (1.861%) 028: dt: 0.1250, sse=789960.3, rms=4.263 (1.195%) rms = 4.2324/4.2633, sse=782652.7/789960.3, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=782652.7, rms=4.232 (0.724%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 103.1855240; border_hi = 59.7828250; border_low = 37.3484800; outside_low = 10.0000000; outside_hi = 54.1742400; sigma = 0.5; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 4920 vertices, nripped=6898 mean border=51.1, 2606 (28) missing vertices, mean dist 0.1 [0.1 (%41.2)->0.2 (%58.8))] %46 local maxima, %20 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0257 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=mrphy, 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=869355.2, rms=4.587 rms = 8.1028/4.5870, sse=2111379.4/869355.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=785539.4, rms=4.245 (7.461%) rms = 4.7299/4.2448, sse=905632.1/785539.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 031: dt: 0.1250, sse=763023.1, rms=4.148 (2.270%) 032: dt: 0.1250, sse=743871.6, rms=4.066 (1.998%) rms = 4.0476/4.0655, sse=739717.0/743871.7, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=739717.0, rms=4.048 (0.442%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 103.1855240; border_hi = 59.7828250; border_low = 37.3484800; outside_low = 10.0000000; outside_hi = 54.1742400; sigma = 0.25; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=146407 Gdiag_no=-1 vno start=0, stop=146407 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 3562 vertices, nripped=6898 mean border=50.3, 4578 (27) missing vertices, mean dist 0.0 [0.2 (%46.3)->0.2 (%53.7))] %47 local maxima, %19 large gradients and %26 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0173 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=mrphy, 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=774949.4, rms=4.201 rms = 6.9630/4.2009, sse=1630367.3/774949.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 034: dt: 0.2500, sse=725549.9, rms=3.985 (5.145%) rms = 4.4796/3.9848, sse=840447.3/725549.9, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 035: dt: 0.1250, sse=705470.5, rms=3.893 (2.291%) 036: dt: 0.1250, sse=684584.6, rms=3.798 (2.440%) rms = 3.7824/3.7984, sse=680876.1/684584.6, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=680876.1, rms=3.782 (0.423%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Pinning medial wall to white surface removing intersecting faces 000: 16 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 4.32 minutes #VMPC# mris_place_surfaces VmPeak 1623592 mris_place_surface done @#@FSTIME 2022:09:05:20:21:22 mris_place_surface N 28 e 272.00 S 0.84 U 271.06 P 99% M 1351264 F 0 R 416104 W 0 c 1340 w 1 I 0 O 10304 L 1.41 1.26 1.20 @#@FSLOADPOST 2022:09:05:20:25:54 mris_place_surface N 28 1.16 1.21 1.18 #-------------------------------------------- #@# T1PialSurf rh Mon Sep 5 20:25:54 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --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 7.2.0 7.2.0 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --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 280992 0.32125 0.12821 0.000841 2.4984 Corner 842976 60.00000 16.40021 0.127929 179.5276 Edge 421488 0.87579 0.21795 0.021955 3.1781 Hinge 421488 12.77121 14.64448 0.000011 179.9627 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=76207, wmmin=5, clip=110 MRIfindBrightNonWM(): 15306 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 69.267 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 INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRIcopyHeader(): source has ctab MRISripSegs(): -2 2 0.5 ripped 0 vertex 70249: xyz = (36.4828,0.408059,10.3136) oxyz = (36.4828,0.408059,10.3136) wxzy = (36.4828,0.408059,10.3136) pxyz = (36.4828,0.408059,10.3136) CBVO Creating mask 140498 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 103.1855240; border_hi = 57.7828250; border_low = 35.3484800; outside_low = 10.0000000; outside_hi = 52.1742400; sigma = 2; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=2 had to be increased for 391 vertices, nripped=7204 mean border=53.6, 217 (217) missing vertices, mean dist 1.4 [0.0 (%0.0)->2.1 (%100.0))] %15 local maxima, %49 large gradients and %31 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1548 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=mrphy, 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=37651212.0, rms=37.516 001: dt: 0.5000, sse=25018022.0, rms=30.541 (18.591%) 002: dt: 0.5000, sse=17366104.0, rms=25.401 (16.830%) 003: dt: 0.5000, sse=13204477.0, rms=22.108 (12.965%) 004: dt: 0.5000, sse=10707790.0, rms=19.870 (10.120%) 005: dt: 0.5000, sse=8903255.0, rms=18.081 (9.004%) 006: dt: 0.5000, sse=7322565.5, rms=16.354 (9.555%) 007: dt: 0.5000, sse=5955135.5, rms=14.696 (10.137%) 008: dt: 0.5000, sse=4688841.5, rms=12.973 (11.725%) 009: dt: 0.5000, sse=3636710.2, rms=11.343 (12.562%) 010: dt: 0.5000, sse=2776340.8, rms=9.811 (13.510%) 011: dt: 0.5000, sse=2279106.2, rms=8.803 (10.267%) 012: dt: 0.5000, sse=2022624.2, rms=8.234 (6.470%) 013: dt: 0.5000, sse=1933002.0, rms=8.024 (2.553%) 014: dt: 0.5000, sse=1858981.5, rms=7.845 (2.230%) rms = 7.8102/7.8447, sse=1845638.3/1858981.5, time step reduction 1 of 3 to 0.250 0 0 1 015: dt: 0.5000, sse=1845638.4, rms=7.810 (0.441%) 016: dt: 0.2500, sse=1237623.8, rms=6.160 (21.124%) 017: dt: 0.2500, sse=1150750.9, rms=5.889 (4.412%) rms = 5.9873/5.8886, sse=1182595.3/1150750.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 018: dt: 0.1250, sse=1022503.8, rms=5.462 (7.252%) 019: dt: 0.1250, sse=854977.5, rms=4.846 (11.263%) 020: dt: 0.1250, sse=810489.7, rms=4.669 (3.654%) 021: dt: 0.1250, sse=798330.3, rms=4.619 (1.073%) rms = 4.6002/4.6192, sse=793844.1/798330.3, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=793844.1, rms=4.600 (0.412%) maximum number of reductions reached, breaking from loop positioning took 2.1 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 103.1855240; border_hi = 57.7828250; border_low = 35.3484800; outside_low = 10.0000000; outside_hi = 52.1742400; sigma = 1; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=1 had to be increased for 5404 vertices, nripped=7204 mean border=50.8, 2162 (18) missing vertices, mean dist 0.1 [0.1 (%42.7)->0.4 (%57.3))] %40 local maxima, %24 large gradients and %29 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0439 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=mrphy, 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=1264162.2, rms=6.087 rms = 8.3126/6.0865, sse=2117859.4/1264162.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=1059101.1, rms=5.415 (11.032%) rms = 5.5867/5.4150, sse=1109494.7/1059101.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 024: dt: 0.1250, sse=1017089.8, rms=5.267 (2.740%) 025: dt: 0.1250, sse=954832.0, rms=5.038 (4.339%) 026: dt: 0.1250, sse=931520.0, rms=4.950 (1.758%) 027: dt: 0.1250, sse=911161.5, rms=4.871 (1.578%) rms = 4.8331/4.8715, sse=901276.9/911161.5, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=901276.9, rms=4.833 (0.788%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 103.1855240; border_hi = 57.7828250; border_low = 35.3484800; outside_low = 10.0000000; outside_hi = 52.1742400; sigma = 0.5; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 5356 vertices, nripped=7204 mean border=49.5, 2875 (15) missing vertices, mean dist 0.1 [0.1 (%41.3)->0.3 (%58.7))] %44 local maxima, %20 large gradients and %29 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0256 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=mrphy, 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=1002028.0, rms=5.209 rms = 8.2058/5.2088, sse=2071096.8/1002028.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=914093.1, rms=4.880 (6.307%) rms = 5.2260/4.8803, sse=1005922.3/914093.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 030: dt: 0.1250, sse=891407.8, rms=4.792 (1.808%) 031: dt: 0.1250, sse=868685.1, rms=4.703 (1.860%) rms = 4.6858/4.7029, sse=864302.4/868685.0, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=864302.4, rms=4.686 (0.364%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 103.1855240; border_hi = 57.7828250; border_low = 35.3484800; outside_low = 10.0000000; outside_hi = 52.1742400; sigma = 0.25; max_thickness = 10; step_size=0.3; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=140498 Gdiag_no=-1 vno start=0, stop=140498 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 3658 vertices, nripped=7204 mean border=48.7, 5163 (15) missing vertices, mean dist 0.0 [0.2 (%46.4)->0.2 (%53.6))] %44 local maxima, %19 large gradients and %28 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0169 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=mrphy, 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=896803.9, rms=4.813 rms = 7.1108/4.8127, sse=1622268.6/896804.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=838561.6, rms=4.580 (4.827%) rms = 4.8761/4.5804, sse=911170.6/838561.6, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 034: dt: 0.1250, sse=818035.0, rms=4.496 (1.851%) 035: dt: 0.1250, sse=789394.2, rms=4.376 (2.650%) rms = 4.3378/4.3765, sse=780084.0/789394.3, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=780084.1, rms=4.338 (0.884%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Pinning medial wall to white surface removing intersecting faces 000: 17 intersecting 001: 3 intersecting step 1 with no progress (num=3, old_num=3) 002: 3 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 4.13 minutes #VMPC# mris_place_surfaces VmPeak 1592924 mris_place_surface done @#@FSTIME 2022:09:05:20:25:55 mris_place_surface N 28 e 261.09 S 0.99 U 260.05 P 99% M 1320872 F 0 R 417234 W 0 c 423 w 1 I 0 O 9888 L 1.16 1.21 1.18 @#@FSLOADPOST 2022:09:05:20:30:16 mris_place_surface N 28 1.22 1.22 1.19 #@# white curv lh Mon Sep 5 20:30:16 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 2022:09:05:20:30:16 mris_place_surface N 5 e 2.20 S 0.12 U 2.07 P 99% M 200768 F 0 R 54292 W 0 c 37 w 1 I 0 O 1144 L 1.22 1.22 1.19 @#@FSLOADPOST 2022:09:05:20:30:18 mris_place_surface N 5 1.20 1.22 1.18 #@# white area lh Mon Sep 5 20:30:18 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2022:09:05:20:30:18 mris_place_surface N 3 e 1.11 S 0.10 U 0.99 P 98% M 200892 F 0 R 54294 W 0 c 150 w 1 I 0 O 1144 L 1.20 1.22 1.18 @#@FSLOADPOST 2022:09:05:20:30:19 mris_place_surface N 3 1.20 1.22 1.18 #@# pial curv lh Mon Sep 5 20:30:19 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 2022:09:05:20:30:19 mris_place_surface N 5 e 2.14 S 0.10 U 2.02 P 99% M 200748 F 0 R 54292 W 0 c 285 w 1 I 0 O 1144 L 1.20 1.22 1.18 @#@FSLOADPOST 2022:09:05:20:30:21 mris_place_surface N 5 1.20 1.22 1.18 #@# pial area lh Mon Sep 5 20:30:21 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2022:09:05:20:30:21 mris_place_surface N 3 e 1.45 S 0.12 U 1.32 P 99% M 200740 F 0 R 54293 W 0 c 5 w 1 I 0 O 1144 L 1.20 1.22 1.18 @#@FSLOADPOST 2022:09:05:20:30:23 mris_place_surface N 3 1.26 1.23 1.19 #@# thickness lh Mon Sep 5 20:30:23 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 146407 vertices processed 25000 of 146407 vertices processed 50000 of 146407 vertices processed 75000 of 146407 vertices processed 100000 of 146407 vertices processed 125000 of 146407 vertices processed 0 of 146407 vertices processed 25000 of 146407 vertices processed 50000 of 146407 vertices processed 75000 of 146407 vertices processed 100000 of 146407 vertices processed 125000 of 146407 vertices processed thickness calculation complete, 7:114 truncations. 