Wed May 27 09:19:07 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/recon-all -i /data/pt_02904/Diffusion/surface_segmentation/input/sub-20/ses-0/sub-20_ses-0_T1w_MPRAGE.nii.gz -s sub-20_ses-0 -sd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 -all subjid sub-20_ses-0 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Actual FREESURFER_HOME /software/freesurfer/7.4.1/debian-bullseye-amd64 build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 Linux silbermond 6.1.0-45-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.170-1 (2026-04-30) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1541529 maxlocks unlimited maxsignal 1541529 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 376Gi 9.2Gi 354Gi 18Mi 15Gi 367Gi Swap: 9.3Gi 0B 9.3Gi ######################################## program versions used 7.4.1 (freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.4.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.4.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/05/27-19:19:07-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: flores Machine: silbermond Platform: Linux PlatformVersion: 6.1.0-45-amd64 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 /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0 mri_convert /data/pt_02904/Diffusion/surface_segmentation/input/sub-20/ses-0/sub-20_ses-0_T1w_MPRAGE.nii.gz /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig/001.mgz mri_convert /data/pt_02904/Diffusion/surface_segmentation/input/sub-20/ses-0/sub-20_ses-0_T1w_MPRAGE.nii.gz /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig/001.mgz reading from /data/pt_02904/Diffusion/surface_segmentation/input/sub-20/ses-0/sub-20_ses-0_T1w_MPRAGE.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig/001.mgz... @#@FSTIME 2026:05:27:21:19:07 mri_convert N 2 e 3.14 S 0.01 U 3.07 P 98% M 28388 F 0 R 653 W 0 c 6 w 69 I 15312 O 15232 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:27:21:19:11 mri_convert N 2 12.00 12.00 12.00 #-------------------------------------------- #@# MotionCor Wed May 27 09:19:11 PM CEST 2026 Found 1 runs /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig/001.mgz /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz mri_info /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz type: MGH dimensions: 176 x 240 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -88.0, xend: 88.0 ystart: -120.0, yend: 120.0 zstart: -128.0, zend: 128.0 TR: 2300.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 30.0018 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.9306 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1.0000 0.0000 0.0000 -87.5000 0.0000 1.0000 0.0000 -89.9982 0.0000 0.0000 1.0000 -128.9306 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 1.0000 0.0000 0.0000 87.5000 0.0000 1.0000 0.0000 89.9982 0.0000 0.0000 1.0000 128.9306 0.0000 0.0000 0.0000 1.0000 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0 mri_convert /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz --conform mri_convert /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz --conform reading from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 667 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz... @#@FSTIME 2026:05:27:21:19:15 mri_convert N 3 e 5.10 S 0.04 U 5.04 P 99% M 39096 F 0 R 5923 W 0 c 31 w 128 I 0 O 11800 L 11.92 11.99 11.99 @#@FSLOADPOST 2026:05:27:21:19:20 mri_convert N 3 11.93 11.99 12.00 mri_add_xform_to_header -c /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/transforms/talairach.xfm /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2026:05:27:21:19:20 mri_add_xform_to_header N 4 e 1.71 S 0.01 U 1.68 P 98% M 23352 F 0 R 494 W 0 c 11 w 129 I 11800 O 11800 L 11.93 11.99 12.00 @#@FSLOADPOST 2026:05:27:21:19:22 mri_add_xform_to_header N 4 11.93 11.99 12.00 mri_info /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz orig.mgz ======================================== Volume information for /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2300.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 30.0018 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.9306 talairach xfm : /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 128.5000 0.0000 0.0000 1.0000 -97.9982 0.0000 -1.0000 0.0000 127.0694 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 128.5000 -0.0000 -0.0000 -1.0000 127.0694 -0.0000 1.0000 -0.0000 97.9982 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Wed May 27 09:19:22 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /bin/bc /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 Linux silbermond 6.1.0-45-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.170-1 (2026-04-30) x86_64 GNU/Linux Wed May 27 09:19:22 PM CEST 2026 tmpdir is ./tmp.mri_nu_correct.mni.207473 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.207473/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.207473/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.207473/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.207473/nu0.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Wed May 27 09:24:45 PM CEST 2026 mri_nu_correct.mni done @#@FSTIME 2026:05:27:21:19:22 mri_nu_correct.mni N 12 e 323.26 S 0.27 U 322.91 P 99% M 519496 F 0 R 20558 W 0 c 796 w 343 I 11320 O 22776 L 11.93 11.99 12.00 @#@FSLOADPOST 2026:05:27:21:24:45 mri_nu_correct.mni N 12 12.06 12.01 12.00 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Wed May 27 09:24:45 PM CEST 2026 Ended at Wed May 27 09:25:20 PM CEST 2026 talairach_avi done @#@FSTIME 2026:05:27:21:24:45 talairach_avi N 4 e 34.66 S 1.21 U 26.94 P 81% M 255376 F 0 R 31546 W 0 c 79 w 2637 I 175160 O 296032 L 12.06 12.01 12.00 @#@FSLOADPOST 2026:05:27:21:25:20 talairach_avi N 4 12.03 12.01 12.00 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /software/freesurfer/7.4.1/debian-bookworm-amd64/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.4.1 --src: orig.mgz src image (geometry). --trg: /software/freesurfer/7.4.1/debian-bookworm-amd64/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 1.05291 -0.02685 -0.00398 -0.70178; 0.06463 1.01834 0.24453 -34.33842; -0.03821 -0.27898 1.08628 -4.96341; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Wed May 27 09:25:22 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7531, pval=0.6675 >= threshold=0.0050) @#@FSTIME 2026:05:27:21:25:22 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 57% M 5840 F 0 R 235 W 0 c 0 w 13 I 0 O 0 L 12.03 12.01 12.00 @#@FSLOADPOST 2026:05:27:21:25:22 talairach_afd N 4 12.03 12.01 12.00 awk -f /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/extract_talairach_avi_QA.awk /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/transforms/talairach_avi.log tal_QC_AZS /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/transforms/talairach_avi.log TalAviQA: 0.97715 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed May 27 09:25:22 PM CEST 2026 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /bin/bc /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.4.1 Linux silbermond 6.1.0-45-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.170-1 (2026-04-30) x86_64 GNU/Linux Wed May 27 09:25:22 PM CEST 2026 tmpdir is ./tmp.mri_nu_correct.mni.211252 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.211252/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.211252/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.211252/ones.mgz 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.211252/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.211252/ones.mgz sysname Linux hostname silbermond machine x86_64 user flores input ./tmp.mri_nu_correct.mni.211252/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.211252/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.211252/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.211252/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.211252/sum.junk --avgwf ./tmp.mri_nu_correct.mni.211252/input.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.211252/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.211252/sum.junk --avgwf ./tmp.mri_nu_correct.mni.211252/input.mean.dat sysname Linux hostname silbermond machine x86_64 user flores whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.211252/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.211252/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.211252/ones.mgz --i ./tmp.mri_nu_correct.mni.211252/nu0.mgz --sum ./tmp.mri_nu_correct.mni.211252/sum.junk --avgwf ./tmp.mri_nu_correct.mni.211252/output.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.211252/ones.mgz --i ./tmp.mri_nu_correct.mni.211252/nu0.mgz --sum ./tmp.mri_nu_correct.mni.211252/sum.junk --avgwf ./tmp.mri_nu_correct.mni.211252/output.mean.dat sysname Linux hostname silbermond machine x86_64 user flores whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.211252/ones.mgz Loading ./tmp.mri_nu_correct.mni.211252/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.211252/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.211252/nu0.mgz ./tmp.mri_nu_correct.mni.211252/nu0.mgz mul 1.16887778927390105861 Saving result to './tmp.mri_nu_correct.mni.211252/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.211252/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.211252/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.211252/nu0.