71014 vertices at 0 distance 134825 vertices at 1 distance 64206 vertices at 2 distance 16606 vertices at 3 distance 4191 vertices at 4 distance 1205 vertices at 5 distance 408 vertices at 6 distance 152 vertices at 7 distance 59 vertices at 8 distance 43 vertices at 9 distance 35 vertices at 10 distance 15 vertices at 11 distance 21 vertices at 12 distance 19 vertices at 13 distance 4 vertices at 14 distance 4 vertices at 15 distance 2 vertices at 16 distance 1 vertices at 17 distance 1 vertices at 18 distance 2 vertices at 19 distance 1 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2022:09:05:20:30:23 mris_place_surface N 6 e 38.57 S 0.16 U 38.39 P 99% M 200956 F 0 R 61916 W 0 c 99 w 1 I 0 O 1144 L 1.26 1.23 1.19 @#@FSLOADPOST 2022:09:05:20:31:02 mris_place_surface N 6 1.15 1.21 1.18 #@# area and vertex vol lh Mon Sep 5 20:31:02 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc lh /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.volume masking with /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Total face volume 212181 Total vertex volume 212064 (mask=0) #@# P7T_020_001bc lh 212064 vertexvol Done @#@FSTIME 2022:09:05:20:31:02 vertexvol N 4 e 2.31 S 0.22 U 1.93 P 93% M 334572 F 7 R 94789 W 0 c 151 w 30 I 1128 O 3432 L 1.15 1.21 1.18 @#@FSLOADPOST 2022:09:05:20:31:04 vertexvol N 4 1.13 1.20 1.18 #@# white curv rh Mon Sep 5 20:31:04 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 2022:09:05:20:31:04 mris_place_surface N 5 e 2.09 S 0.14 U 1.94 P 99% M 193212 F 0 R 52129 W 0 c 31 w 1 I 0 O 1104 L 1.13 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:31:06 mris_place_surface N 5 1.13 1.20 1.18 #@# white area rh Mon Sep 5 20:31:06 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2022:09:05:20:31:06 mris_place_surface N 3 e 1.43 S 0.17 U 1.24 P 99% M 193180 F 0 R 52130 W 0 c 114 w 1 I 0 O 1104 L 1.13 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:31:08 mris_place_surface N 3 1.12 1.20 1.18 #@# pial curv rh Mon Sep 5 20:31:08 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 2022:09:05:20:31:08 mris_place_surface N 5 e 2.49 S 0.15 U 2.34 P 99% M 193180 F 0 R 52129 W 0 c 17 w 1 I 0 O 1104 L 1.12 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:31:10 mris_place_surface N 5 1.12 1.20 1.18 #@# pial area rh Mon Sep 5 20:31:10 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2022:09:05:20:31:10 mris_place_surface N 3 e 1.06 S 0.11 U 0.93 P 99% M 193120 F 0 R 52127 W 0 c 21 w 1 I 0 O 1104 L 1.12 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:31:11 mris_place_surface N 3 1.12 1.20 1.18 #@# thickness rh Mon Sep 5 20:31:11 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 140498 vertices processed 25000 of 140498 vertices processed 50000 of 140498 vertices processed 75000 of 140498 vertices processed 100000 of 140498 vertices processed 125000 of 140498 vertices processed 0 of 140498 vertices processed 25000 of 140498 vertices processed 50000 of 140498 vertices processed 75000 of 140498 vertices processed 100000 of 140498 vertices processed 125000 of 140498 vertices processed thickness calculation complete, 11:128 truncations. 68869 vertices at 0 distance 127577 vertices at 1 distance 62527 vertices at 2 distance 16221 vertices at 3 distance 3925 vertices at 4 distance 1111 vertices at 5 distance 383 vertices at 6 distance 154 vertices at 7 distance 73 vertices at 8 distance 50 vertices at 9 distance 22 vertices at 10 distance 26 vertices at 11 distance 7 vertices at 12 distance 11 vertices at 13 distance 14 vertices at 14 distance 12 vertices at 15 distance 3 vertices at 16 distance 4 vertices at 17 distance 2 vertices at 18 distance 3 vertices at 19 distance 2 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2022:09:05:20:31:11 mris_place_surface N 6 e 37.58 S 0.18 U 37.39 P 99% M 193284 F 0 R 59447 W 0 c 50 w 1 I 0 O 1104 L 1.12 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:31:49 mris_place_surface N 6 1.17 1.20 1.18 #@# area and vertex vol rh Mon Sep 5 20:31:49 UTC 2022 cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc rh /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.volume masking with /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Total face volume 206199 Total vertex volume 206050 (mask=0) #@# P7T_020_001bc rh 206050 vertexvol Done @#@FSTIME 2022:09:05:20:31:49 vertexvol N 4 e 2.74 S 0.31 U 2.41 P 99% M 321528 F 0 R 91076 W 0 c 177 w 22 I 0 O 3312 L 1.17 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:31:52 vertexvol N 4 1.17 1.20 1.18 #----------------------------------------- #@# Curvature Stats lh Mon Sep 5 20:31:52 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm P7T_020_001bc 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 [ P7T_020_001bc/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 [ 266 ] Gb_filter = 0 WARN: S lookup min: -0.061098 WARN: S explicit min: 0.000000 vertex = 2227 @#@FSTIME 2022:09:05:20:31:52 mris_curvature_stats N 11 e 3.23 S 0.13 U 2.87 P 93% M 200948 F 5 R 54417 W 0 c 67 w 6 I 856 O 9192 L 1.17 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:31:55 mris_curvature_stats N 11 1.16 1.20 1.18 #----------------------------------------- #@# Curvature Stats rh Mon Sep 5 20:31:55 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm P7T_020_001bc 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 [ P7T_020_001bc/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 [ 278 ] Gb_filter = 0 WARN: S lookup min: -0.859771 WARN: S explicit min: 0.000000 vertex = 149 @#@FSTIME 2022:09:05:20:31:55 mris_curvature_stats N 11 e 3.43 S 0.16 U 3.27 P 99% M 192892 F 0 R 52248 W 0 c 11 w 1 I 0 O 8872 L 1.16 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:31:59 mris_curvature_stats N 11 1.15 1.20 1.18 #-------------------------------------------- #@# Cortical ribbon mask Mon Sep 5 20:31:59 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc SUBJECTS_DIR is /home/marcantf/software/freesurfer/subjects loading input data... Running hemis serially Processing left hemi MRIcopyHeader(): source has ctab computing distance to left white surface MRIcopyHeader(): source has ctab computing distance to left pial surface Processing right hemi MRIcopyHeader(): source has ctab computing distance to right white surface MRIcopyHeader(): source has ctab computing distance to right pial surface hemi masks overlap voxels = 255 MRIcopyHeader(): source has ctab writing volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/ribbon.mgz mris_volmask took 14.55 minutes writing ribbon files MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab @#@FSTIME 2022:09:05:20:31:59 mris_volmask N 12 e 872.75 S 1.67 U 870.66 P 99% M 1469828 F 5 R 942225 W 0 c 7338 w 6 I 1080 O 2456 L 1.15 1.20 1.18 @#@FSLOADPOST 2022:09:05:20:46:32 mris_volmask N 12 1.21 1.15 1.16 #----------------------------------------- #@# Cortical Parc 2 lh Mon Sep 5 20:46:32 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 P7T_020_001bc lh ../surf/lh.sphere.reg /home/marcantf/software/freesurfer/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 7.2.0 7.2.0 reading atlas from /home/marcantf/software/freesurfer/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... MRIcopyHeader(): source has ctab 16 labels changed using aseg relabeling using gibbs priors... 000: 9572 changed, 146407 examined... 001: 2264 changed, 37393 examined... 002: 682 changed, 11880 examined... 003: 270 changed, 3968 examined... 004: 105 changed, 1563 examined... 005: 51 changed, 626 examined... 006: 23 changed, 301 examined... 007: 8 changed, 130 examined... 008: 3 changed, 40 examined... 009: 4 changed, 21 examined... 010: 2 changed, 20 examined... 011: 3 changed, 10 examined... 012: 1 changed, 12 examined... 013: 0 changed, 8 examined... 0 labels changed using aseg 000: 250 total segments, 167 labels (2206 vertices) changed 001: 100 total segments, 17 labels (59 vertices) changed 002: 84 total segments, 1 labels (2 vertices) changed 003: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 977 vertices marked for relabeling... 977 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. @#@FSTIME 2022:09:05:20:46:32 mris_ca_label N 11 e 17.51 S 1.57 U 15.59 P 98% M 2074004 F 0 R 890135 W 0 c 772 w 137 I 42432 O 2296 L 1.21 1.15 1.16 @#@FSLOADPOST 2022:09:05:20:46:49 mris_ca_label N 11 1.30 1.17 1.17 #----------------------------------------- #@# Cortical Parc 2 rh Mon Sep 5 20:46:49 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 P7T_020_001bc rh ../surf/rh.sphere.reg /home/marcantf/software/freesurfer/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 7.2.0 7.2.0 reading atlas from /home/marcantf/software/freesurfer/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... MRIcopyHeader(): source has ctab 104 labels changed using aseg relabeling using gibbs priors... 000: 9616 changed, 140498 examined... 001: 2147 changed, 37533 examined... 002: 686 changed, 11543 examined... 003: 316 changed, 3910 examined... 004: 147 changed, 1799 examined... 005: 71 changed, 851 examined... 006: 51 changed, 405 examined... 007: 33 changed, 272 examined... 008: 16 changed, 186 examined... 009: 5 changed, 100 examined... 010: 1 changed, 28 examined... 011: 0 changed, 6 examined... 50 labels changed using aseg 000: 226 total segments, 145 labels (2362 vertices) changed 001: 84 total segments, 4 labels (6 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 617 vertices marked for relabeling... 617 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. @#@FSTIME 2022:09:05:20:46:49 mris_ca_label N 11 e 16.97 S 1.24 U 15.11 P 96% M 1898044 F 0 R 707340 W 0 c 1424 w 131 I 42776 O 2208 L 1.30 1.17 1.17 @#@FSLOADPOST 2022:09:05:20:47:06 mris_ca_label N 11 1.23 1.17 1.16 #----------------------------------------- #@# Cortical Parc 3 lh Mon Sep 5 20:47:06 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 P7T_020_001bc lh ../surf/lh.sphere.reg /home/marcantf/software/freesurfer/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 7.2.0 7.2.0 reading atlas from /home/marcantf/software/freesurfer/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... MRIcopyHeader(): source has ctab 2046 labels changed using aseg relabeling using gibbs priors... 000: 2150 changed, 146407 examined... 001: 515 changed, 9905 examined... 002: 162 changed, 2884 examined... 003: 86 changed, 912 examined... 004: 41 changed, 461 examined... 005: 27 changed, 228 examined... 006: 27 changed, 138 examined... 007: 14 changed, 135 examined... 008: 7 changed, 85 examined... 009: 7 changed, 43 examined... 010: 3 changed, 46 examined... 011: 1 changed, 18 examined... 012: 1 changed, 7 examined... 013: 1 changed, 7 examined... 014: 0 changed, 7 examined... 365 labels changed using aseg 000: 57 total segments, 24 labels (235 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 706 vertices marked for relabeling... 706 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. @#@FSTIME 2022:09:05:20:47:06 mris_ca_label N 11 e 12.95 S 0.67 U 11.92 P 97% M 1074304 F 0 R 337059 W 0 c 880 w 133 I 42976 O 2296 L 1.23 1.17 1.16 @#@FSLOADPOST 2022:09:05:20:47:19 mris_ca_label N 11 1.18 1.16 1.16 #----------------------------------------- #@# Cortical Parc 3 rh Mon Sep 5 20:47:19 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 P7T_020_001bc rh ../surf/rh.sphere.reg /home/marcantf/software/freesurfer/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 7.2.0 7.2.0 reading atlas from /home/marcantf/software/freesurfer/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... MRIcopyHeader(): source has ctab 2159 labels changed using aseg relabeling using gibbs priors... 000: 2172 changed, 140498 examined... 001: 487 changed, 10004 examined... 002: 137 changed, 2728 examined... 003: 84 changed, 806 examined... 004: 55 changed, 432 examined... 005: 41 changed, 286 examined... 006: 35 changed, 220 examined... 007: 30 changed, 193 examined... 008: 22 changed, 163 examined... 009: 18 changed, 123 examined... 010: 15 changed, 89 examined... 011: 10 changed, 65 examined... 012: 8 changed, 55 examined... 013: 9 changed, 49 examined... 014: 4 changed, 41 examined... 015: 7 changed, 21 examined... 016: 5 changed, 32 examined... 017: 4 changed, 21 examined... 018: 4 changed, 20 examined... 019: 3 changed, 16 examined... 020: 4 changed, 16 examined... 021: 4 changed, 19 examined... 022: 2 changed, 15 examined... 023: 1 changed, 11 examined... 024: 0 changed, 7 examined... 531 labels changed using aseg 000: 63 total segments, 28 labels (371 vertices) changed 001: 37 total segments, 2 labels (3 vertices) changed 002: 35 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 12 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 439 vertices marked for relabeling... 439 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. @#@FSTIME 2022:09:05:20:47:19 mris_ca_label N 11 e 12.86 S 0.70 U 11.81 P 97% M 1084972 F 0 R 390531 W 0 c 829 w 129 I 42952 O 2200 L 1.18 1.16 1.16 @#@FSLOADPOST 2022:09:05:20:47:32 mris_ca_label N 11 1.15 1.15 1.16 #----------------------------------------- #@# WM/GM Contrast lh Mon Sep 5 20:47:32 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts pctsurfcon --s P7T_020_001bc --lh-only Log file is /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts/pctsurfcon.log Mon Sep 5 20:47:32 UTC 2022 setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts /home/marcantf/software/freesurfer/bin/pctsurfcon pctsurfcon 7.2.0 Linux mrphys-gpu1 4.15.0-180-generic #189-Ubuntu SMP Wed May 18 14:13:57 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/marcantf/software/freesurfer mri_vol2surf --mov /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8573/lh.wm.mgh --regheader P7T_020_001bc --cortex srcvol = /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 Done loading volume Computing registration from header. Using /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99966 -0.01743 -0.01918 0.00001; -0.01917 -0.00033 0.99982 -0.00001; 0.01743 -0.99985 -0.00000 0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Reading surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 123025 Masking with /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Writing to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8573/lh.wm.mgh Dim: 146407 1 1 mri_vol2surf --mov /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8573/lh.gm.mgh --projfrac 0.3 --regheader P7T_020_001bc --cortex srcvol = /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 Done loading volume Computing registration from header. Using /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99966 -0.01743 -0.01918 0.00001; -0.01917 -0.00033 0.99982 -0.00001; 0.01743 -0.99985 -0.00000 0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Reading surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Done reading source surface Reading thickness /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 139322 Masking with /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Writing to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8573/lh.gm.mgh Dim: 146407 1 1 mri_concat /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8573/lh.wm.mgh /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8573/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.w-g.pct.mgh mri_segstats --in /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.w-g.pct.mgh --annot P7T_020_001bc lh aparc --sum /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/stats/lh.w-g.pct.stats --snr 7.2.0 cwd cmdline mri_segstats --in /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.w-g.pct.mgh --annot P7T_020_001bc lh aparc --sum /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/stats/lh.w-g.pct.stats --snr sysname Linux hostname mrphys-gpu1 machine x86_64 user marcantf whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.annot Seg base 1000 Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.w-g.pct.mgh Vertex Area is 0.630339 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 @#@FSTIME 2022:09:05:20:47:32 pctsurfcon N 3 e 6.73 S 0.61 U 5.86 P 96% M 436500 F 15 R 285630 W 0 c 247 w 80 I 2752 O 3568 L 1.15 1.15 1.16 @#@FSLOADPOST 2022:09:05:20:47:39 pctsurfcon N 3 1.13 1.14 1.16 #----------------------------------------- #@# WM/GM Contrast rh Mon Sep 5 20:47:39 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts pctsurfcon --s P7T_020_001bc --rh-only Log file is /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts/pctsurfcon.log Mon Sep 5 20:47:39 UTC 2022 setenv SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects cd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/scripts /home/marcantf/software/freesurfer/bin/pctsurfcon pctsurfcon 7.2.0 Linux mrphys-gpu1 4.15.0-180-generic #189-Ubuntu SMP Wed May 18 14:13:57 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/marcantf/software/freesurfer mri_vol2surf --mov /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8645/rh.wm.mgh --regheader P7T_020_001bc --cortex srcvol = /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 Done loading volume Computing registration from header. Using /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99966 -0.01743 -0.01918 0.00001; -0.01917 -0.00033 0.99982 -0.00001; 0.01743 -0.99985 -0.00000 0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Reading surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 119923 Masking with /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Writing to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8645/rh.wm.mgh Dim: 140498 1 1 mri_vol2surf --mov /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8645/rh.gm.mgh --projfrac 0.3 --regheader P7T_020_001bc --cortex srcvol = /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 Done loading volume Computing registration from header. Using /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99966 -0.01743 -0.01918 0.00001; -0.01917 -0.00033 0.99982 -0.00001; 0.01743 -0.99985 -0.00000 0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Reading surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Done reading source surface Reading thickness /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 134171 Masking with /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Writing to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8645/rh.gm.mgh Dim: 140498 1 1 mri_concat /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8645/rh.wm.mgh /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/tmp.pctsurfcon.8645/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.w-g.pct.mgh mri_segstats --in /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.w-g.pct.mgh --annot P7T_020_001bc rh aparc --sum /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/stats/rh.w-g.pct.stats --snr 7.2.0 cwd cmdline mri_segstats --in /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.w-g.pct.mgh --annot P7T_020_001bc rh aparc --sum /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/stats/rh.w-g.pct.stats --snr sysname Linux hostname mrphys-gpu1 machine x86_64 user marcantf whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.annot Seg base 2000 Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.w-g.pct.mgh Vertex Area is 0.642493 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 @#@FSTIME 2022:09:05:20:47:39 pctsurfcon N 3 e 6.27 S 0.62 U 5.64 P 99% M 429788 F 0 R 279895 W 0 c 146 w 67 I 8 O 3424 L 1.13 1.14 1.16 @#@FSLOADPOST 2022:09:05:20:47:45 pctsurfcon N 3 1.28 1.18 1.17 #----------------------------------------- #@# Relabel Hypointensities Mon Sep 5 20:47:45 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... MRIcopyHeader(): source has ctab 9965 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... MRIcopyHeader(): source has ctab 10734 voxels changed to hypointensity... MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab 20231 hypointense voxels neighboring cortex changed @#@FSTIME 2022:09:05:20:47:45 mri_relabel_hypointensities N 3 e 52.54 S 1.39 U 51.08 P 99% M 966660 F 7 R 760080 W 0 c 251 w 8 I 1632 O 1864 L 1.28 1.18 1.17 @#@FSLOADPOST 2022:09:05:20:48:38 mri_relabel_hypointensities N 3 1.27 1.19 1.17 #----------------------------------------- #@# APas-to-ASeg Mon Sep 5 20:48:38 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/ribbon.mgz --threads 1 --lh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label --lh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white --lh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial --rh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label --rh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white --rh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects outvol aseg.mgz 16 avail.processors, using 1 Loading aseg.presurf.hypos.mgz MRIcopyHeader(): source has ctab Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/ribbon.mgz Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 nrelabeled = 622406 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1176488 mri_surf2volseg done @#@FSTIME 2022:09:05:20:48:38 mri_surf2volseg N 20 e 56.45 S 0.65 U 55.51 P 99% M 1135408 F 6 R 311367 W 0 c 507 w 7 I 1160 O 1904 L 1.27 1.19 1.17 @#@FSLOADPOST 2022:09:05:20:49:35 mri_surf2volseg N 20 1.19 1.17 1.17 mri_brainvol_stats P7T_020_001bc ComputeBrainVolumeStats2 VoxelVol=0.216, KeepCSF=1 #CBVS2 MaskVol 1294940.1 #CBVS2 BrainSegVol 971185.3 #CBVS2 BrainSegVolNotVent 942741.8 #CBVS2 SupraTentVol 891121.9 #CBVS2 SupraTentVolNotVent 862678.4 #CBVS2 lhCtxGM 212456.0 #CBVS2 rhCtxGM 206357.1 #CBVS2 lhCerebralWM 200326.6 #CBVS2 rhCerebralWM 196552.0 #CBVS2 SubCortGMVol 47512.2 #CBVS2 CerebellumVol 80063.4 #CBVS2 CerebellumGMVol 63839.0 #CBVS2 VentChorVol 24975.6 #CBVS2 3rd4th5thCSF 3467.9 #CBVS2 AllCSF 28443.5 #CBVS2 CCVol 3321.6 @#@FSTIME 2022:09:05:20:49:35 mri_brainvol_stats N 1 e 6.73 S 0.31 U 6.26 P 97% M 322724 F 17 R 152098 W 0 c 81 w 21 I 3992 O 8 L 1.19 1.17 1.17 @#@FSLOADPOST 2022:09:05:20:49:41 mri_brainvol_stats N 1 1.17 1.17 1.17 #----------------------------------------- #@# AParc-to-ASeg aparc Mon Sep 5 20:49:41 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.annot 1000 --lh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label --lh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white --lh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial --rh-annot /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.annot 2000 --rh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label --rh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white --rh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects outvol aparc+aseg.mgz 16 avail.processors, using 1 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8328 vertices from lh hemi Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.annot Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8603 vertices from rh hemi Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 nrelabeled = 1936453 ndotcheck = 78260 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1138380 mri_surf2volseg done @#@FSTIME 2022:09:05:20:49:41 mri_surf2volseg N 25 e 744.56 S 0.53 U 743.63 P 99% M 1097468 F 2 R 298245 W 0 c 4196 w 3 I 376 O 2144 L 1.17 1.17 1.17 @#@FSLOADPOST 2022:09:05:21:02:06 mri_surf2volseg N 25 1.11 1.14 1.16 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Mon Sep 5 21:02:06 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label --lh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white --lh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial --rh-annot /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label --rh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white --rh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects outvol aparc.a2009s+aseg.mgz 16 avail.processors, using 1 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8328 vertices from lh hemi Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.a2009s.annot Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8603 vertices from rh hemi Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.a2009s.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 nrelabeled = 1936453 ndotcheck = 78260 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1138468 mri_surf2volseg done @#@FSTIME 2022:09:05:21:02:06 mri_surf2volseg N 25 e 743.08 S 0.58 U 742.15 P 99% M 1097292 F 0 R 298110 W 0 c 7767 w 1 I 0 O 2312 L 1.11 1.14 1.16 @#@FSLOADPOST 2022:09:05:21:14:29 mri_surf2volseg N 25 1.25 1.22 1.19 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Mon Sep 5 21:14:29 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label --lh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white --lh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial --rh-annot /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label --rh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white --rh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects outvol aparc.DKTatlas+aseg.mgz 16 avail.processors, using 1 Loading aseg.mgz MRIcopyHeader(): source has ctab Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8328 vertices from lh hemi Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.DKTatlas.annot Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8603 vertices from rh hemi Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.DKTatlas.