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 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 9 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 2, i2 = 53 #mri_make_uchar# mapping 5 137 to 3 110 : b -1.66373 m 0.817958 : thresh 2.034 maxsat 313.786 : nzero 9663815 nsat 0 Wed May 27 09:31:22 PM CEST 2026 mri_nu_correct.mni done @#@FSTIME 2026:05:27:21:25:22 mri_nu_correct.mni N 9 e 360.25 S 1.08 U 359.10 P 99% M 614168 F 0 R 167881 W 0 c 379 w 898 I 46648 O 56008 L 12.03 12.01 12.00 @#@FSLOADPOST 2026:05:27:21:31:22 mri_nu_correct.mni N 9 11.94 11.98 11.99 mri_add_xform_to_header -c /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2026:05:27:21:31:23 mri_add_xform_to_header N 4 e 1.11 S 0.02 U 1.07 P 98% M 23416 F 0 R 496 W 0 c 4 w 139 I 8960 O 8960 L 11.94 11.98 11.99 @#@FSLOADPOST 2026:05:27:21:31:24 mri_add_xform_to_header N 4 11.95 11.98 11.99 #-------------------------------------------- #@# Intensity Normalization Wed May 27 09:31:24 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.05291 -0.02685 -0.00398 -0.70178; 0.06463 1.01834 0.24453 -34.33842; -0.03821 -0.27898 1.08628 -4.96341; 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 = 21 Starting OpenSpline(): npoints = 21 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 64 (64), valley at 43 (43) csf peak at 32, setting threshold to 53 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 66 (66), valley at 43 (43) csf peak at 34, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 42 seconds. @#@FSTIME 2026:05:27:21:31:24 mri_normalize N 7 e 163.29 S 0.30 U 162.97 P 99% M 585828 F 0 R 11565 W 0 c 147 w 133 I 8960 O 8640 L 11.95 11.98 11.99 @#@FSLOADPOST 2026:05:27:21:34:07 mri_normalize N 7 12.04 12.01 12.00 #-------------------------------------------- #@# Skull Stripping Wed May 27 09:34:07 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_em_register -skull nu.mgz /software/freesurfer/7.4.1/debian-bookworm-amd64/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 '/software/freesurfer/7.4.1/debian-bookworm-amd64/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 2 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=7.0 skull bounding box = (50, 37, 14) --> (206, 255, 213) finding center of left hemi white matter using (102, 110, 114) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (83,83,89) --> (121, 136,138) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 108 +- 5.2 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.295 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.294552 @ (0.000, 0.000, 0.000) max log p = -4.277734 @ (-5.263, 5.263, -5.263) max log p = -4.203688 @ (2.632, -2.632, 2.632) max log p = -4.170557 @ (1.316, -1.316, -3.947) max log p = -4.160554 @ (0.658, 0.658, 0.658) max log p = -4.138567 @ (0.329, 2.961, 2.961) max log p = -4.138567 @ (0.000, 0.000, 0.000) max log p = -4.138567 @ (0.000, 0.000, 0.000) Found translation: (-0.3, 4.9, -3.0): log p = -4.139 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.999, old_max_log_p =-4.139 (thresh=-4.1) 1.06375 0.00000 0.00000 -8.32520; 0.00000 1.03837 0.27823 -24.58315; 0.00000 -0.27532 1.02750 31.66764; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 24 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.888, old_max_log_p =-3.999 (thresh=-4.0) 1.06375 0.00000 0.00000 -8.32520; 0.00000 1.21985 0.18311 -37.57032; 0.00000 -0.10832 0.98094 15.11435; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 24 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.888, old_max_log_p =-3.888 (thresh=-3.9) 1.06375 0.00000 0.00000 -8.32520; 0.00000 1.21985 0.18311 -37.57032; 0.00000 -0.10832 0.98094 15.11435; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 2 minutes and 25 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.824, old_max_log_p =-3.888 (thresh=-3.9) 1.08080 0.07409 0.04988 -25.72988; -0.06696 1.16228 0.23711 -27.72684; -0.03408 -0.19370 0.98327 28.38912; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 17 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.824, old_max_log_p =-3.824 (thresh=-3.8) 1.08080 0.07409 0.04988 -25.72988; -0.06696 1.16228 0.23711 -27.72684; -0.03408 -0.19370 0.98327 28.38912; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 2 minutes and 11 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.787, old_max_log_p =-3.824 (thresh=-3.8) 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 59 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.787, old_max_log_p =-3.787 (thresh=-3.8) 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 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: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.787 (old=-4.295) transform before final EM align: 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.2 tol 0.000000 final transform: 1.08326 0.05693 0.03774 -22.88961; -0.04982 1.16001 0.25395 -32.44095; -0.02421 -0.21273 0.98189 29.78332; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 784172 FSRUNTIME@ mri_em_register 0.2910 hours 1 threads registration took 17 minutes and 28 seconds. @#@FSTIME 2026:05:27:21:34:07 mri_em_register N 4 e 1047.70 S 1.07 U 1046.60 P 99% M 630904 F 0 R 117649 W 0 c 341 w 45 I 0 O 32 L 12.04 12.01 12.00 @#@FSLOADPOST 2026:05:27:21:51:35 mri_em_register N 4 12.00 12.00 12.00 mri_watershed -T1 -brain_atlas /software/freesurfer/7.4.1/debian-bookworm-amd64/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=110 z=111 r=84 first estimation of the main basin volume: 2499116 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=110, y=96, z=70, Imax=255 CSF=17, 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=14112425740 voxels, voxel volume =1.000 = 14112425740 mmm3 = 14112425.984 cm3 done. PostAnalyze...Basin Prior 105 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=114, z=105, r=9353 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 45234 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=11 , nb = 3024 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = 3276 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=22 , nb = 19620 LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=20 , nb = 18792 OTHER CSF_MIN=0, CSF_intensity=13, CSF_MAX=26 , nb = 522 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 21, 35, 47, 63 after analyzing : 21, 43, 47, 48 RIGHT_CER before analyzing : 11, 20, 44, 67 after analyzing : 11, 36, 44, 43 LEFT_CER before analyzing : 10, 16, 39, 65 after analyzing : 10, 31, 39, 39 RIGHT_BRAIN before analyzing : 22, 33, 45, 63 after analyzing : 22, 41, 45, 46 LEFT_BRAIN before analyzing : 20, 33, 47, 64 after analyzing : 20, 42, 47, 47 OTHER before analyzing : 26, 22, 7, 61 after analyzing : 22, 24, 25, 33 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 69.859, std = 7.900 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.42, sigma = 4.07 after rotation: sse = 2.42, sigma = 4.07 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.48, its var is 3.62 before Erosion-Dilatation 0.30% 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...44 iterations mri_strip_skull: done peeling brain Brain Size = 1690144 voxels, voxel volume = 1.000 mm3 = 1690144 mmm3 = 1690.144 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed done @#@FSTIME 2026:05:27:21:51:35 mri_watershed N 6 e 25.83 S 0.72 U 25.10 P 99% M 822080 F 0 R 189463 W 0 c 60 w 63 I 8640 O 2704 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:27:21:52:01 mri_watershed N 6 12.00 12.00 12.00 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed May 27 09:52:02 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /software/freesurfer/7.4.1/debian-bookworm-amd64/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 '/software/freesurfer/7.4.1/debian-bookworm-amd64/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (60, 52, 26) --> (195, 197, 192) finding center of left hemi white matter using (105, 100, 109) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (88,82,89) --> (121, 117,129) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 108 +- 4.6 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -3.955 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.923901 @ (0.000, 0.000, 0.000) max log p = -3.798784 @ (-5.263, 5.263, -5.263) max log p = -3.678796 @ (2.632, 2.632, 2.632) max log p = -3.660171 @ (3.947, -1.316, -1.316) max log p = -3.660171 @ (0.000, 0.000, 0.000) max log p = -3.660171 @ (0.000, 0.000, 0.000) max log p = -3.660171 @ (0.000, 0.000, 0.000) max log p = -3.660171 @ (0.000, 0.000, 0.000) Found translation: (1.3, 6.6, -3.9): log p = -3.660 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.573, old_max_log_p =-3.660 (thresh=-3.7) 1.00000 0.00000 0.00000 1.31579; 0.00000 1.04996 0.15634 -16.15105; 0.00000 -0.11161 0.99651 9.01428; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 6 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.559, old_max_log_p =-3.573 (thresh=-3.6) 1.07500 0.00000 0.00000 -8.09570; 0.00000 1.12871 0.16807 -26.30916; 0.00000 -0.10324 0.92177 16.24477; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 5 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.559, old_max_log_p =-3.559 (thresh=-3.6) 1.07500 0.00000 0.00000 -8.09570; 0.00000 1.12871 0.16807 -26.30916; 0.00000 -0.10324 0.92177 16.24477; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 2 minutes and 5 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.401, old_max_log_p =-3.559 (thresh=-3.6) 1.07442 -0.03524 -0.00733 -5.12306; 0.03517 1.07647 0.22385 -31.05856; 0.00000 -0.17794 0.94371 24.13932; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 3 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.401, old_max_log_p =-3.401 (thresh=-3.4) 1.07442 -0.03524 -0.00733 -5.12306; 0.03517 1.07647 0.22385 -31.05856; 0.00000 -0.17794 0.94371 24.13932; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 2 minutes and 3 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.358, old_max_log_p =-3.401 (thresh=-3.4) 1.07820 -0.03536 -0.00735 -6.52581; 0.03504 1.07545 0.20764 -28.24871; 0.00058 -0.16030 0.94725 21.69023; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 49 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.358, old_max_log_p =-3.358 (thresh=-3.4) 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 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: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.358 (old=-3.955) transform before final EM align: 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 771616 FSRUNTIME@ mri_em_register 0.2575 hours 1 threads registration took 15 minutes and 27 seconds. @#@FSTIME 2026:05:27:21:52:02 mri_em_register N 7 e 927.22 S 1.05 U 926.13 P 99% M 618432 F 0 R 113103 W 0 c 1104 w 35 I 2704 O 32 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:27:22:07:29 mri_em_register N 7 12.08 12.04 12.02 #-------------------------------------- #@# CA Normalize Wed May 27 10:07:29 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /software/freesurfer/7.4.1/debian-bookworm-amd64/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 '/software/freesurfer/7.4.1/debian-bookworm-amd64/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=22.0 skull bounding box = (60, 52, 26) --> (195, 197, 192) finding center of left hemi white matter using (105, 100, 109) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (88,82,89) --> (121, 117,129) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 108 +- 4.6 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246437 sample points... INFO: compute sample coordinates transform 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 50, 27) --> (189, 157, 200) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 3659 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 52, 26) --> (129, 157, 200) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 6 of 3381 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 131, 55) --> (175, 174, 111) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 37 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 131, 52) --> (129, 174, 112) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 13 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 122, 92) --> (145, 187, 123) Brain_Stem: limiting intensities to 94.0 --> 132.0 0 of 14 (0.0%) samples deleted using 7104 total control points for intensity normalization... bias field = 0.985 +- 0.038 54 of 7098 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 50, 27) --> (189, 157, 200) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 3967 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 52, 26) --> (129, 157, 200) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 9 of 3670 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 131, 55) --> (175, 174, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 67 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 131, 52) --> (129, 174, 112) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 85 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 122, 92) --> (145, 187, 123) Brain_Stem: limiting intensities to 88.0 --> 132.0 3 of 106 (2.8%) samples deleted using 7895 total control points for intensity normalization... bias field = 1.024 +- 0.044 88 of 7825 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 50, 27) --> (189, 157, 200) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 3942 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 52, 26) --> (129, 157, 200) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 12 of 3681 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 131, 55) --> (175, 174, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 94 (6.