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 nrelabeled = 1936453 ndotcheck = 78260 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1138384 mri_surf2volseg done @#@FSTIME 2022:09:05:21:14:29 mri_surf2volseg N 25 e 758.32 S 0.63 U 756.86 P 99% M 1097504 F 0 R 298090 W 0 c 14881 w 1 I 0 O 2136 L 1.25 1.22 1.19 @#@FSLOADPOST 2022:09:05:21:27:08 mri_surf2volseg N 25 1.19 1.17 1.17 #----------------------------------------- #@# WMParc Mon Sep 5 21:27:08 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 1 --lh-annot /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.annot 3000 --lh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label --lh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white --lh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial --rh-annot /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.annot 4000 --rh-cortex-mask /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label --rh-white /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white --rh-pial /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects outvol wmparc.mgz 16 avail.processors, using 1 Loading aparc+aseg.mgz MRIcopyHeader(): source has ctab Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8328 vertices from lh hemi Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.aparc.annot Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8603 vertices from rh hemi Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.aparc.annot Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 nrelabeled = 1822023 ndotcheck = 22458 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1138388 mri_surf2volseg done @#@FSTIME 2022:09:05:21:27:08 mri_surf2volseg N 25 e 276.92 S 0.74 U 276.00 P 99% M 1097380 F 0 R 298094 W 0 c 4568 w 1 I 0 O 2384 L 1.19 1.17 1.17 @#@FSLOADPOST 2022:09:05:21:31:45 mri_surf2volseg N 25 1.16 1.17 1.18 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 P7T_020_001bc --surf-wm-vol --ctab /home/marcantf/software/freesurfer/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 7.2.0 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 P7T_020_001bc --surf-wm-vol --ctab /home/marcantf/software/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname mrphys-gpu1 machine x86_64 user marcantf whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1009967 mm^3 (det: 1.928880 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 0.216 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2022:09:05:21:31:45 mri_segstats N 24 e 501.93 S 1.95 U 499.88 P 99% M 549076 F 0 R 2823635 W 0 c 616 w 3 I 56 O 24 L 1.16 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:40:07 mri_segstats N 24 1.14 1.14 1.16 #----------------------------------------- #@# Parcellation Stats lh Mon Sep 5 21:40:07 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 212181 Total vertex volume 212064 (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) = 1009967 mm^3 (det: 1.928880 ) 1480 932 2101 2.310 0.399 0.098 0.020 8 1.3 bankssts 937 583 1488 2.313 0.614 0.107 0.018 11 0.7 caudalanteriorcingulate 5014 2977 6522 2.169 0.548 0.110 0.029 45 6.1 caudalmiddlefrontal 2624 1724 3667 1.924 0.370 0.138 0.036 43 3.4 cuneus 524 345 1083 2.355 0.632 0.120 0.036 6 0.7 entorhinal 4131 2805 6709 2.110 0.492 0.125 0.032 56 5.2 fusiform 7450 4673 11455 2.200 0.450 0.113 0.025 91 7.6 inferiorparietal 3781 2537 6253 2.160 0.624 0.131 0.040 56 6.1 inferiortemporal 1684 1102 2477 2.128 0.718 0.129 0.029 23 2.0 isthmuscingulate 9918 5931 12418 1.926 0.487 0.118 0.029 112 11.5 lateraloccipital 3136 2094 5728 2.421 0.539 0.127 0.033 44 3.9 lateralorbitofrontal 4800 3289 6980 1.958 0.398 0.138 0.036 73 6.6 lingual 2241 1539 3791 2.228 0.543 0.131 0.041 44 2.9 medialorbitofrontal 3988 2621 7267 2.295 0.535 0.123 0.035 66 5.1 middletemporal 985 616 1790 2.463 0.626 0.124 0.036 14 1.2 parahippocampal 2506 1488 3811 2.338 0.488 0.091 0.019 14 2.0 paracentral 2389 1569 4413 2.461 0.445 0.116 0.025 26 2.4 parsopercularis 1163 791 2210 2.218 0.459 0.118 0.032 20 1.3 parsorbitalis 1869 1184 3040 2.271 0.427 0.101 0.022 15 1.6 parstriangularis 2432 1634 2914 1.869 0.385 0.132 0.032 30 3.2 pericalcarine 6134 3687 7569 1.855 0.515 0.106 0.026 65 5.9 postcentral 1819 1219 3001 2.225 0.709 0.125 0.027 28 2.0 posteriorcingulate 8517 5063 12555 2.316 0.549 0.105 0.025 73 8.4 precentral 6108 4085 9551 2.168 0.422 0.127 0.028 86 7.3 precuneus 1032 720 2115 2.528 0.772 0.140 0.035 19 1.3 rostralanteriorcingulate 9929 6458 15729 2.179 0.468 0.126 0.030 142 11.7 rostralmiddlefrontal 15106 9300 23417 2.363 0.568 0.117 0.031 179 18.4 superiorfrontal 9437 5725 12786 2.058 0.442 0.117 0.026 104 9.9 superiorparietal 5943 3829 11072 2.446 0.575 0.107 0.024 57 5.9 superiortemporal 5797 3534 8688 2.225 0.511 0.123 0.034 80 7.8 supramarginal 545 400 1213 2.178 0.470 0.159 0.054 25 1.0 frontalpole 743 546 1928 2.631 0.607 0.149 0.051 16 1.5 temporalpole 688 451 1076 2.145 0.432 0.136 0.040 8 1.0 transversetemporal 3229 2077 5246 2.473 0.798 0.122 0.038 33 4.3 insula @#@FSTIME 2022:09:05:21:40:07 mris_anatomical_stats N 14 e 18.70 S 0.32 U 18.17 P 98% M 537660 F 9 R 154953 W 0 c 81 w 10 I 1648 O 24 L 1.14 1.14 1.16 @#@FSLOADPOST 2022:09:05:21:40:25 mris_anatomical_stats N 14 1.10 1.13 1.16 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 P7T_020_001bc lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 212181 Total vertex volume 212064 (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) = 1009967 mm^3 (det: 1.928880 ) 1480 875 2101 2.310 0.399 0.114 0.032 21 1.6 bankssts 937 711 1488 2.313 0.614 0.160 0.052 68 1.8 caudalanteriorcingulate 5014 3088 6522 2.169 0.548 0.111 0.027 86 5.5 caudalmiddlefrontal 2624 2164 3667 1.924 0.370 0.150 0.037 38 3.9 cuneus 524 673 1083 2.355 0.632 0.285 0.077 13 2.3 entorhinal 4131 3611 6709 2.110 0.492 0.160 0.043 81 7.1 fusiform 7450 5569 11455 2.200 0.450 0.132 0.030 91 9.1 inferiorparietal 3781 3397 6253 2.160 0.624 0.162 0.043 58 6.9 inferiortemporal 1684 1319 2477 2.128 0.718 0.184 0.061 98 4.2 isthmuscingulate 9918 6969 12418 1.926 0.487 0.128 0.031 164 12.7 lateraloccipital 3136 2704 5728 2.421 0.539 0.174 0.048 95 6.0 lateralorbitofrontal 4800 4053 6980 1.958 0.398 0.161 0.043 116 8.1 lingual 2241 1987 3791 2.228 0.543 0.187 0.055 68 5.0 medialorbitofrontal 3988 3671 7267 2.295 0.535 0.165 0.044 63 7.1 middletemporal 985 859 1790 2.463 0.626 0.209 0.069 32 3.0 parahippocampal 2506 1756 3811 2.338 0.488 0.108 0.022 19 2.5 paracentral 2389 1997 4413 2.461 0.445 0.152 0.039 45 3.6 parsopercularis 1163 1221 2210 2.218 0.459 0.182 0.040 19 2.0 parsorbitalis 1869 1469 3040 2.271 0.427 0.151 0.040 31 3.2 parstriangularis 2432 1516 2914 1.869 0.385 0.132 0.037 57 3.3 pericalcarine 6134 4406 7569 1.855 0.515 0.119 0.024 61 6.0 postcentral 1819 1494 3001 2.225 0.709 0.166 0.045 54 3.1 posteriorcingulate 8517 5683 12555 2.316 0.549 0.107 0.024 95 8.1 precentral 6108 4665 9551 2.168 0.422 0.148 0.036 103 9.1 precuneus 1032 945 2115 2.528 0.772 0.206 0.059 34 2.5 rostralanteriorcingulate 9929 7767 15729 2.179 0.468 0.147 0.032 168 13.7 rostralmiddlefrontal 15106 10404 23417 2.363 0.568 0.126 0.031 264 18.8 superiorfrontal 9437 6536 12786 2.058 0.442 0.122 0.025 129 9.6 superiorparietal 5943 5068 11072 2.446 0.575 0.159 0.045 100 11.1 superiortemporal 5797 4060 8688 2.225 0.511 0.132 0.034 92 7.7 supramarginal 545 733 1213 2.178 0.470 0.241 0.109 17 1.2 frontalpole 743 1036 1928 2.631 0.607 0.249 0.056 16 1.8 temporalpole 688 555 1076 2.145 0.432 0.160 0.057 16 1.2 transversetemporal 3229 2084 5246 2.473 0.798 0.150 0.052 88 5.9 insula @#@FSTIME 2022:09:05:21:40:25 mris_anatomical_stats N 14 e 18.61 S 0.33 U 18.25 P 99% M 537544 F 0 R 154957 W 0 c 447 w 1 I 0 O 24 L 1.10 1.13 1.16 @#@FSLOADPOST 2022:09:05:21:40:44 mris_anatomical_stats N 14 1.08 1.12 1.16 #----------------------------------------- #@# Parcellation Stats rh Mon Sep 5 21:40:44 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 206199 Total vertex volume 206050 (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) = 1009967 mm^3 (det: 1.928880 ) 1208 793 1665 2.128 0.372 0.117 0.025 10 1.4 bankssts 916 575 1269 2.152 0.479 0.125 0.030 12 1.0 caudalanteriorcingulate 4802 2928 5781 2.034 0.562 0.117 0.032 43 7.0 caudalmiddlefrontal 2464 1690 3730 1.975 0.360 0.154 0.040 47 4.0 cuneus 413 278 1022 2.493 0.520 0.109 0.032 3 0.5 entorhinal 3419 2278 6005 2.302 0.483 0.126 0.030 48 4.2 fusiform 7803 5157 13644 2.284 0.431 0.123 0.025 103 8.4 inferiorparietal 3158 2024 4546 1.934 0.511 0.130 0.041 97 5.2 inferiortemporal 1649 1087 2271 1.987 0.700 0.132 0.038 28 2.3 isthmuscingulate 7955 5236 11303 1.927 0.383 0.129 0.028 112 9.0 lateraloccipital 2823 1863 4915 2.442 0.602 0.128 0.036 35 4.0 lateralorbitofrontal 5425 3790 8250 2.020 0.507 0.153 0.043 86 9.5 lingual 2675 1787 4416 2.181 0.545 0.134 0.038 49 3.8 medialorbitofrontal 3351 2147 5145 2.039 0.555 0.119 0.034 56 4.7 middletemporal 974 632 1503 2.206 0.587 0.126 0.041 14 1.4 parahippocampal 2513 1553 4035 2.375 0.492 0.107 0.025 19 2.7 paracentral 1793 1189 3334 2.507 0.367 0.109 0.023 17 1.7 parsopercularis 1288 944 2541 2.233 0.465 0.151 0.037 26 2.1 parsorbitalis 2129 1364 3471 2.279 0.440 0.111 0.023 22 2.1 parstriangularis 2524 1717 3294 1.934 0.493 0.128 0.039 31 3.4 pericalcarine 6641 3960 7667 1.808 0.496 0.108 0.025 68 7.1 postcentral 1549 1059 2485 2.229 0.625 0.130 0.034 23 2.4 posteriorcingulate 8223 5030 12520 2.354 0.552 0.109 0.025 76 9.0 precentral 6377 4170 9828 2.220 0.469 0.128 0.030 74 8.0 precuneus 820 536 1612 2.570 0.418 0.127 0.031 15 1.0 rostralanteriorcingulate 11108 7389 18032 2.151 0.446 0.134 0.033 190 15.1 rostralmiddlefrontal 14466 9203 24453 2.409 0.548 0.121 0.031 171 19.0 superiorfrontal 9152 5694 12497 2.022 0.404 0.122 0.027 117 10.3 superiorparietal 4796 3066 7598 2.184 0.507 0.119 0.034 60 6.9 superiortemporal 4775 3003 7496 2.244 0.495 0.122 0.028 62 5.5 supramarginal 652 522 1705 2.505 0.409 0.172 0.047 22 1.1 frontalpole 701 559 2351 2.831 0.809 0.190 0.073 16 2.2 temporalpole 504 319 805 2.220 0.303 0.114 0.024 6 0.5 transversetemporal 2849 1816 4861 2.609 0.749 0.116 0.035 37 4.0 insula @#@FSTIME 2022:09:05:21:40:44 mris_anatomical_stats N 14 e 17.05 S 0.28 U 16.75 P 99% M 517724 F 0 R 145542 W 0 c 193 w 1 I 0 O 24 L 1.08 1.12 1.16 @#@FSLOADPOST 2022:09:05:21:41:01 mris_anatomical_stats N 14 1.19 1.15 1.17 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 P7T_020_001bc rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 206199 Total vertex volume 206050 (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) = 1009967 mm^3 (det: 1.928880 ) 1208 782 1665 2.128 0.372 0.140 0.044 24 1.9 bankssts 916 633 1269 2.152 0.479 0.168 0.056 61 1.9 caudalanteriorcingulate 4802 2938 5781 2.034 0.562 0.105 0.027 60 5.4 caudalmiddlefrontal 2464 2163 3730 1.975 0.360 0.169 0.043 46 4.2 cuneus 413 556 1022 2.493 0.520 0.291 0.085 10 2.1 entorhinal 3419 3046 6005 2.302 0.483 0.171 0.046 86 6.7 fusiform 7803 6590 13644 2.284 0.431 0.153 0.036 129 11.2 inferiorparietal 3158 2825 4546 1.934 0.511 0.168 0.044 58 5.6 inferiortemporal 1649 1261 2271 1.987 0.700 0.179 0.058 46 3.9 isthmuscingulate 7955 6436 11303 1.927 0.383 0.153 0.034 203 11.2 lateraloccipital 2823 2233 4915 2.442 0.602 0.178 0.054 70 6.5 lateralorbitofrontal 5425 4601 8250 2.020 0.507 0.170 0.048 107 10.6 lingual 2675 2370 4416 2.181 0.545 0.185 0.055 72 6.1 medialorbitofrontal 3351 2980 5145 2.039 0.555 0.173 0.049 61 7.4 middletemporal 974 738 1503 2.206 0.587 0.180 0.058 27 2.4 parahippocampal 2513 1784 4035 2.375 0.492 0.124 0.028 41 3.0 paracentral 1793 1475 3334 2.507 0.367 0.169 0.047 35 3.6 parsopercularis 1288 1341 2541 2.233 0.465 0.194 0.047 32 2.6 parsorbitalis 2129 1635 3471 2.279 0.440 0.154 0.041 60 3.5 parstriangularis 2524 1674 3294 1.934 0.493 0.142 0.037 60 3.7 pericalcarine 6641 4618 7667 1.808 0.496 0.113 0.025 61 6.7 postcentral 1549 1200 2485 2.229 0.625 0.182 0.056 61 3.5 posteriorcingulate 8223 5597 12520 2.354 0.552 0.112 0.027 106 8.7 precentral 6377 4629 9828 2.220 0.469 0.143 0.035 123 9.6 precuneus 820 742 1612 2.570 0.418 0.184 0.057 24 1.7 rostralanteriorcingulate 11108 9241 18032 2.151 0.446 0.156 0.036 195 16.4 rostralmiddlefrontal 14466 10974 24453 2.409 0.548 0.141 0.037 266 21.4 superiorfrontal 9152 6632 12497 2.022 0.404 0.128 0.028 122 10.1 superiorparietal 4796 3987 7598 2.184 0.507 0.164 0.046 111 9.1 superiortemporal 4775 3499 7496 2.244 0.495 0.137 0.034 77 6.6 supramarginal 652 871 1705 2.505 0.409 0.238 0.053 12 1.5 frontalpole 701 1214 2351 2.831 0.809 0.327 0.077 20 2.6 temporalpole 504 428 805 2.220 0.303 0.129 0.029 3 0.6 transversetemporal 2849 1923 4861 2.609 0.749 0.157 0.052 87 5.8 insula @#@FSTIME 2022:09:05:21:41:01 mris_anatomical_stats N 14 e 17.16 S 0.26 U 16.89 P 99% M 517724 F 0 R 145544 W 0 c 44 w 1 I 0 O 24 L 1.19 1.15 1.17 @#@FSLOADPOST 2022:09:05:21:41:18 mris_anatomical_stats N 14 1.23 1.16 1.17 #----------------------------------------- #@# Parcellation Stats 2 lh Mon Sep 5 21:41:18 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 212181 Total vertex volume 212064 (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) = 1009967 mm^3 (det: 1.928880 ) 1543 1068 2669 2.232 0.405 0.134 0.030 26 1.9 G_and_S_frontomargin 2057 1291 3147 2.120 0.471 0.120 0.023 23 2.0 G_and_S_occipital_inf 2114 1199 2756 2.018 0.609 0.101 0.024 15 2.3 G_and_S_paracentral 1422 938 2543 2.342 0.466 0.120 0.031 19 1.5 G_and_S_subcentral 871 637 1789 2.205 0.445 0.142 0.037 26 1.1 G_and_S_transv_frontopol 1923 1321 3582 2.564 0.530 0.117 0.026 20 1.9 G_and_S_cingul-Ant 1515 954 2510 2.620 0.362 0.090 0.015 10 1.0 G_and_S_cingul-Mid-Ant 1531 983 2491 2.461 0.448 0.113 0.025 15 1.5 G_and_S_cingul-Mid-Post 642 441 1499 2.635 0.518 0.138 0.032 11 0.9 G_cingul-Post-dorsal 322 209 523 2.373 0.727 0.142 0.033 6 0.3 G_cingul-Post-ventral 2280 1508 3454 1.944 0.386 0.149 0.042 47 3.1 G_cuneus 1311 904 3119 2.604 0.413 0.130 0.031 20 1.5 G_front_inf-Opercular 452 318 1133 2.540 0.322 0.135 0.036 8 0.5 G_front_inf-Orbital 999 658 2169 2.545 0.378 0.118 0.028 13 1.0 G_front_inf-Triangul 5665 3459 9283 2.179 0.619 0.132 0.039 93 8.5 G_front_middle 10388 6326 17627 2.374 0.642 0.128 0.039 162 15.1 G_front_sup 544 370 1089 2.738 0.760 0.138 0.050 8 0.9 G_Ins_lg_and_S_cent_ins 528 361 1627 3.238 0.769 0.136 0.041 8 0.7 G_insular_short 2640 1633 4759 2.293 0.456 0.131 0.034 46 3.5 G_occipital_middle 1700 1001 2374 2.092 0.477 0.125 0.027 24 1.8 G_occipital_sup 1702 1207 3423 2.240 0.433 0.142 0.039 36 2.5 G_oc-temp_lat-fusifor 3393 2385 5467 1.963 0.391 0.149 0.041 64 5.2 G_oc-temp_med-Lingual 1243 785 2396 2.405 0.694 0.124 0.039 17 1.7 G_oc-temp_med-Parahip 2184 1506 4690 2.385 0.528 0.130 0.041 41 3.0 G_orbital 3136 1827 5678 2.421 0.516 0.116 0.035 52 3.8 G_pariet_inf-Angular 3154 1952 5247 2.213 0.589 0.142 0.045 62 5.7 G_pariet_inf-Supramar 4316 2576 6673 2.154 0.505 0.119 0.029 53 5.1 G_parietal_sup 2327 1322 3071 1.910 0.535 0.107 0.029 32 2.3 G_postcentral 3217 1795 5520 2.468 0.649 0.109 0.033 36 3.9 G_precentral 2937 2033 5610 2.213 0.453 0.142 0.039 66 4.4 G_precuneus 820 568 1551 2.154 0.617 0.147 0.055 21 1.7 G_rectus 574 365 615 1.778 0.784 0.126 0.051 6 1.1 G_subcallosal 477 311 906 2.363 0.321 0.134 0.036 6 0.6 G_temp_sup-G_T_transv 1920 1287 5113 2.817 0.538 0.127 0.030 28 2.1 G_temp_sup-Lateral 686 456 1547 2.791 0.584 0.085 0.021 3 0.5 G_temp_sup-Plan_polar 1043 657 1750 2.369 0.411 0.092 0.017 6 0.7 G_temp_sup-Plan_tempo 1966 1344 3872 2.298 0.691 0.139 0.043 33 3.6 G_temporal_inf 2405 1600 5168 2.398 0.583 0.138 0.044 57 3.6 G_temporal_middle 406 246 429 1.966 0.394 0.078 0.013 1 0.2 Lat_Fis-ant-Horizont 269 178 407 2.321 0.463 0.128 0.024 3 0.3 Lat_Fis-ant-Vertical 1381 850 1533 2.095 0.374 0.102 0.023 7 1.3 Lat_Fis-post 3211 1847 3216 1.623 0.462 0.120 0.034 38 4.2 Pole_occipital 1550 1064 3212 2.371 0.555 0.134 0.047 30 2.7 Pole_temporal 2938 1971 3539 2.005 0.490 0.124 0.028 26 3.7 S_calcarine 3092 1896 3199 1.916 0.495 0.098 0.019 17 2.7 S_central 1319 806 1465 2.031 0.327 0.089 0.013 7 0.8 S_cingul-Marginalis 514 323 792 2.814 0.371 0.103 0.023 2 0.5 S_circular_insula_ant 1390 845 1687 2.328 0.508 0.094 0.025 7 1.4 S_circular_insula_inf 1566 957 1928 2.363 0.457 0.097 0.018 7 1.2 S_circular_insula_sup 721 481 873 1.906 0.497 0.109 0.040 6 0.9 S_collat_transv_ant 554 346 528 1.673 0.317 0.108 0.022 4 0.5 S_collat_transv_post 2521 1595 3303 2.110 0.349 0.105 0.019 17 2.2 S_front_inf 2009 1268 2414 1.993 0.348 0.108 0.022 18 2.1 S_front_middle 5041 3154 6537 2.279 0.389 0.105 0.022 40 4.7 S_front_sup 250 155 290 2.385 0.330 0.114 0.021 1 0.3 S_interm_prim-Jensen 2817 1794 3263 1.973 0.274 0.114 0.020 25 2.5 S_intrapariet_and_P_trans 1705 1073 1855 1.931 0.302 0.116 0.025 12 2.0 S_oc_middle_and_Lunatus 1128 696 1255 1.969 0.269 0.097 0.016 6 0.7 S_oc_sup_and_transversal 658 406 864 2.081 0.396 0.083 0.016 3 0.5 S_occipital_ant 924 609 1120 1.972 0.431 0.121 0.028 9 1.4 S_oc-temp_lat 1971 1303 2573 2.061 0.433 0.117 0.026 17 2.1 S_oc-temp_med_and_Lingual 501 322 516 1.937 0.302 0.120 0.025 3 0.6 S_orbital_lateral 421 274 659 2.420 0.684 0.118 0.038 4 0.5 S_orbital_med-olfact 1188 790 1692 2.107 0.449 0.125 0.025 15 1.3 S_orbital-H_Shaped 2577 1645 3246 2.056 0.383 0.115 0.022 22 2.3 S_parieto_occipital 1268 771 821 1.372 0.469 0.124 0.024 23 1.2 S_pericallosal 2601 1657 2941 1.900 0.327 0.115 0.024 23 2.7 S_postcentral 2566 1594 3537 2.344 0.341 0.096 0.018 16 2.0 S_precentral-inf-part 1477 921 1787 2.062 0.369 0.094 0.014 9 0.9 S_precentral-sup-part 784 533 1069 2.219 0.431 0.125 0.031 15 0.7 S_suborbital 1277 822 1603 2.122 0.327 0.112 0.022 8 1.3 S_subparietal 1005 659 1137 1.941 0.365 0.114 0.023 8 1.0 S_temporal_inf 6229 3913 7985 2.142 0.410 0.101 0.019 40 5.3 S_temporal_sup 303 204 347 1.848 0.338 0.136 0.034 2 0.5 S_temporal_transverse @#@FSTIME 2022:09:05:21:41:19 mris_anatomical_stats N 14 e 19.47 S 0.33 U 19.09 P 99% M 537564 F 0 R 147441 W 0 c 858 w 1 I 0 O 40 L 1.23 1.16 1.17 @#@FSLOADPOST 2022:09:05:21:41:38 mris_anatomical_stats N 14 1.16 1.15 1.16 #----------------------------------------- #@# Parcellation Stats 2 rh Mon Sep 5 21:41:38 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 206199 Total vertex volume 206050 (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) = 1009967 mm^3 (det: 1.928880 ) 1119 795 1965 2.164 0.398 0.146 0.037 22 1.7 G_and_S_frontomargin 1484 980 2269 2.019 0.421 0.127 0.025 18 1.6 G_and_S_occipital_inf 1715 1035 2333 1.993 0.709 0.124 0.032 17 2.5 G_and_S_paracentral 1456 957 2559 2.275 0.518 0.128 0.032 22 1.8 G_and_S_subcentral 1414 1092 3295 2.440 0.422 0.167 0.040 41 2.2 G_and_S_transv_frontopol 3257 2096 5471 2.457 0.426 0.113 0.024 34 3.3 G_and_S_cingul-Ant 2140 1377 3580 2.459 0.392 0.109 0.026 17 2.3 G_and_S_cingul-Mid-Ant 1575 1041 2742 2.465 0.387 0.113 0.030 14 1.7 G_and_S_cingul-Mid-Post 622 432 1399 2.640 0.563 0.159 0.047 15 1.2 G_cingul-Post-dorsal 437 290 650 2.071 0.419 0.140 0.046 8 0.6 G_cingul-Post-ventral 2191 1554 3492 1.974 0.389 0.163 0.046 48 3.9 G_cuneus 1228 872 2943 2.589 0.400 0.119 0.026 16 1.4 G_front_inf-Opercular 357 261 956 2.643 0.413 0.156 0.033 6 0.6 G_front_inf-Orbital 691 463 1440 2.410 0.409 0.115 0.028 8 0.7 G_front_inf-Triangul 6799 4377 10870 2.042 0.590 0.146 0.042 132 12.5 G_front_middle 8688 5578 16080 2.411 0.638 0.138 0.040 145 14.4 G_front_sup 528 371 1107 2.555 0.792 0.168 0.067 13 1.6 G_Ins_lg_and_S_cent_ins 518 339 1422 3.222 0.913 0.108 0.043 11 0.5 G_insular_short 2075 1437 4296 2.305 0.391 0.143 0.030 40 2.5 G_occipital_middle 1655 1059 2693 2.093 0.393 0.124 0.025 25 1.7 G_occipital_sup 1782 1224 3544 2.332 0.476 0.145 0.036 33 2.5 G_oc-temp_lat-fusifor 3195 2332 5548 2.033 0.525 0.168 0.052 62 6.5 G_oc-temp_med-Lingual 871 574 1917 2.437 0.619 0.118 0.039 12 1.1 G_oc-temp_med-Parahip 2436 1722 4965 2.333 0.623 0.146 0.043 48 4.0 G_orbital 2760 1888 6438 2.557 0.415 0.140 0.031 53 3.5 G_pariet_inf-Angular 2347 1485 4465 2.371 0.573 0.138 0.040 45 4.0 G_pariet_inf-Supramar 3399 2044 5049 2.108 0.451 0.130 0.035 51 4.6 G_parietal_sup 2429 1338 2959 1.858 0.550 0.115 0.032 31 3.1 G_postcentral 3036 1825 5541 2.434 0.679 0.119 0.030 42 3.8 G_precentral 2947 1988 5559 2.297 0.485 0.147 0.039 50 4.8 G_precuneus 685 474 1438 2.349 0.467 0.144 0.046 15 1.1 G_rectus 296 174 369 2.022 0.784 0.108 0.040 3 0.4 G_subcallosal 385 242 673 2.219 0.271 0.111 0.022 5 0.3 G_temp_sup-G_T_transv 1546 1021 3046 2.280 0.493 0.139 0.038 31 2.2 G_temp_sup-Lateral 580 391 1096 2.357 0.876 0.121 0.037 5 0.9 G_temp_sup-Plan_polar 841 510 1277 2.193 0.469 0.096 0.023 7 0.6 G_temp_sup-Plan_tempo 1865 1177 3047 1.986 0.559 0.147 0.056 93 4.1 G_temporal_inf 1761 1128 2908 2.026 0.512 0.124 0.037 41 2.4 G_temporal_middle 477 286 559 2.052 0.389 0.088 0.014 2 0.3 Lat_Fis-ant-Horizont 184 117 248 2.239 0.416 0.089 0.014 1 0.1 Lat_Fis-ant-Vertical 1603 998 1876 2.116 0.399 0.115 0.023 13 1.7 Lat_Fis-post 4103 2742 5939 1.880 0.413 0.133 0.032 68 5.1 Pole_occipital 1467 1084 3966 2.563 0.768 0.167 0.068 31 4.3 Pole_temporal 2847 1847 3400 2.046 0.542 0.122 0.033 29 3.8 S_calcarine 3426 2117 3582 1.935 0.520 0.098 0.019 19 3.2 S_central 1396 888 1782 2.123 0.412 0.103 0.019 10 1.1 S_cingul-Marginalis 465 286 667 2.897 0.329 0.088 0.016 2 0.4 S_circular_insula_ant 998 606 1261 2.380 0.573 0.085 0.020 4 0.9 S_circular_insula_inf 1286 760 1578 2.456 0.349 0.085 0.016 5 0.9 S_circular_insula_sup 520 336 745 2.132 0.423 0.091 0.014 2 0.3 S_collat_transv_ant 542 342 503 1.703 0.269 0.126 0.024 4 0.6 S_collat_transv_post 2224 1420 3079 2.135 0.371 0.109 0.022 21 1.9 S_front_inf 2963 1897 3522 2.063 0.372 0.120 0.027 30 3.6 S_front_middle 3790 2304 4963 2.327 0.347 0.089 0.017 19 2.5 S_front_sup 403 250 469 1.988 0.276 0.087 0.013 1 0.3 S_interm_prim-Jensen 3601 2302 4428 2.002 0.284 0.115 0.021 35 3.3 S_intrapariet_and_P_trans 1142 745 1287 1.869 0.313 0.119 0.026 9 1.3 S_oc_middle_and_Lunatus 1361 842 1437 1.877 0.263 0.107 0.020 11 1.2 S_oc_sup_and_transversal 782 514 908 1.848 0.294 0.123 0.023 7 1.0 S_occipital_ant 624 424 742 1.856 0.287 0.108 0.020 4 0.6 S_oc-temp_lat 2109 1338 2629 2.181 0.480 0.115 0.027 17 2.3 S_oc-temp_med_and_Lingual 638 411 861 2.148 0.414 0.126 0.027 8 0.8 S_orbital_lateral 426 276 641 2.274 0.810 0.118 0.034 4 0.6 S_orbital_med-olfact 1126 763 1788 2.265 0.416 0.134 0.032 13 1.7 S_orbital-H_Shaped 2458 1562 3190 2.142 0.375 0.112 0.022 19 2.4 S_parieto_occipital 1114 701 818 1.422 0.544 0.139 0.039 22 1.9 S_pericallosal 2387 1478 2481 1.881 0.322 0.104 0.018 18 1.9 S_postcentral 1853 1149 2309 2.263 0.353 0.103 0.019 10 1.7 S_precentral-inf-part 2041 1231 2452 2.318 0.304 0.090 0.016 9 1.5 S_precentral-sup-part 354 239 385 1.715 0.241 0.124 0.019 3 0.3 S_suborbital 1330 869 1775 2.122 0.357 0.115 0.022 14 1.2 S_subparietal 785 502 773 1.689 0.348 0.097 0.018 4 0.7 S_temporal_inf 5732 3634 7353 2.106 0.394 0.109 0.024 43 6.1 S_temporal_sup 228 157 250 1.831 0.299 0.135 0.025 2 0.3 S_temporal_transverse @#@FSTIME 2022:09:05:21:41:38 mris_anatomical_stats N 14 e 17.80 S 0.31 U 17.46 P 99% M 517820 F 0 R 145544 W 0 c 595 w 1 I 0 O 40 L 1.16 1.15 1.16 @#@FSLOADPOST 2022:09:05:21:41:56 mris_anatomical_stats N 14 1.12 1.14 1.16 #----------------------------------------- #@# Parcellation Stats 3 lh Mon Sep 5 21:41:56 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 212181 Total vertex volume 212064 (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) = 1009967 mm^3 (det: 1.928880 ) 1904 1195 3208 2.493 0.540 0.103 0.019 21 1.3 caudalanteriorcingulate 5390 3175 7043 2.171 0.542 0.110 0.030 51 6.5 caudalmiddlefrontal 3547 2304 4791 1.932 0.375 0.132 0.033 53 4.2 cuneus 461 294 870 2.332 0.623 0.121 0.039 6 0.7 entorhinal 3768 2566 6199 2.102 0.495 0.123 0.030 50 4.6 fusiform 7611 4686 11723 2.235 0.459 0.113 0.025 95 7.9 inferiorparietal 3757 2540 6242 2.166 0.619 0.132 0.042 56 6.2 inferiortemporal 1619 1062 2397 2.153 0.710 0.130 0.029 23 2.0 isthmuscingulate 9863 5911 12249 1.919 0.486 0.119 0.029 112 11.4 lateraloccipital 3621 2472 6653 2.317 0.563 0.134 0.036 57 4.8 lateralorbitofrontal 4939 3367 7147 1.956 0.396 0.138 0.036 75 6.8 lingual 2233 1529 3526 2.107 0.596 0.139 0.046 46 3.6 medialorbitofrontal 5543 3598 9446 2.272 0.514 0.119 0.032 79 6.8 middletemporal 1018 641 1833 2.444 0.634 0.123 0.035 14 1.1 parahippocampal 2877 1711 4559 2.385 0.502 0.092 0.020 17 2.5 paracentral 2274 1486 4142 2.471 0.436 0.117 0.025 25 2.3 parsopercularis 1043 710 1960 2.330 0.475 0.112 0.028 15 1.0 parsorbitalis 2330 1478 3630 2.235 0.436 0.112 0.023 22 2.3 parstriangularis 2424 1631 2929 1.875 0.390 0.131 0.032 29 3.1 pericalcarine 7077 4249 8569 1.860 0.500 0.109 0.027 77 7.2 postcentral 2028 1340 3224 2.228 0.690 0.123 0.027 29 2.2 posteriorcingulate 8179 4880 12183 2.327 0.550 0.104 0.024 68 7.9 precentral 6028 4040 9706 2.178 0.421 0.126 0.028 86 7.1 precuneus 1406 965 2725 2.492 0.739 0.135 0.037 25 1.8 rostralanteriorcingulate 7209 4690 11792 2.191 0.480 0.126 0.031 105 8.7 rostralmiddlefrontal 16287 10125 24945 2.296 0.557 0.119 0.032 214 20.2 superiorfrontal 7534 4561 10416 2.091 0.449 0.116 0.026 81 7.8 superiorparietal 7689 5010 14540 2.437 0.572 0.112 0.027 81 8.5 superiortemporal 5276 3279 7803 2.190 0.504 0.126 0.035 72 7.5 supramarginal 717 470 1101 2.124 0.442 0.134 0.039 8 1.0 transversetemporal 2427 1563 4512 2.760 0.673 0.111 0.031 21 2.7 insula @#@FSTIME 2022:09:05:21:41:56 mris_anatomical_stats N 14 e 18.48 S 0.28 U 18.19 P 99% M 537672 F 0 R 154962 W 0 c 77 w 1 I 0 O 24 L 1.12 1.14 1.16 @#@FSLOADPOST 2022:09:05:21:42:14 mris_anatomical_stats N 14 1.09 1.13 1.16 #----------------------------------------- #@# Parcellation Stats 3 rh Mon Sep 5 21:42:14 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 P7T_020_001bc rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 206199 Total vertex volume 206050 (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) = 1009967 mm^3 (det: 1.928880 ) 1260 792 2007 2.290 0.529 0.128 0.033 18 1.5 caudalanteriorcingulate 5078 3101 6149 2.044 0.562 0.117 0.032 45 7.3 caudalmiddlefrontal 3044 2065 4453 1.977 0.350 0.146 0.036 50 4.4 cuneus 363 246 939 2.492 0.519 0.109 0.033 3 0.5 entorhinal 3303 2208 5696 2.273 0.469 0.123 0.027 43 3.6 fusiform 7752 5122 13579 2.288 0.431 0.123 0.025 103 8.5 inferiorparietal 3353 2153 4918 1.970 0.534 0.132 0.043 104 5.8 inferiortemporal 1633 1080 2287 1.998 0.689 0.132 0.038 27 2.3 isthmuscingulate 8066 5294 11420 1.925 0.384 0.128 0.028 113 9.0 lateraloccipital 3491 2365 6154 2.309 0.585 0.136 0.039 53 5.6 lateralorbitofrontal 5249 3668 8003 2.019 0.504 0.154 0.043 83 9.3 lingual 1995 1345 3425 2.179 0.577 0.141 0.042 42 3.0 medialorbitofrontal 4231 2724 6403 2.049 0.538 0.118 0.033 62 