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 131, 52) --> (129, 174, 112) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 21 of 120 (17.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 122, 92) --> (145, 187, 123) Brain_Stem: limiting intensities to 88.0 --> 132.0 40 of 187 (21.4%) samples deleted using 8024 total control points for intensity normalization... bias field = 1.024 +- 0.041 60 of 7796 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 51 seconds. @#@FSTIME 2026:05:27:22:07:29 mri_ca_normalize N 8 e 110.78 S 0.68 U 110.09 P 99% M 904228 F 0 R 136860 W 0 c 190 w 57 I 0 O 3944 L 12.08 12.04 12.02 @#@FSLOADPOST 2026:05:27:22:09:20 mri_ca_normalize N 8 12.01 12.03 12.01 #-------------------------------------- #@# CA Reg Wed May 27 10:09:20 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /software/freesurfer/7.4.1/debian-bookworm-amd64/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 '/software/freesurfer/7.4.1/debian-bookworm-amd64/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 0.902483 #GCAMreg# pass 0 level1 5 level2 1 tsec 568.635 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 0.689861 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 0.702834 #GCAMreg# pass 0 level1 4 level2 1 tsec 249.205 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 0.674405 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 0.714404 #GCAMreg# pass 0 level1 3 level2 1 tsec 64.323 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 0.714373 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 0.826894 #GCAMreg# pass 0 level1 2 level2 1 tsec 97.807 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 0.79045 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 0.886222 #GCAMreg# pass 0 level1 1 level2 1 tsec 229.55 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 0.851803 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 0.800043 #GCAMreg# pass 0 level1 0 level2 1 tsec 66.787 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 0.79452 GCAMregister done in 28.4563 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.13293 (21) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (1257 voxels, overlap=0.743) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (1257 voxels, peak = 16), gca=15.6 gca peak = 0.17690 (16) mri peak = 0.12371 (21) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (594 voxels, overlap=0.905) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (594 voxels, peak = 18), gca=17.5 gca peak = 0.28275 (96) mri peak = 0.10800 (77) Right_Pallidum (52): linear fit = 0.80 x + 0.0 (638 voxels, overlap=0.096) Right_Pallidum (52): linear fit = 0.80 x + 0.0 (638 voxels, peak = 76), gca=76.3 gca peak = 0.18948 (93) mri peak = 0.08786 (98) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (640 voxels, overlap=0.953) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (640 voxels, peak = 96), gca=96.3 gca peak = 0.20755 (55) mri peak = 0.09273 (63) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (550 voxels, overlap=0.234) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (550 voxels, peak = 62), gca=62.4 gca peak = 0.31831 (58) mri peak = 0.08154 (66) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (608 voxels, overlap=0.623) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (608 voxels, peak = 65), gca=64.7 gca peak = 0.11957 (102) mri peak = 0.14035 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57671 voxels, overlap=0.576) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57671 voxels, peak = 106), gca=105.6 gca peak = 0.11429 (102) mri peak = 0.14837 (105) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (59737 voxels, overlap=0.597) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (59737 voxels, peak = 105), gca=104.5 gca peak = 0.14521 (59) mri peak = 0.04831 (63) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (17877 voxels, overlap=0.976) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (17877 voxels, peak = 63), gca=63.4 gca peak = 0.14336 (58) mri peak = 0.05772 (63) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (16051 voxels, overlap=0.956) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (16051 voxels, peak = 62), gca=62.4 gca peak = 0.13305 (70) mri peak = 0.09834 (74) Right_Caudate (50): linear fit = 1.12 x + 0.0 (856 voxels, overlap=0.457) Right_Caudate (50): linear fit = 1.12 x + 0.0 (856 voxels, peak = 78), gca=78.1 gca peak = 0.15761 (71) mri peak = 0.18831 (79) Left_Caudate (11): linear fit = 1.05 x + 0.0 (1038 voxels, overlap=0.643) Left_Caudate (11): linear fit = 1.05 x + 0.0 (1038 voxels, peak = 75), gca=74.9 gca peak = 0.13537 (57) mri peak = 0.03724 (57) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (15387 voxels, overlap=0.941) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (15387 voxels, peak = 60), gca=59.6 gca peak = 0.13487 (56) mri peak = 0.04347 (62) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (19828 voxels, overlap=0.847) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (19828 voxels, peak = 62), gca=62.4 gca peak = 0.19040 (84) mri peak = 0.08288 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7352 voxels, overlap=0.306) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7352 voxels, peak = 91), gca=91.1 gca peak = 0.18871 (83) mri peak = 0.08852 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7402 voxels, overlap=0.193) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7402 voxels, peak = 90), gca=90.1 gca peak = 0.24248 (57) mri peak = 0.08093 (73) Left_Amygdala (18): linear fit = 1.21 x + 0.0 (427 voxels, overlap=0.257) Left_Amygdala (18): linear fit = 1.21 x + 0.0 (427 voxels, peak = 69), gca=68.7 gca peak = 0.35833 (56) mri peak = 0.06557 (68) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (522 voxels, overlap=0.305) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (522 voxels, peak = 67), gca=67.5 gca peak = 0.12897 (85) mri peak = 0.05802 (98) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (5346 voxels, overlap=0.783) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (5346 voxels, peak = 91), gca=90.5 gca peak = 0.13127 (83) mri peak = 0.06017 (98) Right_Thalamus (49): linear fit = 1.17 x + 0.0 (4346 voxels, overlap=0.545) Right_Thalamus (49): linear fit = 1.17 x + 0.0 (4346 voxels, peak = 98), gca=97.5 gca peak = 0.12974 (78) mri peak = 0.08193 (84) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2340 voxels, overlap=0.770) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2340 voxels, peak = 85), gca=85.4 gca peak = 0.17796 (79) mri peak = 0.06924 (79) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2056 voxels, overlap=0.862) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2056 voxels, peak = 83), gca=82.6 gca peak = 0.10999 (80) mri peak = 0.06917 (91) Brain_Stem (16): linear fit = 1.14 x + 0.0 (11743 voxels, overlap=0.210) Brain_Stem (16): linear fit = 1.14 x + 0.0 (11743 voxels, peak = 92), gca=91.6 gca peak = 0.13215 (88) mri peak = 0.09827 (95) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (885 voxels, overlap=0.246) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (885 voxels, peak = 100), gca=99.9 gca peak = 0.11941 (89) mri peak = 0.07630 (95) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1075 voxels, overlap=0.364) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1075 voxels, peak = 97), gca=97.5 gca peak = 0.20775 (25) mri peak = 0.09528 (20) gca peak = 0.13297 (21) mri peak = 0.12807 (22) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (203 voxels, overlap=0.827) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (203 voxels, peak = 24), gca=24.0 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 1.13 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.07 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 5.82918 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 0.809432 #GCAMreg# pass 0 level1 5 level2 1 tsec 1511.5 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 0.650861 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 0.648668 #GCAMreg# pass 0 level1 4 level2 1 tsec 1894.38 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 0.553719 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 0.557319 #GCAMreg# pass 0 level1 3 level2 1 tsec 1071.16 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 0.515328 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 0.536706 #GCAMreg# pass 0 level1 2 level2 1 tsec 69.058 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 0.536706 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 0.592563 #GCAMreg# pass 0 level1 1 level2 1 tsec 73.758 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 0.589675 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 0.516458 #GCAMreg# pass 0 level1 0 level2 1 tsec 435.798 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 0.488859 GCAMregister done in 106.773 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 0.480388 #GCAMreg# pass 0 level1 5 level2 1 tsec 76.811 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 0.480357 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 0.479075 #GCAMreg# pass 0 level1 4 level2 1 tsec 88.201 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 0.478772 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 0.4725 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 9 after 5 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 8 after 14 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 346.86 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 0.454439 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.449742 #GCAMreg# pass 0 level1 2 level2 1 tsec 72.849 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 0.449742 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 0.459315 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 1 level2 1 tsec 78.945 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 