5.6 middletemporal 1082 706 1661 2.203 0.595 0.128 0.042 16 1.6 parahippocampal 2779 1717 4465 2.381 0.490 0.111 0.028 24 3.3 paracentral 2110 1387 3777 2.480 0.365 0.108 0.022 19 1.9 parsopercularis 953 675 1782 2.310 0.470 0.134 0.031 15 1.2 parsorbitalis 2072 1324 3312 2.254 0.446 0.114 0.024 21 2.2 parstriangularis 2461 1680 3296 1.962 0.491 0.128 0.038 33 3.5 pericalcarine 7557 4531 8649 1.795 0.506 0.111 0.026 78 8.4 postcentral 1608 1097 2534 2.225 0.632 0.130 0.033 23 2.4 posteriorcingulate 7809 4787 12038 2.352 0.557 0.109 0.025 73 8.7 precentral 6442 4225 10154 2.234 0.468 0.129 0.030 78 8.0 precuneus 1130 761 2364 2.558 0.449 0.129 0.033 20 1.3 rostralanteriorcingulate 8234 5462 13254 2.134 0.459 0.137 0.034 145 11.7 rostralmiddlefrontal 17336 11193 29384 2.378 0.527 0.122 0.030 225 21.8 superiorfrontal 7535 4674 10461 2.054 0.380 0.123 0.028 99 8.6 superiorparietal 6220 4102 10789 2.236 0.585 0.130 0.039 84 10.6 superiortemporal 4573 2865 7144 2.241 0.491 0.121 0.028 59 5.1 supramarginal 508 322 819 2.231 0.304 0.112 0.024 6 0.5 transversetemporal 2668 1689 4736 2.723 0.684 0.107 0.030 32 2.9 insula @#@FSTIME 2022:09:05:21:42:15 mris_anatomical_stats N 14 e 17.20 S 0.28 U 16.90 P 99% M 517720 F 0 R 149147 W 0 c 98 w 1 I 0 O 24 L 1.09 1.13 1.16 @#@FSLOADPOST 2022:09:05:21:42:32 mris_anatomical_stats N 14 1.26 1.17 1.17 #-------------------------------------------- #@# ASeg Stats Mon Sep 5 21:42:32 UTC 2022 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc 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 /home/marcantf/software/freesurfer/ASegStatsLUT.txt --subject P7T_020_001bc setting seed for random number genererator to 1234 7.2.0 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 /home/marcantf/software/freesurfer/ASegStatsLUT.txt --subject P7T_020_001bc sysname Linux hostname mrphys-gpu1 machine x86_64 user marcantf whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1009967 mm^3 (det: 1.928880 ) Computing euler number orig.nofix lheno = -236, rheno = -266 orig.nofix lhholes = 119, rhholes = 134 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 0.216 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2022:09:05:21:42:32 mri_segstats N 32 e 260.41 S 1.28 U 258.72 P 99% M 635540 F 0 R 1700299 W 0 c 11442 w 1 I 0 O 24 L 1.26 1.17 1.17 @#@FSLOADPOST 2022:09:05:21:46:52 mri_segstats N 32 1.29 1.22 1.19 /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label #-------------------------------------------- #@# BA_exvivo Labels lh Mon Sep 5 21:46:52 UTC 2022 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4332 mri_label2label: Done @#@FSTIME 2022:09:05:21:46:52 mri_label2label N 12 e 6.00 S 0.32 U 5.32 P 94% M 580324 F 0 R 166099 W 0 c 363 w 53 I 16184 O 256 L 1.29 1.22 1.19 @#@FSLOADPOST 2022:09:05:21:46:58 mri_label2label N 12 1.27 1.21 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 363 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8272 mri_label2label: Done @#@FSTIME 2022:09:05:21:46:58 mri_label2label N 12 e 6.43 S 0.27 U 6.12 P 99% M 580580 F 0 R 166165 W 0 c 35 w 3 I 632 O 464 L 1.27 1.21 1.19 @#@FSLOADPOST 2022:09:05:21:47:05 mri_label2label N 12 1.25 1.21 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4131 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:05 mri_label2label N 12 e 5.68 S 0.34 U 5.31 P 99% M 580332 F 0 R 166096 W 0 c 184 w 3 I 320 O 232 L 1.25 1.21 1.18 @#@FSLOADPOST 2022:09:05:21:47:11 mri_label2label N 12 1.31 1.22 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 174 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6157 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:11 mri_label2label N 12 e 6.53 S 0.38 U 6.12 P 99% M 580340 F 0 R 166130 W 0 c 18 w 3 I 472 O 352 L 1.31 1.22 1.19 @#@FSLOADPOST 2022:09:05:21:47:17 mri_label2label N 12 1.26 1.21 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 578 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6362 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:17 mri_label2label N 12 e 5.86 S 0.25 U 5.59 P 99% M 580344 F 0 R 166130 W 0 c 6 w 3 I 456 O 424 L 1.26 1.21 1.19 @#@FSLOADPOST 2022:09:05:21:47:23 mri_label2label N 12 1.24 1.21 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4210 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:23 mri_label2label N 12 e 5.84 S 0.29 U 5.51 P 99% M 580348 F 0 R 166095 W 0 c 30 w 3 I 320 O 240 L 1.24 1.21 1.18 @#@FSLOADPOST 2022:09:05:21:47:29 mri_label2label N 12 1.22 1.21 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 3132 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 16721 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:29 mri_label2label N 12 e 9.66 S 0.27 U 9.35 P 99% M 581156 F 0 R 166291 W 0 c 37 w 3 I 1056 O 1240 L 1.22 1.21 1.18 @#@FSLOADPOST 2022:09:05:21:47:39 mri_label2label N 12 1.18 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 359 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4540 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:39 mri_label2label N 12 e 5.71 S 0.31 U 5.36 P 99% M 580456 F 0 R 166102 W 0 c 38 w 4 I 328 O 304 L 1.18 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:47:44 mri_label2label N 12 1.17 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 503 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3925 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:44 mri_label2label N 12 e 5.56 S 0.35 U 5.20 P 99% M 580328 F 0 R 169842 W 0 c 25 w 4 I 272 O 288 L 1.17 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:47:50 mri_label2label N 12 1.16 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 2265 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6906 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:50 mri_label2label N 12 e 5.93 S 0.30 U 5.57 P 98% M 580364 F 0 R 166125 W 0 c 457 w 3 I 376 O 584 L 1.16 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:47:56 mri_label2label N 12 1.13 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 4013 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 12127 mri_label2label: Done @#@FSTIME 2022:09:05:21:47:56 mri_label2label N 12 e 7.34 S 0.27 U 6.99 P 99% M 580728 F 0 R 166204 W 0 c 455 w 3 I 664 O 1008 L 1.13 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:48:03 mri_label2label N 12 1.12 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 628 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2646 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:03 mri_label2label N 12 e 6.52 S 0.49 U 5.91 P 98% M 580316 F 0 R 166069 W 0 c 430 w 3 I 168 O 224 L 1.12 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:48:10 mri_label2label N 12 1.11 1.18 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1329 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:10 mri_label2label N 12 e 5.25 S 0.31 U 4.89 P 99% M 580300 F 0 R 169803 W 0 c 184 w 4 I 120 O 80 L 1.11 1.18 1.17 @#@FSLOADPOST 2022:09:05:21:48:15 mri_label2label N 12 1.18 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject P7T_020_001bc --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1238 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:15 mri_label2label N 12 e 5.20 S 0.35 U 4.84 P 99% M 580188 F 0 R 169798 W 0 c 7 w 3 I 112 O 80 L 1.18 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:48:21 mri_label2label N 12 1.17 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 478 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:21 mri_label2label N 12 e 5.12 S 0.34 U 4.76 P 99% M 580244 F 0 R 166028 W 0 c 218 w 4 I 40 O 40 L 1.17 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:48:26 mri_label2label N 12 1.22 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 824 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:26 mri_label2label N 12 e 5.18 S 0.30 U 4.85 P 99% M 580204 F 0 R 166038 W 0 c 110 w 4 I 72 O 72 L 1.22 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:48:31 mri_label2label N 12 1.20 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1971 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:31 mri_label2label N 12 e 5.32 S 0.32 U 4.98 P 99% M 580140 F 0 R 166050 W 0 c 38 w 3 I 176 O 144 L 1.20 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:48:36 mri_label2label N 12 1.18 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2325 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:36 mri_label2label N 12 e 5.84 S 0.39 U 5.41 P 99% M 580320 F 0 R 166055 W 0 c 98 w 3 I 200 O 176 L 1.18 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:48:42 mri_label2label N 12 1.17 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 1636 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 5513 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:42 mri_label2label N 12 e 5.69 S 0.35 U 5.29 P 99% M 580216 F 0 R 166103 W 0 c 99 w 4 I 360 O 464 L 1.17 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:48:48 mri_label2label N 12 1.23 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 1788 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 4707 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:48 mri_label2label N 12 e 7.08 S 0.50 U 6.56 P 99% M 580156 F 0 R 166085 W 0 c 33 w 3 I 272 O 400 L 1.23 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:48:55 mri_label2label N 12 1.22 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 742 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 2028 mri_label2label: Done @#@FSTIME 2022:09:05:21:48:55 mri_label2label N 12 e 6.74 S 0.40 U 6.30 P 99% M 580080 F 0 R 166046 W 0 c 443 w 3 I 128 O 184 L 1.22 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:49:02 mri_label2label N 12 1.18 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 353 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1359 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:02 mri_label2label N 12 e 5.22 S 0.38 U 4.81 P 99% M 580184 F 0 R 169794 W 0 c 90 w 4 I 96 O 120 L 1.18 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:49:07 mri_label2label N 12 1.17 1.19 1.18 mris_label2annot --s P7T_020_001bc --ctab /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average/colortable_vpnl.txt Number of ctab entries 9 7.2.0 cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label cmdline mris_label2annot --s P7T_020_001bc --ctab /home/marcantf/software/freesurfer/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 mrphys-gpu1 machine x86_64 user marcantf subject P7T_020_001bc hemi lh SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects ColorTable /home/marcantf/software/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 128703 unhit vertices Writing annot to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.mpm.vpnl.annot @#@FSTIME 2022:09:05:21:49:07 mris_label2annot N 26 e 1.01 S 0.09 U 0.85 P 92% M 169436 F 4 R 46532 W 0 c 21 w 6 I 832 O 2296 L 1.17 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:49:08 mris_label2annot N 26 1.17 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1061 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:08 mri_label2label N 12 e 5.24 S 0.31 U 4.91 P 99% M 580204 F 0 R 166041 W 0 c 89 w 3 I 96 O 64 L 1.17 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:49:14 mri_label2label N 12 1.15 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2215 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:14 mri_label2label N 12 e 5.34 S 0.33 U 4.98 P 99% M 580344 F 0 R 169815 W 0 c 77 w 4 I 192 O 128 L 1.15 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:49:19 mri_label2label N 12 1.14 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1519 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:19 mri_label2label N 12 e 5.37 S 0.34 U 4.98 P 99% M 580376 F 0 R 169808 W 0 c 468 w 7 I 136 O 88 L 1.14 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:49:24 mri_label2label N 12 1.13 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2046 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:24 mri_label2label N 12 e 6.33 S 0.43 U 5.84 P 99% M 580144 F 0 R 169814 W 0 c 662 w 3 I 184 O 128 L 1.13 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:49:31 mri_label2label N 12 1.19 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 205 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2524 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:31 mri_label2label N 12 e 5.69 S 0.39 U 5.27 P 99% M 580332 F 0 R 166064 W 0 c 376 w 3 I 208 O 176 L 1.19 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:49:37 mri_label2label N 12 1.17 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1579 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:37 mri_label2label N 12 e 6.56 S 0.49 U 5.98 P 98% M 580260 F 0 R 166045 W 0 c 837 w 4 I 144 O 96 L 1.17 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:49:43 mri_label2label N 12 1.16 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 1389 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8424 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:43 mri_label2label N 12 e 6.50 S 0.32 U 6.11 P 98% M 580712 F 0 R 166159 W 0 c 575 w 4 I 616 O 608 L 1.16 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:49:50 mri_label2label N 12 1.15 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2010 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:50 mri_label2label N 12 e 5.40 S 0.35 U 5.04 P 99% M 580212 F 0 R 166054 W 0 c 16 w 4 I 168 O 136 L 1.15 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:49:55 mri_label2label N 12 1.13 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 202 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1353 mri_label2label: Done @#@FSTIME 2022:09:05:21:49:55 mri_label2label N 12 e 5.47 S 0.33 U 5.07 P 98% M 580100 F 0 R 169796 W 0 c 268 w 3 I 104 O 104 L 1.13 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:50:01 mri_label2label N 12 1.11 1.17 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 1554 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4959 mri_label2label: Done @#@FSTIME 2022:09:05:21:50:01 mri_label2label N 12 e 5.63 S 0.29 U 5.29 P 99% M 580328 F 0 R 166095 W 0 c 112 w 4 I 304 O 424 L 1.11 1.17 1.17 @#@FSLOADPOST 2022:09:05:21:50:06 mri_label2label N 12 1.10 1.17 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 1911 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5245 mri_label2label: Done @#@FSTIME 2022:09:05:21:50:06 mri_label2label N 12 e 5.77 S 0.31 U 5.41 P 99% M 580284 F 0 R 166095 W 0 c 902 w 4 I 296 O 440 L 1.10 1.17 1.17 @#@FSLOADPOST 2022:09:05:21:50:12 mri_label2label N 12 1.10 1.16 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 634 mri_label2label: Done @#@FSTIME 2022:09:05:21:50:12 mri_label2label N 12 e 6.79 S 0.47 U 6.30 P 99% M 580000 F 0 R 166027 W 0 c 9 w 3 I 48 O 56 L 1.10 1.16 1.17 @#@FSLOADPOST 2022:09:05:21:50:19 mri_label2label N 12 1.09 1.16 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 474 mri_label2label: Done @#@FSTIME 2022:09:05:21:50:19 mri_label2label N 12 e 6.70 S 0.47 U 6.19 P 99% M 580036 F 0 R 166030 W 0 c 34 w 3 I 48 O 32 L 1.09 1.16 1.17 @#@FSLOADPOST 2022:09:05:21:50:26 mri_label2label N 12 1.23 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 146407 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 462 mri_label2label: Done @#@FSTIME 2022:09:05:21:50:26 mri_label2label N 12 e 6.11 S 0.40 U 5.69 P 99% M 580084 F 0 R 166031 W 0 c 81 w 3 I 48 O 32 L 1.23 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:50:32 mri_label2label N 12 1.21 1.19 1.18 mris_label2annot --s P7T_020_001bc --hemi lh --ctab /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label cmdline mris_label2annot --s P7T_020_001bc --hemi lh --ctab /home/marcantf/software/freesurfer/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 mrphys-gpu1 machine x86_64 user marcantf subject P7T_020_001bc hemi lh SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects ColorTable /home/marcantf/software/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 98596 unhit vertices Writing annot to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.BA_exvivo.annot @#@FSTIME 2022:09:05:21:50:32 mris_label2annot N 38 e 1.37 S 0.14 U 1.18 P 96% M 170212 F 0 R 46784 W 0 c 175 w 2 I 8 O 2296 L 1.21 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:50:33 mris_label2annot N 38 1.21 1.19 1.18 mris_label2annot --s P7T_020_001bc --hemi lh --ctab /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label cmdline mris_label2annot --s P7T_020_001bc --hemi lh --ctab /home/marcantf/software/freesurfer/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 mrphys-gpu1 machine x86_64 user marcantf subject P7T_020_001bc hemi lh SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects ColorTable /home/marcantf/software/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 118436 unhit vertices Writing annot to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2022:09:05:21:50:34 mris_label2annot N 38 e 1.30 S 0.13 U 1.14 P 97% M 169940 F 0 R 46691 W 0 c 191 w 1 I 0 O 2296 L 1.21 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:50:35 mris_label2annot N 38 1.21 1.19 1.18 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab P7T_020_001bc lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 212181 Total vertex volume 212064 (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) = 1009967 mm^3 (det: 1.928880 ) 1128 626 1438 1.834 0.556 0.123 0.037 19 1.5 BA1_exvivo 3613 2205 4513 1.990 0.448 0.114 0.026 38 3.8 BA2_exvivo 1060 649 882 1.719 0.343 0.116 0.025 8 1.1 BA3a_exvivo 2330 1414 2691 1.728 0.506 0.099 0.025 21 2.1 BA3b_exvivo 1920 1092 3095 2.487 0.575 0.089 0.021 9 1.7 BA4a_exvivo 1270 777 1801 2.453 0.383 0.091 0.018 6 1.0 BA4p_exvivo 13168 7815 19567 2.304 0.636 0.113 0.030 127 16.6 BA6_exvivo 2494 1634 4279 2.393 0.385 0.109 0.024 25 2.2 BA44_exvivo 2940 1916 5243 2.328 0.456 0.117 0.026 33 2.9 BA45_exvivo 4457 2917 5626 1.860 0.455 0.129 0.035 61 6.0 V1_exvivo 9849 6303 12409 1.853 0.427 0.135 0.034 140 12.9 V2_exvivo 2430 1483 3899 2.222 0.465 0.116 0.025 26 2.7 MT_exvivo 626 402 1217 2.550 0.610 0.123 0.041 8 0.8 perirhinal_exvivo 526 342 1219 2.498 0.807 0.120 0.035 7 0.7 entorhinal_exvivo @#@FSTIME 2022:09:05:21:50:35 mris_anatomical_stats N 12 e 6.89 S 0.49 U 6.35 P 99% M 532712 F 0 R 149987 W 0 c 544 w 1 I 0 O 24 L 1.21 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:50:42 mris_anatomical_stats N 12 1.18 1.18 1.18 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab P7T_020_001bc lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 212181 Total vertex volume 212064 (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) = 1009967 mm^3 (det: 1.928880 ) 664 358 910 1.906 0.576 0.124 0.035 11 0.9 BA1_exvivo 1437 869 1844 1.987 0.408 0.101 0.022 16 1.1 BA2_exvivo 876 540 695 1.676 0.306 0.118 0.026 7 0.9 BA3a_exvivo 1429 878 1378 1.571 0.276 0.089 0.017 8 1.1 BA3b_exvivo 1850 1063 2920 2.480 0.568 0.087 0.020 8 1.6 BA4a_exvivo 1027 629 1397 2.368 0.373 0.095 0.019 6 0.9 BA4p_exvivo 7013 4058 10484 2.334 0.648 0.110 0.029 66 8.3 BA6_exvivo 1508 1000 2777 2.469 0.401 0.121 0.028 18 1.5 BA44_exvivo 1182 772 2446 2.485 0.485 0.125 0.029 16 1.3 BA45_exvivo 4769 3129 6052 1.848 0.459 0.128 0.034 65 6.4 V1_exvivo 5031 3231 6176 1.785 0.419 0.143 0.039 78 7.3 V2_exvivo 587 366 955 2.230 0.430 0.105 0.025 7 0.6 MT_exvivo 267 152 413 2.584 0.666 0.118 0.043 4 0.4 perirhinal_exvivo 331 212 725 2.581 0.641 0.098 0.024 2 0.3 entorhinal_exvivo @#@FSTIME 2022:09:05:21:50:42 mris_anatomical_stats N 12 e 5.88 S 0.30 U 5.54 P 99% M 532668 F 0 R 146229 W 0 c 505 w 1 I 0 O 24 L 1.18 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:50:48 mris_anatomical_stats N 12 1.16 1.18 1.18 #-------------------------------------------- #@# BA_exvivo Labels rh Mon Sep 5 21:50:48 UTC 2022 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 270 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4232 mri_label2label: Done @#@FSTIME 2022:09:05:21:50:48 mri_label2label N 12 e 6.69 S 0.44 U 6.04 P 96% M 567236 F 0 R 162523 W 0 c 79 w 55 I 16160 O 272 L 1.16 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:50:55 mri_label2label N 12 1.15 1.17 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 321 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7008 mri_label2label: Done @#@FSTIME 2022:09:05:21:50:55 mri_label2label N 12 e 7.44 S 0.51 U 6.91 P 99% M 567348 F 0 R 162572 W 0 c 26 w 3 I 520 O 424 L 1.15 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:51:02 mri_label2label N 12 1.13 1.17 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4072 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:02 mri_label2label N 12 e 6.89 S 0.43 U 6.44 P 99% M 567364 F 0 R 162527 W 0 c 34 w 3 I 312 O 240 L 1.13 1.17 1.17 @#@FSLOADPOST 2022:09:05:21:51:09 mri_label2label N 12 1.12 1.16 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 233 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4755 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:09 mri_label2label N 12 e 5.74 S 0.31 U 5.36 P 98% M 567332 F 0 R 162539 W 0 c 577 w 3 I 352 O 304 L 1.12 1.16 1.17 @#@FSLOADPOST 2022:09:05:21:51:15 mri_label2label N 12 1.11 1.16 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 341 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6088 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:15 mri_label2label N 12 e 5.80 S 0.33 U 5.44 P 99% M 567376 F 0 R 162560 W 0 c 280 w 3 I 440 O 384 L 1.11 1.16 1.17 @#@FSLOADPOST 2022:09:05:21:51:21 mri_label2label N 12 1.10 1.16 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4612 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:21 mri_label2label N 12 e 5.51 S 0.29 U 5.20 P 99% M 567404 F 0 R 162538 W 0 c 320 w 3 I 344 O 280 L 1.10 1.16 1.17 @#@FSLOADPOST 2022:09:05:21:51:26 mri_label2label N 12 1.23 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 1742 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13998 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:26 mri_label2label N 12 e 8.18 S 0.28 U 7.87 P 99% M 567916 F 0 R 162681 W 0 c 253 w 4 I 936 O 992 L 1.23 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:51:34 mri_label2label N 12 1.21 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 343 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7255 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:34 mri_label2label N 12 e 6.09 S 0.32 U 5.72 P 99% M 567428 F 0 R 162581 W 0 c 461 w 3 I 528 O 456 L 1.21 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:51:41 mri_label2label N 12 1.19 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 540 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5895 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:41 mri_label2label N 12 e 5.68 S 0.33 U 5.33 P 99% M 567416 F 0 R 162556 W 0 c 38 w 5 I 416 O 408 L 1.19 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:51:46 mri_label2label N 12 1.16 1.17 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 1789 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6516 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:46 mri_label2label N 12 e 5.63 S 0.30 U 5.31 P 99% M 567476 F 0 R 162554 W 0 c 32 w 3 I 376 O 536 L 1.16 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:51:52 mri_label2label N 12 1.15 1.17 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 2853 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10869 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:52 mri_label2label N 12 e 6.88 S 0.25 U 6.57 P 99% M 567812 F 0 R 162621 W 0 c 690 w 3 I 640 O 888 L 1.15 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:51:59 mri_label2label N 12 1.14 1.17 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 362 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2294 mri_label2label: Done @#@FSTIME 2022:09:05:21:51:59 mri_label2label N 12 e 5.51 S 0.28 U 5.13 P 98% M 567080 F 0 R 162489 W 0 c 416 w 3 I 160 O 184 L 1.14 1.17 1.17 @#@FSLOADPOST 2022:09:05:21:52:05 mri_label2label N 12 1.21 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1045 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:05 mri_label2label N 12 e 5.01 S 0.32 U 4.66 P 99% M 567016 F 0 R 162469 W 0 c 23 w 4 I 96 O 56 L 1.21 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:52:10 mri_label2label N 12 1.19 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject P7T_020_001bc --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 755 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:10 mri_label2label N 12 e 5.08 S 0.27 U 4.79 P 99% M 567132 F 0 R 162473 W 0 c 287 w 4 I 72 O 40 L 1.19 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:52:15 mri_label2label N 12 1.18 1.17 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 702 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:15 mri_label2label N 12 e 4.96 S 0.31 U 4.62 P 99% M 567160 F 0 R 166071 W 0 c 380 w 4 I 56 O 64 L 1.18 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:52:20 mri_label2label N 12 1.16 1.17 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 198 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 919 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:20 mri_label2label N 12 e 5.01 S 0.34 U 4.66 P 99% M 567096 F 0 R 166069 W 0 c 24 w 4 I 72 O 80 L 1.16 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:52:25 mri_label2label N 12 1.15 1.17 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 145 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1668 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:25 mri_label2label N 12 e 5.09 S 0.33 U 4.74 P 99% M 567020 F 0 R 162477 