0.458987 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 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 0.448544 iter 0, gcam->neg = 734 after 14 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 80.688 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 0.415468 label assignment complete, 0 changed (0.00%) GCAMregister done in 24.9953 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 0.398573 #GCAMreg# pass 0 level1 5 level2 1 tsec 40.029 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 0.398573 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 0.398761 #GCAMreg# pass 0 level1 4 level2 1 tsec 37.484 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 0.398761 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 0.399152 #GCAMreg# pass 0 level1 3 level2 1 tsec 74.145 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 0.399064 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.393669 #GCAMreg# pass 0 level1 2 level2 1 tsec 69.185 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 0.393669 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 0.401833 #GCAMreg# pass 0 level1 1 level2 1 tsec 35.322 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 0.401833 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 0.388105 iter 0, gcam->neg = 547 after 15 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 83.649 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 0.380168 GCAMregister done in 15.9003 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4645 tmin = 22.7646 Calls to gcamLabelEnergy 4147 tmin = 1.63308 Calls to gcamJacobianEnergy 4645 tmin = 17.384 Calls to gcamSmoothnessEnergy 4645 tmin = 25.9298 Calls to gcamLogLikelihoodTerm 604 tmin = 6.45873 Calls to gcamLabelTerm 553 tmin = 10.1969 Calls to gcamJacobianTerm 604 tmin = 14.898 Calls to gcamSmoothnessTerm 604 tmin = 5.00493 Calls to gcamComputeGradient 604 tmin = 74.6445 Calls to gcamComputeMetricProperties 6356 tmin = 23.8073 mri_ca_register took 3 hours, 2 minutes and 17 seconds. #VMPC# mri_ca_register VmPeak 2013408 FSRUNTIME@ mri_ca_register 3.0380 hours 1 threads @#@FSTIME 2026:05:27:22:09:20 mri_ca_register N 9 e 10936.69 S 2.18 U 10934.39 P 99% M 1339100 F 0 R 378009 W 0 c 5631 w 95 I 0 O 63416 L 12.01 12.03 12.01 @#@FSLOADPOST 2026:05:28:01:11:37 mri_ca_register N 9 12.02 12.03 12.00 #-------------------------------------- #@# SubCort Seg Thu May 28 01:11:37 AM CEST 2026 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /software/freesurfer/7.4.1/debian-bookworm-amd64/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname silbermond machine x86_64 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.05 Atlas used for the 3D morph was /software/freesurfer/7.4.1/debian-bookworm-amd64/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 = 0.11422 (21) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (891 voxels, overlap=0.888) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (891 voxels, peak = 19), gca=18.7 gca peak = 0.20380 (13) mri peak = 0.12436 (16) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (487 voxels, overlap=0.686) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (487 voxels, peak = 15), gca=15.4 gca peak = 0.26283 (96) mri peak = 0.08380 (85) Right_Pallidum (52): linear fit = 0.89 x + 0.0 (534 voxels, overlap=0.381) Right_Pallidum (52): linear fit = 0.89 x + 0.0 (534 voxels, peak = 86), gca=85.9 gca peak = 0.15814 (97) mri peak = 0.14912 (98) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (684 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (684 voxels, peak = 100), gca=100.4 gca peak = 0.27624 (56) mri peak = 0.09410 (68) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (709 voxels, overlap=0.292) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (709 voxels, peak = 64), gca=63.6 gca peak = 0.28723 (59) mri peak = 0.08926 (62) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (714 voxels, overlap=0.551) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (714 voxels, peak = 65), gca=64.6 gca peak = 0.07623 (103) mri peak = 0.15223 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (37976 voxels, overlap=0.569) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (37976 voxels, peak = 105), gca=104.5 gca peak = 0.07837 (105) mri peak = 0.15699 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39997 voxels, overlap=0.572) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39997 voxels, peak = 105), gca=105.0 gca peak = 0.10165 (58) mri peak = 0.05381 (63) Left_Cerebral_Cortex (3): linear fit = 1.07 x + 0.0 (23453 voxels, overlap=0.948) Left_Cerebral_Cortex (3): linear fit = 1.07 x + 0.0 (23453 voxels, peak = 62), gca=61.8 gca peak = 0.11113 (58) mri peak = 0.05765 (61) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22191 voxels, overlap=0.917) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22191 voxels, peak = 59), gca=59.4 gca peak = 0.27796 (67) mri peak = 0.13736 (79) Right_Caudate (50): linear fit = 1.14 x + 0.0 (910 voxels, overlap=0.059) Right_Caudate (50): linear fit = 1.14 x + 0.0 (910 voxels, peak = 77), gca=76.7 gca peak = 0.14473 (69) mri peak = 0.19960 (79) Left_Caudate (11): linear fit = 1.04 x + 0.0 (991 voxels, overlap=0.679) Left_Caudate (11): linear fit = 1.04 x + 0.0 (991 voxels, peak = 72), gca=72.1 gca peak = 0.14301 (56) mri peak = 0.05034 (60) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (14272 voxels, overlap=0.981) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (14272 voxels, peak = 59), gca=58.5 gca peak = 0.14610 (55) mri peak = 0.05337 (64) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (17263 voxels, overlap=0.746) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (17263 voxels, peak = 62), gca=62.4 gca peak = 0.16309 (85) mri peak = 0.10803 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6245 voxels, overlap=0.427) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6245 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.10532 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5985 voxels, overlap=0.366) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5985 voxels, peak = 89), gca=89.5 gca peak = 0.30461 (58) mri peak = 0.08501 (71) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (667 voxels, overlap=0.064) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (667 voxels, peak = 70), gca=70.5 gca peak = 0.32293 (57) mri peak = 0.08985 (70) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (639 voxels, overlap=0.050) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (639 voxels, peak = 69), gca=68.7 gca peak = 0.11083 (90) mri peak = 0.06418 (87) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (4001 voxels, overlap=0.979) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (4001 voxels, peak = 91), gca=91.3 gca peak = 0.11393 (83) mri peak = 0.05891 (98) Right_Thalamus (49): linear fit = 1.12 x + 0.0 (4875 voxels, overlap=0.523) Right_Thalamus (49): linear fit = 1.12 x + 0.0 (4875 voxels, peak = 93), gca=93.4 gca peak = 0.08575 (81) mri peak = 0.09103 (84) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2230 voxels, overlap=0.655) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2230 voxels, peak = 86), gca=86.3 gca peak = 0.08618 (78) mri peak = 0.08161 (79) Right_Putamen (51): linear fit = 1.04 x + 0.0 (941 voxels, overlap=0.761) Right_Putamen (51): linear fit = 1.04 x + 0.0 (941 voxels, peak = 82), gca=81.5 gca peak = 0.08005 (78) mri peak = 0.06969 (91) Brain_Stem (16): linear fit = 1.13 x + 0.0 (12687 voxels, overlap=0.367) Brain_Stem (16): linear fit = 1.13 x + 0.0 (12687 voxels, peak = 89), gca=88.5 gca peak = 0.12854 (88) mri peak = 0.08802 (100) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1395 voxels, overlap=0.346) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1395 voxels, peak = 97), gca=97.2 gca peak = 0.15703 (87) mri peak = 0.07399 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1409 voxels, overlap=0.490) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1409 voxels, peak = 96), gca=96.1 gca peak = 0.17522 (25) mri peak = 0.25000 (20) gca peak = 0.17113 (14) mri peak = 0.15278 (24) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (143 voxels, overlap=0.851) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (143 voxels, peak = 21), gca=20.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) 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 1.12 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.20 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17693 (19) mri peak = 0.11422 (21) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (891 voxels, overlap=0.927) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (891 voxels, peak = 20), gca=20.4 gca peak = 0.18351 (15) mri peak = 0.12436 (16) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (487 voxels, overlap=0.799) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (487 voxels, peak = 15), gca=14.6 gca peak = 0.27209 (86) mri peak = 0.08380 (85) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (534 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (534 voxels, peak = 84), gca=83.8 gca peak = 0.16762 (98) mri peak = 0.14912 (98) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (684 voxels, overlap=0.997) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (684 voxels, peak = 98), gca=98.0 gca peak = 0.24486 (63) mri peak = 0.09410 (68) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (709 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (709 voxels, peak = 62), gca=62.1 gca peak = 0.30464 (62) mri peak = 0.08926 (62) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (714 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (714 voxels, peak = 61), gca=61.1 gca peak = 0.07884 (105) mri peak = 0.15223 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37976 voxels, overlap=0.627) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37976 voxels, peak = 104), gca=104.5 gca peak = 0.07837 (105) mri peak = 0.15699 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39997 voxels, overlap=0.572) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39997 voxels, peak = 105), gca=105.0 gca peak = 0.09431 (62) mri peak = 0.05381 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23453 voxels, overlap=0.988) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23453 voxels, peak = 64), gca=63.5 gca peak = 0.11127 (60) mri peak = 0.05765 (61) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22191 voxels, overlap=0.952) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22191 voxels, peak = 62), gca=61.5 gca peak = 0.21856 (76) mri peak = 0.13736 (79) Right_Caudate (50): linear fit = 1.00 x + 0.0 (910 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (910 voxels, peak = 76), gca=76.0 gca peak = 0.16719 (81) mri peak = 0.19960 (79) Left_Caudate (11): linear fit = 0.99 x + 0.0 (991 voxels, overlap=0.997) Left_Caudate (11): linear fit = 0.99 x + 0.0 (991 voxels, peak = 80), gca=79.8 gca peak = 0.13133 (58) mri peak = 0.05034 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (14272 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (14272 voxels, peak = 59), gca=59.4 gca peak = 0.14016 (63) mri peak = 0.05337 (64) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (17263 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (17263 voxels, peak = 62), gca=62.1 gca peak = 0.15236 (90) mri peak = 0.10803 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6245 voxels, overlap=0.881) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6245 voxels, peak = 91), gca=91.3 gca peak = 0.16794 (90) mri peak = 0.10532 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5985 voxels, overlap=0.841) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5985 voxels, peak = 91), gca=91.3 gca peak = 0.22728 (69) mri peak = 0.08501 (71) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (667 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (667 voxels, peak = 68), gca=68.0 gca peak = 0.22100 (69) mri peak = 0.08985 (70) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (639 voxels, overlap=1.005) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (639 voxels, peak = 70), gca=70.0 gca peak = 0.10534 (91) mri peak = 0.06418 (87) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4001 voxels, overlap=0.976) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4001 voxels, peak = 91), gca=90.5 gca peak = 0.10705 (91) mri peak = 0.05891 (98) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4875 voxels, overlap=0.993) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4875 voxels, peak = 91), gca=91.5 gca peak = 0.07448 (88) mri peak = 0.09103 (84) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2230 voxels, overlap=0.868) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2230 voxels, peak = 88), gca=88.0 gca peak = 0.11252 (79) mri peak = 0.08161 (79) Right_Putamen (51): linear fit = 0.99 x + 0.0 (941 voxels, overlap=0.877) Right_Putamen (51): linear fit = 0.99 x + 0.0 (941 voxels, peak = 78), gca=77.8 gca peak = 0.07817 (89) mri peak = 0.06969 (91) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12687 voxels, overlap=0.861) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12687 voxels, peak = 90), gca=90.3 gca peak = 0.11659 (97) mri peak = 0.08802 (100) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1395 voxels, overlap=0.810) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1395 voxels, peak = 98), gca=98.5 gca peak = 0.14494 (96) mri peak = 0.07399 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1409 voxels, overlap=0.924) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1409 voxels, peak = 96), gca=96.5 gca peak = 0.13281 (32) mri peak = 0.25000 (20) gca peak = 0.12908 (21) mri peak = 0.15278 (24) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (143 voxels, overlap=0.710) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (143 voxels, peak = 21), gca=21.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.17186 (31) gca peak Third_Ventricle = 0.13281 (32) gca peak CSF = 0.18178 (43) gca peak Left_Accumbens_area = 0.74301 (65) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.10623 (35) gca peak Right_Inf_Lat_Vent = 0.23431 (26) gca peak Right_Accumbens_area = 0.29441 (74) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13278 (38) gca peak Fifth_Ventricle = 0.59466 (39) gca peak WM_hypointensities = 0.10795 (77) gca peak non_WM_hypointensities = 0.14635 (41) gca peak Optic_Chiasm = 0.61279 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 67009 voxels changed in iteration 0 of unlikely voxel relabeling 115 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 31178 gm and wm labels changed (%32 to gray, %68 to white out of all changed labels) 344 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 68286 changed. image ll: -2.102, PF=0.500 pass 2: 18340 changed. image ll: -2.102, PF=0.500 pass 3: 4760 changed. 40793 voxels changed in iteration 0 of unlikely voxel relabeling 227 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5968 voxels changed in iteration 0 of unlikely voxel relabeling 94 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5945 voxels changed in iteration 0 of unlikely voxel relabeling 56 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4533 voxels changed in iteration 0 of unlikely voxel relabeling 10 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 1 with volume 5871 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 663 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 4087 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 684 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3024.925696 mri_ca_label stimesec 3.215976 mri_ca_label ru_maxrss 2139364 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 485782 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63408 mri_ca_label ru_oublock 712 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 83 mri_ca_label ru_nivcsw 1745 mri_ca_label took 50 minutes and 28 seconds. mri_ca_label done @#@FSTIME 2026:05:28:01:11:37 mri_ca_label N 10 e 3028.33 S 3.36 U 3024.92 P 99% M 2139364 F 0 R 485786 W 0 c 1745 w 83 I 63408 O 712 L 12.02 12.03 12.00 @#@FSLOADPOST 2026:05:28:02:02:05 mri_ca_label N 10 12.09 12.04 12.01 #-------------------------------------- #@# CC Seg Thu May 28 02:02:05 AM CEST 2026 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/transforms/cc_up.lta sub-20_ses-0 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/transforms/cc_up.lta reading aseg from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/aseg.auto_noCCseg.mgz reading norm from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/norm.mgz 22542 voxels in left wm, 37763 in right wm, xrange [123, 130] searching rotation angles z=[-7 7], y=[-6 8] searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 global minimum found at slice 127.0, rotations (1.48, -0.72) final transformation (x=127.0, yr=1.480, zr=-0.724): 0.99959 0.01264 0.02582 -2.98833; -0.01263 0.99992 -0.00033 34.64812; -0.02582 -0.00000 0.99967 21.31595; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 131] in xformed coordinates best xformed slice 129 min_x_fornix = 139 min_x_fornix = 106 min_x_fornix = 106 min_x_fornix = 136 min_x_fornix = 132 cc center is found at 129 95 110 eigenvectors: 0.00075 -0.00702 0.99998; -0.11696 -0.99311 -0.00688; 0.99314 -0.11695 -0.00156; writing aseg with callosum to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/aseg.auto.mgz... corpus callosum segmentation took 1.1 minutes #VMPC# mri_cc VmPeak 434240 mri_cc done @#@FSTIME 2026:05:28:02:02:05 mri_cc N 7 e 64.60 S 0.24 U 64.35 P 99% M 344556 F 0 R 13197 W 0 c 88 w 41 I 0 O 704 L 12.09 12.04 12.01 @#@FSLOADPOST 2026:05:28:02:03:10 mri_cc N 7 12.03 12.03 12.00 #-------------------------------------- #@# Merge ASeg Thu May 28 02:03:10 AM CEST 2026 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu May 28 02:03:10 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz aseg read with width 256 (src width 256) ************** resampling aseg to account for mismatch with source image *************** normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 715 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 68 (68), valley at 43 (43) csf peak at 16, 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 68 (68), valley at 43 (43) csf peak at 16, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 44 seconds. @#@FSTIME 2026:05:28:02:03:10 mri_normalize N 9 e 230.74 S 1.14 U 229.58 P 99% M 1234360 F 0 R 235236 W 0 c 215 w 62 I 0 O 2712 L 12.03 12.03 12.00 @#@FSLOADPOST 2026:05:28:02:07:01 mri_normalize N 9 12.06 12.03 12.00 #-------------------------------------------- #@# Mask BFS Thu May 28 02:07:01 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1629331 voxels in mask (pct= 9.71) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2026:05:28:02:07:01 mri_mask N 5 e 1.96 S 0.02 U 1.92 P 99% M 74272 F 0 R 2454 W 0 c 7 w 93 I 2712 O 2648 L 12.06 12.03 12.00 @#@FSLOADPOST 2026:05:28:02:07:03 mri_mask N 5 12.06 12.03 12.00 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Thu May 28 02:07:03 AM CEST 2026 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2026:05:28:02:07:03 AntsDenoiseImageFs N 4 e 74.59 S 0.09 U 74.49 P 99% M 351132 F 0 R 4092 W 0 c 46 w 81 I 0 O 2712 L 12.06 12.03 12.00 @#@FSLOADPOST 2026:05:28:02:08:18 AntsDenoiseImageFs N 4 12.09 12.04 12.00 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 414076, nonwhite = 16095220, ambig = 267920, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (105.0): 104.3 +- 5.4 [79.0 --> 125.0] CCS GM (73.0) : 72.1 +- 10.0 [30.0 --> 95.0] white_mean 104.292 white_sigma 5.43196 gray_mean 72.1187 gray_sigma 9.96974 setting bottom of white matter range wm_low to 82.1 setting top of gray matter range gray_hi to 92.1 wm_low 82.0884 wm_hi 125 gray_low 30 gray_hi 92.0582 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=82.0884, wm_hi=125, gray_hi=92.0582 white = 491776, nonwhite = 16160903, ambig = 124537, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 82.0884 wm_hi 125 gray_low 30 gray_hi 92.0582 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 92.0582, wm_low = 82.0884 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=92.0582, wmlow=82.0884 113529 voxels processed (0.68%) 51949 voxels white (0.31%) 61580 voxels non-white (0.37%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=77.0884, gray_hi=92.0582, wsize=13 208108 voxels tested (1.24%) 43742 voxels changed (0.26%) 49279 multi-scale searches (0.29%) Recovering bright white MRIrecoverBrightWhite() wm_low 82.0884 wm_hi 125 slack 5.43196 pct_thresh 0.33 intensity_thresh 130.432 nvox_thresh 8.58 183 voxels tested (0.00%) 98 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=77.0884, hithr=92.0582 smoothing input volume with sigma = 0.250 66705 voxels tested (0.40%) 13750 voxels changed (0.08%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 4224 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 2236 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 5844 filled MRIfindBrightNonWM(): 2281 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 2.0 minutes writing output to wm.seg.mgz... @#@FSTIME 2026:05:28:02:08:18 mri_segment N 5 e 121.13 S 0.42 U 120.70 P 99% M 162196 F 0 R 96093 W 0 c 162 w 33 I 2712 O 848 L 12.09 12.04 12.00 @#@FSLOADPOST 2026:05:28:02:10:19 mri_segment N 5 12.01 12.02 12.00 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.73 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2689 additional wm voxels added 0 additional wm voxels added SEG EDIT: 39488 voxels turned on, 45262 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2026:05:28:02:10:19 mri_edit_wm_with_aseg N 5 e 43.94 S 0.25 U 43.68 P 99% M 463844 F 0 R 40201 W 0 c 55 w 58 I 0 O 768 L 12.01 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:11:03 mri_edit_wm_with_aseg N 5 12.00 12.02 12.00 