W 0 c 177 w 4 I 144 O 128 L 1.15 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:52:30 mri_label2label N 12 1.14 1.16 1.17 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1655 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:30 mri_label2label N 12 e 6.63 S 0.46 U 6.15 P 99% M 566984 F 0 R 162483 W 0 c 66 w 3 I 152 O 112 L 1.14 1.16 1.17 @#@FSLOADPOST 2022:09:05:21:52:37 mri_label2label N 12 1.19 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 1319 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4986 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:37 mri_label2label N 12 e 5.49 S 0.35 U 5.10 P 99% M 567376 F 0 R 162535 W 0 c 113 w 4 I 328 O 408 L 1.19 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:52:42 mri_label2label N 12 1.17 1.17 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 1074 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3793 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:42 mri_label2label N 12 e 5.31 S 0.33 U 4.97 P 99% M 567112 F 0 R 166118 W 0 c 300 w 3 I 248 O 312 L 1.17 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:52:48 mri_label2label N 12 1.16 1.17 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 599 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1827 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:48 mri_label2label N 12 e 5.48 S 0.35 U 5.07 P 98% M 567056 F 0 R 166090 W 0 c 378 w 4 I 112 O 160 L 1.16 1.17 1.18 @#@FSLOADPOST 2022:09:05:21:52:53 mri_label2label N 12 1.39 1.22 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject P7T_020_001bc --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 425 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1450 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:53 mri_label2label N 12 e 5.09 S 0.25 U 4.83 P 99% M 566876 F 0 R 162473 W 0 c 61 w 4 I 96 O 128 L 1.39 1.22 1.19 @#@FSLOADPOST 2022:09:05:21:52:58 mri_label2label N 12 1.36 1.21 1.19 mris_label2annot --s P7T_020_001bc --ctab /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average/colortable_vpnl.txt Number of ctab entries 9 7.2.0 cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label cmdline mris_label2annot --s P7T_020_001bc --ctab /home/marcantf/software/freesurfer/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 mrphys-gpu1 machine x86_64 user marcantf subject P7T_020_001bc hemi rh SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects ColorTable /home/marcantf/software/freesurfer/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 124601 unhit vertices Writing annot to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.mpm.vpnl.annot @#@FSTIME 2022:09:05:21:52:58 mris_label2annot N 26 e 0.87 S 0.09 U 0.78 P 100% M 163316 F 0 R 44642 W 0 c 3 w 1 I 0 O 2200 L 1.36 1.21 1.19 @#@FSLOADPOST 2022:09:05:21:52:59 mris_label2annot N 26 1.36 1.21 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 924 mri_label2label: Done @#@FSTIME 2022:09:05:21:52:59 mri_label2label N 12 e 5.16 S 0.33 U 4.78 P 99% M 566940 F 0 R 162471 W 0 c 460 w 3 I 80 O 64 L 1.36 1.21 1.19 @#@FSLOADPOST 2022:09:05:21:53:04 mri_label2label N 12 1.33 1.21 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2751 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:04 mri_label2label N 12 e 5.31 S 0.30 U 5.00 P 99% M 567136 F 0 R 162502 W 0 c 56 w 3 I 240 O 160 L 1.33 1.21 1.19 @#@FSLOADPOST 2022:09:05:21:53:10 mri_label2label N 12 1.30 1.21 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1716 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:10 mri_label2label N 12 e 5.46 S 0.32 U 5.11 P 99% M 567104 F 0 R 162487 W 0 c 341 w 4 I 152 O 96 L 1.30 1.21 1.19 @#@FSLOADPOST 2022:09:05:21:53:15 mri_label2label N 12 1.36 1.22 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2290 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:15 mri_label2label N 12 e 5.19 S 0.29 U 4.88 P 99% M 567068 F 0 R 162496 W 0 c 108 w 3 I 192 O 152 L 1.36 1.22 1.19 @#@FSLOADPOST 2022:09:05:21:53:21 mri_label2label N 12 1.33 1.22 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1528 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:21 mri_label2label N 12 e 5.10 S 0.25 U 4.83 P 99% M 567060 F 0 R 162478 W 0 c 90 w 4 I 120 O 104 L 1.33 1.22 1.19 @#@FSLOADPOST 2022:09:05:21:53:26 mri_label2label N 12 1.30 1.21 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1538 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:26 mri_label2label N 12 e 5.08 S 0.30 U 4.75 P 99% M 567208 F 0 R 166089 W 0 c 309 w 4 I 136 O 104 L 1.30 1.21 1.19 @#@FSLOADPOST 2022:09:05:21:53:31 mri_label2label N 12 1.28 1.21 1.19 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 827 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7786 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:31 mri_label2label N 12 e 6.11 S 0.32 U 5.76 P 99% M 567492 F 0 R 162588 W 0 c 12 w 3 I 592 O 536 L 1.25 1.20 1.19 @#@FSLOADPOST 2022:09:05:21:53:37 mri_label2label N 12 1.23 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1028 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:37 mri_label2label N 12 e 5.07 S 0.29 U 4.74 P 99% M 566988 F 0 R 162469 W 0 c 643 w 4 I 88 O 64 L 1.23 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:53:42 mri_label2label N 12 1.21 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1223 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:42 mri_label2label N 12 e 5.04 S 0.32 U 4.71 P 99% M 567080 F 0 R 162476 W 0 c 26 w 4 I 104 O 80 L 1.21 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:53:47 mri_label2label N 12 1.20 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 1197 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4429 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:47 mri_label2label N 12 e 5.42 S 0.31 U 5.10 P 99% M 567420 F 0 R 162519 W 0 c 26 w 3 I 280 O 368 L 1.20 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:53:53 mri_label2label N 12 1.18 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 1383 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4820 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:53 mri_label2label N 12 e 5.47 S 0.31 U 5.14 P 99% M 567484 F 0 R 162530 W 0 c 408 w 4 I 296 O 400 L 1.18 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:53:58 mri_label2label N 12 1.17 1.19 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 322 mri_label2label: Done @#@FSTIME 2022:09:05:21:53:58 mri_label2label N 12 e 4.91 S 0.29 U 4.60 P 99% M 566852 F 0 R 162459 W 0 c 380 w 2 I 24 O 32 L 1.17 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:54:03 mri_label2label N 12 1.15 1.18 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 701 mri_label2label: Done @#@FSTIME 2022:09:05:21:54:03 mri_label2label N 12 e 5.12 S 0.34 U 4.74 P 99% M 567056 F 0 R 166066 W 0 c 680 w 3 I 64 O 40 L 1.15 1.18 1.18 @#@FSLOADPOST 2022:09:05:21:54:08 mri_label2label N 12 1.22 1.20 1.18 mri_label2label --srcsubject fsaverage --srclabel /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject P7T_020_001bc --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/marcantf/software/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = P7T_020_001bc 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 /home/marcantf/software/freesurfer/subjects FREESURFER_HOME /home/marcantf/software/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/marcantf/software/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white Reading target registration /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 140498 Number of reverse mapping hits = 0 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 291 mri_label2label: Done @#@FSTIME 2022:09:05:21:54:08 mri_label2label N 12 e 4.94 S 0.28 U 4.66 P 99% M 566996 F 0 R 166061 W 0 c 24 w 2 I 32 O 16 L 1.22 1.20 1.18 @#@FSLOADPOST 2022:09:05:21:54:13 mri_label2label N 12 1.20 1.19 1.18 mris_label2annot --s P7T_020_001bc --hemi rh --ctab /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label cmdline mris_label2annot --s P7T_020_001bc --hemi rh --ctab /home/marcantf/software/freesurfer/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 mrphys-gpu1 machine x86_64 user marcantf subject P7T_020_001bc hemi rh SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects ColorTable /home/marcantf/software/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 95513 unhit vertices Writing annot to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.BA_exvivo.annot @#@FSTIME 2022:09:05:21:54:13 mris_label2annot N 38 e 0.94 S 0.10 U 0.83 P 99% M 163632 F 0 R 44778 W 0 c 76 w 1 I 0 O 2200 L 1.20 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:54:14 mris_label2annot N 38 1.20 1.19 1.18 mris_label2annot --s P7T_020_001bc --hemi rh --ctab /home/marcantf/software/freesurfer/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 /home/marcantf/software/freesurfer/average/colortable_BA.txt Number of ctab entries 15 7.2.0 cwd /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label cmdline mris_label2annot --s P7T_020_001bc --hemi rh --ctab /home/marcantf/software/freesurfer/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 mrphys-gpu1 machine x86_64 user marcantf subject P7T_020_001bc hemi rh SUBJECTS_DIR /home/marcantf/software/freesurfer/subjects ColorTable /home/marcantf/software/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/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 115120 unhit vertices Writing annot to /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2022:09:05:21:54:14 mris_label2annot N 38 e 0.88 S 0.08 U 0.79 P 99% M 163456 F 0 R 44704 W 0 c 48 w 1 I 0 O 2200 L 1.20 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:54:15 mris_label2annot N 38 1.20 1.19 1.18 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab P7T_020_001bc rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 206199 Total vertex volume 206050 (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) = 1009967 mm^3 (det: 1.928880 ) 1047 599 1070 1.555 0.526 0.148 0.044 18 2.1 BA1_exvivo 3382 2023 3887 1.927 0.456 0.107 0.022 31 3.1 BA2_exvivo 1143 716 963 1.718 0.289 0.117 0.027 9 1.3 BA3a_exvivo 2261 1369 2400 1.636 0.403 0.100 0.022 18 2.1 BA3b_exvivo 1805 1024 2744 2.467 0.554 0.105 0.029 15 2.6 BA4a_exvivo 1370 837 2106 2.558 0.394 0.088 0.016 6 1.0 BA4p_exvivo 10457 6478 16535 2.350 0.592 0.117 0.029 103 13.2 BA6_exvivo 3502 2301 6238 2.414 0.426 0.114 0.026 40 3.7 BA44_exvivo 4017 2680 7134 2.266 0.452 0.122 0.026 49 4.2 BA45_exvivo 4461 3090 7000 2.020 0.492 0.140 0.041 85 7.0 V1_exvivo 8770 5954 12164 1.906 0.432 0.144 0.036 127 12.5 V2_exvivo 2109 1415 2966 1.981 0.329 0.128 0.026 23 2.4 MT_exvivo 247 167 459 2.507 0.425 0.104 0.023 2 0.2 perirhinal_exvivo 414 289 1129 2.581 0.777 0.118 0.038 4 0.7 entorhinal_exvivo @#@FSTIME 2022:09:05:21:54:15 mris_anatomical_stats N 12 e 5.53 S 0.36 U 5.17 P 99% M 513280 F 0 R 151490 W 0 c 49 w 1 I 0 O 24 L 1.20 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:54:21 mris_anatomical_stats N 12 1.17 1.19 1.18 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab P7T_020_001bc rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/mri/wm.mgz... reading input surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white... reading input pial surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.pial... reading input white surface /home/marcantf/software/freesurfer/subjects/P7T_020_001bc/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 206199 Total vertex volume 206050 (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) = 1009967 mm^3 (det: 1.928880 ) 652 360 663 1.572 0.413 0.132 0.039 9 1.1 BA1_exvivo 1852 1079 2308 1.989 0.456 0.093 0.021 15 1.6 BA2_exvivo 1052 662 844 1.714 0.296 0.122 0.027 8 1.2 BA3a_exvivo 1767 1086 1713 1.581 0.272 0.091 0.017 12 1.4 BA3b_exvivo 1153 626 1942 2.585 0.563 0.120 0.037 15 2.0 BA4a_exvivo 1168 711 1782 2.579 0.406 0.086 0.015 5 0.9 BA4p_exvivo 6412 3936 9765 2.354 0.581 0.116 0.028 63 7.9 BA6_exvivo 722 503 1404 2.469 0.377 0.123 0.027 8 0.8 BA44_exvivo 902 622 1931 2.422 0.416 0.115 0.027 11 0.9 BA45_exvivo 4270 2929 6569 2.020 0.490 0.135 0.040 76 6.4 V1_exvivo 4694 3299 6847 1.877 0.430 0.160 0.044 84 8.1 V2_exvivo 306 222 579 2.072 0.389 0.168 0.039 5 0.6 MT_exvivo 20 11 25 2.387 0.240 0.081 0.014 0 0.0 perirhinal_exvivo 408 275 1032 2.655 0.573 0.101 0.026 3 0.4 entorhinal_exvivo @#@FSTIME 2022:09:05:21:54:21 mris_anatomical_stats N 12 e 5.53 S 0.27 U 5.25 P 99% M 513340 F 0 R 144384 W 0 c 95 w 1 I 0 O 24 L 1.17 1.19 1.18 @#@FSLOADPOST 2022:09:05:21:54:27 mris_anatomical_stats N 12 1.16 1.18 1.18 Started at Mon Sep 5 12:42:55 UTC 2022 Ended at Mon Sep 5 21:54:27 UTC 2022 #@#%# recon-all-run-time-hours 9.192 recon-all -s P7T_020_001bc finished without error at Mon Sep 5 21:54:27 UTC 2022