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 15 found - 15 modified | TOTAL: 31 pass 2 (xy-): 0 found - 15 modified | TOTAL: 31 pass 1 (yz+): 32 found - 32 modified | TOTAL: 63 pass 2 (yz+): 0 found - 32 modified | TOTAL: 63 pass 1 (yz-): 19 found - 19 modified | TOTAL: 82 pass 2 (yz-): 0 found - 19 modified | TOTAL: 82 pass 1 (xz+): 8 found - 8 modified | TOTAL: 90 pass 2 (xz+): 0 found - 8 modified | TOTAL: 90 pass 1 (xz-): 21 found - 21 modified | TOTAL: 111 pass 2 (xz-): 0 found - 21 modified | TOTAL: 111 Iteration Number : 1 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 13 found - 13 modified | TOTAL: 25 pass 2 (+++): 0 found - 13 modified | TOTAL: 25 pass 1 (+++): 18 found - 18 modified | TOTAL: 43 pass 2 (+++): 0 found - 18 modified | TOTAL: 43 pass 1 (+++): 9 found - 9 modified | TOTAL: 52 pass 2 (+++): 0 found - 9 modified | TOTAL: 52 Iteration Number : 1 pass 1 (++): 121 found - 121 modified | TOTAL: 121 pass 2 (++): 0 found - 121 modified | TOTAL: 121 pass 1 (+-): 116 found - 116 modified | TOTAL: 237 pass 2 (+-): 0 found - 116 modified | TOTAL: 237 pass 1 (--): 104 found - 104 modified | TOTAL: 341 pass 2 (--): 1 found - 105 modified | TOTAL: 342 pass 3 (--): 0 found - 105 modified | TOTAL: 342 pass 1 (-+): 97 found - 97 modified | TOTAL: 439 pass 2 (-+): 0 found - 97 modified | TOTAL: 439 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 4 found - 4 modified | TOTAL: 7 pass 2 (xy-): 0 found - 4 modified | TOTAL: 7 pass 1 (yz+): 0 found - 0 modified | TOTAL: 7 pass 1 (yz-): 3 found - 3 modified | TOTAL: 10 pass 2 (yz-): 0 found - 3 modified | TOTAL: 10 pass 1 (xz+): 4 found - 4 modified | TOTAL: 14 pass 2 (xz+): 0 found - 4 modified | TOTAL: 14 pass 1 (xz-): 2 found - 2 modified | TOTAL: 16 pass 2 (xz-): 0 found - 2 modified | TOTAL: 16 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 (++): 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 (--): 1 found - 1 modified | TOTAL: 5 pass 2 (--): 0 found - 1 modified | TOTAL: 5 pass 1 (-+): 0 found - 0 modified | TOTAL: 5 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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 = 627 (out of 534635: 0.117276) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2026:05:28:02:11:03 mri_pretess N 4 e 5.62 S 0.04 U 5.56 P 99% M 56888 F 0 R 2939 W 0 c 13 w 42 I 0 O 776 L 12.00 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:11:09 mri_pretess N 4 12.00 12.02 12.00 #-------------------------------------------- #@# Fill Thu May 28 02:11:09 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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... done. searching for cutting planes...voxel to talairach voxel transform 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24870; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24870; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1023 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) no need to search using seed (126, 116, 143), TAL = (2.0, 15.0, 12.0) talairach voxel to voxel transform 0.92539 0.03054 0.00050 7.03536; -0.02910 0.89946 -0.19763 29.52017; -0.00549 0.15220 1.02348 -18.03731; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 116, 143) --> (2.0, 15.0, 12.0) done. filling took 1.7 minutes talairach cc position changed to (2.00, 15.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 15.00, 12.00) SRC: (110.59, 102.46, 145.38) search lh wm seed point around talairach space (-16.00, 15.00, 12.00), SRC: (143.91, 101.41, 145.19) 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 2026:05:28:02:11:09 mri_fill N 10 e 103.41 S 1.11 U 102.28 P 99% M 966076 F 0 R 291692 W 0 c 120 w 41 I 0 O 272 L 12.00 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:12:52 mri_fill N 10 12.00 12.01 12.00 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Thu May 28 02:12:52 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 7 found - 7 modified | TOTAL: 7 pass 2 (yz+): 0 found - 7 modified | TOTAL: 7 pass 1 (yz-): 4 found - 4 modified | TOTAL: 11 pass 2 (yz-): 0 found - 4 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 0 found - 0 modified | TOTAL: 12 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 17 (out of 256109: 0.006638) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2026:05:28:02:12:52 mri_pretess N 4 e 3.01 S 0.03 U 2.97 P 99% M 40464 F 0 R 2334 W 0 c 6 w 51 I 0 O 264 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:12:56 mri_pretess N 4 12.00 12.01 12.00 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.4.1 7.4.1 slice 30: 335 vertices, 388 faces slice 40: 4628 vertices, 4830 faces slice 50: 11780 vertices, 12082 faces slice 60: 21254 vertices, 21590 faces slice 70: 31207 vertices, 31561 faces slice 80: 40961 vertices, 41341 faces slice 90: 51947 vertices, 52303 faces slice 100: 63051 vertices, 63441 faces slice 110: 74236 vertices, 74604 faces slice 120: 84919 vertices, 85322 faces slice 130: 95644 vertices, 96029 faces slice 140: 105786 vertices, 106131 faces slice 150: 114958 vertices, 115263 faces slice 160: 122388 vertices, 122657 faces slice 170: 129409 vertices, 129679 faces slice 180: 134997 vertices, 135177 faces slice 190: 138460 vertices, 138513 faces slice 200: 138584 vertices, 138598 faces slice 210: 138584 vertices, 138598 faces slice 220: 138584 vertices, 138598 faces slice 230: 138584 vertices, 138598 faces slice 240: 138584 vertices, 138598 faces slice 250: 138584 vertices, 138598 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2026:05:28:02:12:56 mri_tessellate N 3 e 2.33 S 0.01 U 2.30 P 99% M 44552 F 0 R 1261 W 0 c 4 w 129 I 0 O 6504 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:12:58 mri_tessellate N 3 12.00 12.01 12.00 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 138584 voxel in cpt #1: X=-14 [v=138584,e=415794,f=277196] located at (-26.773920, -22.422523, 19.799313) For the whole surface: X=-14 [v=138584,e=415794,f=277196] One single component has been found nothing to do done @#@FSTIME 2026:05:28:02:12:58 mris_extract_main_component N 2 e 1.19 S 0.12 U 1.05 P 98% M 277352 F 0 R 26100 W 0 c 4 w 245 I 6504 O 9752 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:12:59 mris_extract_main_component N 2 12.00 12.01 12.00 #-------------------------------------------- #@# Tessellate rh Thu May 28 02:12:59 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 9 found - 9 modified | TOTAL: 11 pass 2 (yz+): 0 found - 9 modified | TOTAL: 11 pass 1 (yz-): 5 found - 5 modified | TOTAL: 16 pass 2 (yz-): 0 found - 5 modified | TOTAL: 16 pass 1 (xz+): 1 found - 1 modified | TOTAL: 17 pass 2 (xz+): 0 found - 1 modified | TOTAL: 17 pass 1 (xz-): 1 found - 1 modified | TOTAL: 18 pass 2 (xz-): 0 found - 1 modified | TOTAL: 18 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 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 : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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 = 24 (out of 255498: 0.009393) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2026:05:28:02:12:59 mri_pretess N 4 e 3.01 S 0.00 U 3.00 P 99% M 40468 F 0 R 1660 W 0 c 6 w 34 I 0 O 264 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:13:02 mri_pretess N 4 12.00 12.01 12.00 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.4.1 7.4.1 slice 30: 308 vertices, 358 faces slice 40: 4628 vertices, 4851 faces slice 50: 12379 vertices, 12684 faces slice 60: 22388 vertices, 22749 faces slice 70: 33499 vertices, 33854 faces slice 80: 44664 vertices, 45045 faces slice 90: 56780 vertices, 57160 faces slice 100: 68163 vertices, 68549 faces slice 110: 79186 vertices, 79570 faces slice 120: 89957 vertices, 90340 faces slice 130: 100142 vertices, 100506 faces slice 140: 110102 vertices, 110435 faces slice 150: 118357 vertices, 118669 faces slice 160: 125547 vertices, 125780 faces slice 170: 131674 vertices, 131892 faces slice 180: 136863 vertices, 137036 faces slice 190: 139545 vertices, 139576 faces slice 200: 139578 vertices, 139596 faces slice 210: 139578 vertices, 139596 faces slice 220: 139578 vertices, 139596 faces slice 230: 139578 vertices, 139596 faces slice 240: 139578 vertices, 139596 faces slice 250: 139578 vertices, 139596 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2026:05:28:02:13:02 mri_tessellate N 3 e 2.37 S 0.04 U 2.32 P 99% M 44624 F 0 R 1257 W 0 c 9 w 36 I 0 O 6552 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:13:05 mri_tessellate N 3 12.00 12.01 12.00 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 139578 voxel in cpt #1: X=-18 [v=139578,e=418788,f=279192] located at (28.517883, -25.282745, 21.693977) For the whole surface: X=-18 [v=139578,e=418788,f=279192] One single component has been found nothing to do done @#@FSTIME 2026:05:28:02:13:05 mris_extract_main_component N 2 e 1.28 S 0.14 U 1.11 P 98% M 279060 F 0 R 27600 W 0 c 3 w 199 I 6552 O 9816 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:13:06 mris_extract_main_component N 2 12.00 12.01 12.00 #-------------------------------------------- #@# Smooth1 lh Thu May 28 02:13:06 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:02:13:06 mris_smooth N 5 e 4.30 S 0.17 U 4.11 P 99% M 221116 F 0 R 39144 W 0 c 12 w 36 I 9752 O 9752 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:13:10 mris_smooth N 5 12.00 12.01 12.00 #-------------------------------------------- #@# Smooth1 rh Thu May 28 02:13:10 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:02:13:10 mris_smooth N 5 e 4.26 S 0.17 U 4.08 P 99% M 222608 F 0 R 39127 W 0 c 11 w 35 I 9816 O 9824 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:13:15 mris_smooth N 5 12.08 12.02 12.01 #-------------------------------------------- #@# Inflation1 lh Thu May 28 02:13:15 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.2 mm, total surface area = 74190 mm^2 step 000: RMS=0.148 (target=0.015) step 005: RMS=0.110 (target=0.015) step 010: RMS=0.080 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.034 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.031 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes inflation complete. Not saving sulc mris_inflate utimesec 27.352667 mris_inflate stimesec 1.560266 mris_inflate ru_maxrss 221812 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 463869 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9752 mris_inflate ru_oublock 9752 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 112 mris_inflate ru_nivcsw 67 @#@FSTIME 2026:05:28:02:13:15 mris_inflate N 3 e 28.94 S 1.57 U 27.35 P 99% M 221812 F 0 R 463875 W 0 c 67 w 113 I 9752 O 9752 L 12.08 12.02 12.01 @#@FSLOADPOST 2026:05:28:02:13:44 mris_inflate N 3 12.05 12.02 12.00 #-------------------------------------------- #@# Inflation1 rh Thu May 28 02:13:44 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.8 mm, total surface area = 75289 mm^2 step 000: RMS=0.147 (target=0.015) step 005: RMS=0.110 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.028 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes inflation complete. Not saving sulc mris_inflate utimesec 26.937387 mris_inflate stimesec 0.108005 mris_inflate ru_maxrss 223992 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34564 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9824 mris_inflate ru_oublock 9824 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 156 mris_inflate ru_nivcsw 30 @#@FSTIME 2026:05:28:02:13:44 mris_inflate N 3 e 27.07 S 0.12 U 26.93 P 99% M 224196 F 0 R 34569 W 0 c 30 w 156 I 9824 O 9824 L 12.05 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:14:11 mris_inflate N 3 12.03 12.02 12.00 #-------------------------------------------- #@# QSphere lh Thu May 28 02:14:11 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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: 7.4.1 available threads: 1 scaling brain by 0.306... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.57 (0.00-->6.46) (max @ vno 53734 --> 54723) face area 0.03 +- 0.03 (-0.06-->0.56) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.611, avgs=0 005/300: dt: 0.9000, rms radial error=176.353, avgs=0 010/300: dt: 0.9000, rms radial error=175.796, avgs=0 015/300: dt: 0.9000, rms radial error=175.063, avgs=0 020/300: dt: 0.9000, rms radial error=174.228, avgs=0 025/300: dt: 0.9000, rms radial error=173.336, avgs=0 030/300: dt: 0.9000, rms radial error=172.416, avgs=0 035/300: dt: 0.9000, rms radial error=171.483, avgs=0 040/300: dt: 0.9000, rms radial error=170.543, avgs=0 045/300: dt: 0.9000, rms radial error=169.600, avgs=0 050/300: dt: 0.9000, rms radial error=168.658, avgs=0 055/300: dt: 0.9000, rms radial error=167.718, avgs=0 060/300: dt: 0.9000, rms radial error=166.781, avgs=0 065/300: dt: 0.9000, rms radial error=165.848, avgs=0 070/300: dt: 0.9000, rms radial error=164.919, avgs=0 075/300: dt: 0.9000, rms radial error=163.996, avgs=0 080/300: dt: 0.9000, rms radial error=163.076, avgs=0 085/300: dt: 0.9000, rms radial error=162.162, avgs=0 090/300: dt: 0.9000, rms radial error=161.252, avgs=0 095/300: dt: 0.9000, rms radial error=160.348, avgs=0 100/300: dt: 0.9000, rms radial error=159.448, avgs=0 105/300: dt: 0.9000, rms radial error=158.553, avgs=0 110/300: dt: 0.9000, rms radial error=157.663, avgs=0 115/300: dt: 0.9000, rms radial error=156.777, avgs=0 120/300: dt: 0.9000, rms radial error=155.897, avgs=0 125/300: dt: 0.9000, rms radial error=155.021, avgs=0 130/300: dt: 0.9000, rms radial error=154.150, avgs=0 135/300: dt: 0.9000, rms radial error=153.284, avgs=0 140/300: dt: 0.9000, rms radial error=152.422, avgs=0 145/300: dt: 0.9000, rms radial error=151.565, avgs=0 150/300: dt: 0.9000, rms radial error=150.713, avgs=0 155/300: dt: 0.9000, rms radial error=149.865, avgs=0 160/300: dt: 0.9000, rms radial error=149.022, avgs=0 165/300: dt: 0.9000, rms radial error=148.183, avgs=0 170/300: dt: 0.9000, rms radial error=147.349, avgs=0 175/300: dt: 0.9000, rms radial error=146.520, avgs=0 180/300: dt: 0.9000, rms radial error=145.695, avgs=0 185/300: dt: 0.9000, rms radial error=144.874, avgs=0 190/300: dt: 0.9000, rms radial error=144.058, avgs=0 195/300: dt: 0.9000, rms radial error=143.247, avgs=0 200/300: dt: 0.9000, rms radial error=142.440, avgs=0 205/300: dt: 0.9000, rms radial error=141.638, avgs=0 210/300: dt: 0.9000, rms radial error=140.840, avgs=0 215/300: dt: 0.9000, rms radial error=140.046, avgs=0 220/300: dt: 0.9000, rms radial error=139.257, avgs=0 225/300: dt: 0.9000, rms radial error=138.472, avgs=0 230/300: dt: 0.9000, rms radial error=137.691, avgs=0 235/300: dt: 0.9000, rms radial error=136.915, avgs=0 240/300: dt: 0.9000, rms radial error=136.143, avgs=0 245/300: dt: 0.9000, rms radial error=135.376, avgs=0 250/300: dt: 0.9000, rms radial error=134.612, avgs=0 255/300: dt: 0.9000, rms radial error=133.853, avgs=0 260/300: dt: 0.9000, rms radial error=133.098, avgs=0 265/300: dt: 0.9000, rms radial error=132.348, avgs=0 270/300: dt: 0.9000, rms radial error=131.602, avgs=0 275/300: dt: 0.9000, rms radial error=130.859, avgs=0 280/300: dt: 0.9000, rms radial error=130.121, avgs=0 285/300: dt: 0.9000, rms radial error=129.387, avgs=0 290/300: dt: 0.9000, rms radial error=128.657, avgs=0 295/300: dt: 0.9000, rms radial error=127.932, avgs=0 300/300: dt: 0.9000, rms radial error=127.210, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16241.07 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00035 epoch 2 (K=40.0), pass 1, starting sse = 2653.41 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00024 epoch 3 (K=160.0), pass 1, starting sse = 253.18 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/20 = 0.01154 epoch 4 (K=640.0), pass 1, starting sse = 7.90 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.25/31 = 0.00815 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0620 hours FSRUNTIME@ mris_sphere 0.0620 hours 1 threads #VMPC# mris_sphere VmPeak 480292 mris_sphere done @#@FSTIME 2026:05:28:02:14:11 mris_sphere N 9 e 223.39 S 9.48 U 213.88 P 99% M 227140 F 0 R 2932291 W 0 c 366 w 169 I 9752 O 9752 L 12.03 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:17:54 mris_sphere N 9 12.00 12.01 12.00 #-------------------------------------------- #@# QSphere rh Thu May 28 02:17:54 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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: 7.4.1 available threads: 1 scaling brain by 0.304... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.57 (0.00-->9.55) (max @ vno 64476 --> 65589) face area 0.02 +- 0.03 (-0.30-->0.72) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.715, avgs=0 005/300: dt: 0.9000, rms radial error=176.454, avgs=0 010/300: dt: 0.9000, rms radial error=175.896, avgs=0 015/300: dt: 0.9000, rms radial error=175.162, avgs=0 020/300: dt: 0.9000, rms radial error=174.327, avgs=0 025/300: dt: 0.9000, rms radial error=173.432, avgs=0 030/300: dt: 0.9000, rms radial error=172.510, avgs=0 035/300: dt: 0.9000, rms radial error=171.575, avgs=0 040/300: dt: 0.9000, rms radial error=170.632, avgs=0 045/300: dt: 0.9000, rms radial error=169.687, avgs=0 050/300: dt: 0.9000, rms radial error=168.744, avgs=0 055/300: dt: 0.9000, rms radial error=167.803, avgs=0 060/300: dt: 0.9000, rms radial error=166.865, avgs=0 065/300: dt: 0.9000, rms radial error=165.932, avgs=0 070/300: dt: 0.9000, rms radial error=165.004, avgs=0 075/300: dt: 0.9000, rms radial error=164.080, avgs=0 080/300: dt: 0.9000, rms radial error=163.162, avgs=0 085/300: dt: 0.9000, rms radial error=162.248, avgs=0 090/300: dt: 0.9000, rms radial error=161.340, avgs=0 095/300: dt: 0.9000, rms radial error=160.436, avgs=0 100/300: dt: 0.9000, rms radial error=159.537, avgs=0 105/300: dt: 0.9000, rms radial error=158.643, avgs=0 110/300: dt: 0.9000, rms radial error=157.753, avgs=0 115/300: dt: 0.9000, rms radial error=156.869, avgs=0 120/300: dt: 0.9000, rms radial error=155.989, avgs=0 125/300: dt: 0.9000, rms radial error=155.114, avgs=0 130/300: dt: 0.9000, rms radial error=154.243, avgs=0 135/300: dt: 0.9000, rms radial error=153.378, avgs=0 140/300: dt: 0.9000, rms radial error=152.517, avgs=0 145/300: dt: 0.9000, rms radial error=151.660, avgs=0 150/300: dt: 0.9000, rms radial error=150.808, avgs=0 155/300: dt: 0.9000, rms radial error=149.961, avgs=0 160/300: dt: 0.9000, rms radial error=149.119, avgs=0 165/300: dt: 0.9000, rms radial error=148.281, avgs=0 170/300: dt: 0.9000, rms radial error=147.447, avgs=0 175/300: dt: 0.9000, rms radial error=146.619, avgs=0 180/300: dt: 0.9000, rms radial error=145.794, avgs=0 185/300: dt: 0.9000, rms radial error=144.975, avgs=0 190/300: dt: 0.9000, rms radial error=144.159, avgs=0 195/300: dt: 0.9000, rms radial error=143.349, avgs=0 200/300: dt: 0.9000, rms radial error=142.542, avgs=0 205/300: dt: 0.9000, rms radial error=141.740, avgs=0 210/300: dt: 0.9000, rms radial error=140.943, avgs=0 215/300: dt: 0.9000, rms radial error=140.150, avgs=0 220/300: dt: 0.9000, rms radial error=139.361, avgs=0 225/300: dt: 0.9000, rms radial error=138.577, avgs=0 230/300: dt: 0.9000, rms radial error=137.797, avgs=0 235/300: dt: 0.9000, rms radial error=137.022, avgs=0 240/300: dt: 0.9000, rms radial error=136.251, avgs=0 245/300: dt: 0.9000, rms radial error=135.484, avgs=0 250/300: dt: 0.9000, rms radial error=134.721, avgs=0 255/300: dt: 0.9000, rms radial error=133.963, avgs=0 260/300: dt: 0.9000, rms radial error=133.208, avgs=0 265/300: dt: 0.9000, rms radial error=132.458, avgs=0 270/300: dt: 0.9000, rms radial error=131.713, avgs=0 275/300: dt: 0.9000, rms radial error=130.971, avgs=0 280/300: dt: 0.9000, rms radial error=130.233, avgs=0 285/300: dt: 0.9000, rms radial error=129.500, avgs=0 290/300: dt: 0.9000, rms radial error=128.771, avgs=0 295/300: dt: 0.9000, rms radial error=128.045, avgs=0 300/300: dt: 0.9000, rms radial error=127.324, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16382.12 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00027 epoch 2 (K=40.0), pass 1, starting sse = 2701.27 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00034 epoch 3 (K=160.0), pass 1, starting sse = 258.35 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/19 = 0.00756 epoch 4 (K=640.0), pass 1, starting sse = 10.85 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.27/37 = 0.00742 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0664 hours FSRUNTIME@ mris_sphere 0.0664 hours 1 threads #VMPC# mris_sphere VmPeak 481664 mris_sphere done @#@FSTIME 2026:05:28:02:17:54 mris_sphere N 9 e 239.01 S 10.50 U 228.48 P 99% M 228516 F 0 R 3137740 W 0 c 354 w 82 I 9824 O 9824 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:21:53 mris_sphere N 9 12.02 12.05 12.01 #@# Fix Topology lh Thu May 28 02:21:53 AM CEST 2026 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-20_ses-0 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' 7.4.1 7.4.1 before topology correction, eno=-14 (nv=138584, nf=277196, ne=415794, g=8) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... 2216 ambiguous faces found in tessellation segmenting defects... 19 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 15 into 13 18 defects to be corrected 0 vertices coincident reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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: -9.5410 (-4.7705) -vertex loglikelihood: -6.4212 (-3.2106) -normal dot loglikelihood: -3.6466 (-3.6466) -quad curv loglikelihood: -6.2719 (-3.1360) Total Loglikelihood : -25.8808 CORRECTING DEFECT 0 (vertices=37, convex hull=78, v0=870) After retessellation of defect 0 (v0=870), euler #=-16 (137285,411499,274198) : difference with theory (-15) = 1 CORRECTING DEFECT 1 (vertices=253, convex hull=124, v0=7624) After retessellation of defect 1 (v0=7624), euler #=-15 (137298,411591,274278) : difference with theory (-14) = 1 CORRECTING DEFECT 2 (vertices=35, convex hull=59, v0=28808) After retessellation of defect 2 (v0=28808), euler #=-14 (137314,411663,274335) : difference with theory (-13) = 1 CORRECTING DEFECT 3 (vertices=24, convex hull=15, v0=43964) After retessellation of defect 3 (v0=43964), euler #=-13 (137317,411675,274345) : difference with theory (-12) = 1 CORRECTING DEFECT 4 (vertices=12, convex hull=25, v0=56673) After retessellation of defect 4 (v0=56673), euler #=-12 (137320,411692,274360) : difference with theory (-11) = 1 CORRECTING DEFECT 5 (vertices=29, convex hull=34, v0=60194) After retessellation of defect 5 (v0=60194), euler #=-11 (137327,411724,274386) : difference with theory (-10) = 1 CORRECTING DEFECT 6 (vertices=26, convex hull=25, v0=64780) After retessellation of defect 6 (v0=64780), euler #=-10 (137335,411758,274413) : difference with theory (-9) = 1 CORRECTING DEFECT 7 (vertices=66, convex hull=51, v0=73919) After retessellation of defect 7 (v0=73919), euler #=-9 (137348,411818,274461) : difference with theory (-8) = 1 CORRECTING DEFECT 8 (vertices=29, convex hull=22, v0=86570) After retessellation of defect 8 (v0=86570), euler #=-8 (137351,411836,274477) : difference with theory (-7) = 1 CORRECTING DEFECT 9 (vertices=20, convex hull=24, v0=90944) After retessellation of defect 9 (v0=90944), euler #=-7 (137355,411853,274491) : difference with theory (-6) = 1 CORRECTING DEFECT 10 (vertices=28, convex hull=24, v0=92939) After retessellation of defect 10 (v0=92939), euler #=-6 (137360,411877,274511) : difference with theory (-5) = 1 CORRECTING DEFECT 11 (vertices=27, convex hull=63, v0=94196) After retessellation of defect 11 (v0=94196), euler #=-5 (137376,411950,274569) : difference with theory (-4) = 1 CORRECTING DEFECT 12 (vertices=142, convex hull=84, v0=94234) After retessellation of defect 12 (v0=94234), euler #=-4 (137385,412009,274620) : difference with theory (-3) = 1 CORRECTING DEFECT 13 (vertices=48, convex hull=78, v0=96180) After retessellation of defect 13 (v0=96180), euler #=-2 (137408,412114,274704) : difference with theory (-2) = 0 CORRECTING DEFECT 14 (vertices=335, convex hull=71, v0=96264) After retessellation of defect 14 (v0=96264), euler #=-1 (137426,412202,274775) : difference with theory (-1) = 0 CORRECTING DEFECT 15 (vertices=25, convex hull=30, v0=100371) After retessellation of defect 15 (v0=100371), euler #=0 (137431,412224,274793) : difference with theory (0) = 0 CORRECTING DEFECT 16 (vertices=19, convex hull=34, v0=102591) After retessellation of defect 16 (v0=102591), euler #=1 (137443,412272,274830) : difference with theory (1) = 0 CORRECTING DEFECT 17 (vertices=159, convex hull=117, v0=103579) After retessellation of defect 17 (v0=103579), euler #=2 (137487,412455,274970) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.09-->5.27) (max @ vno 97751 --> 97766) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.09-->5.27) (max @ vno 97751 --> 97766) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 53 mutations (37.9%), 87 crossovers (62.1%), 92 vertices were eliminated building final representation... 1097 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=137487, nf=274970, ne=412455, g=0) writing corrected surface to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 62 intersecting terminating search with 0 intersecting topology fixing took 3.0 minutes FSRUNTIME@ mris_fix_topology lh 0.0494 hours 1 threads #VMPC# mris_fix_topology VmPeak 757420 @#@FSTIME 2026:05:28:02:21:53 mris_fix_topology N 14 e 178.06 S 0.68 U 177.33 P 99% M 738468 F 0 R 175827 W 0 c 141 w 261 I 9752 O 12936 L 12.02 12.05 12.01 @#@FSLOADPOST 2026:05:28:02:24:52 mris_fix_topology N 14 12.00 12.02 12.00 #@# Fix Topology rh Thu May 28 02:24:52 AM CEST 2026 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-20_ses-0 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' 7.4.1 7.4.1 before topology correction, eno=-18 (nv=139578, nf=279192, ne=418788, g=10) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 1841 ambiguous faces found in tessellation segmenting defects... 15 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 15 defects to be corrected 0 vertices coincident reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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: -9.6487 (-4.8243) -vertex loglikelihood: -6.4180 (-3.2090) -normal dot loglikelihood: -3.6566 (-3.6566) -quad curv loglikelihood: -6.2480 (-3.1240) Total Loglikelihood : -25.9712 CORRECTING DEFECT 0 (vertices=51, convex hull=89, v0=1921) After retessellation of defect 0 (v0=1921), euler #=-12 (138485,415104,276607) : difference with theory (-12) = 0 CORRECTING DEFECT 1 (vertices=306, convex hull=251, v0=51403) normal vector of length zero at vertex 138789 with 3 faces normal vector of length zero at vertex 138798 with 3 faces After retessellation of defect 1 (v0=51403), euler #=-11 (138557,415442,276874) : difference with theory (-11) = 0 CORRECTING DEFECT 2 (vertices=66, convex hull=39, v0=57404) After retessellation of defect 2 (v0=57404), euler #=-10 (138574,415506,276922) : difference with theory (-10) = 0 CORRECTING DEFECT 3 (vertices=7, convex hull=12, v0=63216) After retessellation of defect 3 (v0=63216), euler #=-9 (138576,415514,276929) : difference with theory (-9) = 0 CORRECTING DEFECT 4 (vertices=35, convex hull=22, v0=64254) After retessellation of defect 4 (v0=64254), euler #=-8 (138577,415523,276938) : difference with theory (-8) = 0 CORRECTING DEFECT 5 (vertices=8, convex hull=20, v0=76311) After retessellation of defect 5 (v0=76311), euler #=-7 (138578,415532,276947) : difference with theory (-7) = 0 CORRECTING DEFECT 6 (vertices=24, convex hull=65, v0=91555) After retessellation of defect 6 (v0=91555), euler #=-6 (138594,415602,277002) : difference with theory (-6) = 0 CORRECTING DEFECT 7 (vertices=36, convex hull=65, v0=96786) After retessellation of defect 7 (v0=96786), euler #=-5 (138614,415685,277066) : difference with theory (-5) = 0 CORRECTING DEFECT 8 (vertices=15, convex hull=28, v0=96811) After retessellation of defect 8 (v0=96811), euler #=-4 (138619,415708,277085) : difference with theory (-4) = 0 CORRECTING DEFECT 9 (vertices=354, convex hull=135, v0=99806) After retessellation of defect 9 (v0=99806), euler #=-3 (138667,415911,277241) : difference with theory (-3) = 0 CORRECTING DEFECT 10 (vertices=61, convex hull=39, v0=103881) After retessellation of defect 10 (v0=103881), euler #=-2 (138677,415953,277274) : difference with theory (-2) = 0 CORRECTING DEFECT 11 (vertices=30, convex hull=53, v0=118324) After retessellation of defect 11 (v0=118324), euler #=-1 (138686,415999,277312) : difference with theory (-1) = 0 CORRECTING DEFECT 12 (vertices=59, convex hull=61, v0=131120) After retessellation of defect 12 (v0=131120), euler #=0 (138703,416079,277376) : difference with theory (0) = 0 CORRECTING DEFECT 13 (vertices=22, convex hull=44, v0=132126) After retessellation of defect 13 (v0=132126), euler #=1 (138715,416130,277416) : difference with theory (1) = 0 CORRECTING DEFECT 14 (vertices=37, convex hull=28, v0=135573) After retessellation of defect 14 (v0=135573), euler #=2 (138721,416157,277438) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.10-->9.11) (max @ vno 58353 --> 58439) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.10-->9.11) (max @ vno 58353 --> 58439) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 65 mutations (36.7%), 112 crossovers (63.3%), 74 vertices were eliminated building final representation... 857 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138721, nf=277438, ne=416157, g=0) writing corrected surface to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 146 intersecting 001: 2 intersecting terminating search with 0 intersecting topology fixing took 2.2 minutes FSRUNTIME@ mris_fix_topology rh 0.0371 hours 1 threads #VMPC# mris_fix_topology VmPeak 758240 @#@FSTIME 2026:05:28:02:24:52 mris_fix_topology N 14 e 133.67 S 0.67 U 132.96 P 99% M 741376 F 0 R 175079 W 0 c 90 w 304 I 0 O 13048 L 12.00 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:27:05 mris_fix_topology N 14 12.01 12.02 12.00 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 137487 - 412455 + 274970 = 2 --> 0 holes F =2V-4: 274970 = 274974-4 (0) 2E=3F: 824910 = 824910 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 138721 - 416157 + 277438 = 2 --> 0 holes F =2V-4: 277438 = 277442-4 (0) 2E=3F: 832314 = 832314 (0) total defect index = 0 Thu May 28 02:27:07 AM CEST 2026 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/defect2seg --s sub-20_ses-0 --cortex freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 defect2seg 7.4.1 Linux silbermond 6.1.0-45-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.170-1 (2026-04-30) x86_64 GNU/Linux pid 256348 mri_label2label --label-cortex /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.nofix /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/aseg.presurf.mgz 0 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 10 non-cortical segments detected only using segment with 7602 vertices erasing segment 0 (vno[0] = 45940) erasing segment 2 (vno[0] = 58051) erasing segment 3 (vno[0] = 95244) erasing segment 4 (vno[0] = 97365) erasing segment 5 (vno[0] = 98309) erasing segment 6 (vno[0] = 116064) erasing segment 7 (vno[0] = 116066) erasing segment 8 (vno[0] = 117425) erasing segment 9 (vno[0] = 119773) mri_label2vol --defects /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.nofix /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.defect_labels /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz 1000 0 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz mris_defects_pointset -s /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.nofix -d /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.defect_labels -o /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.defects.pointset --label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label Reading in surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.nofix Reading in defect segmentation /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.defect_labels Reading in label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 181676 mris_defects_pointset done mri_label2label --label-cortex /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.nofix /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/aseg.presurf.mgz 0 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 18 non-cortical segments detected only using segment with 7315 vertices erasing segment 1 (vno[0] = 52517) erasing segment 2 (vno[0] = 62125) erasing segment 3 (vno[0] = 65500) erasing segment 4 (vno[0] = 82014) erasing segment 5 (vno[0] = 82045) erasing segment 6 (vno[0] = 84109) erasing segment 7 (vno[0] = 93628) erasing segment 8 (vno[0] = 99780) erasing segment 9 (vno[0] = 99806) erasing segment 10 (vno[0] = 100715) erasing segment 11 (vno[0] = 100814) erasing segment 12 (vno[0] = 101876) erasing segment 13 (vno[0] = 103822) erasing segment 14 (vno[0] = 103946) erasing segment 15 (vno[0] = 104739) erasing segment 16 (vno[0] = 106534) erasing segment 17 (vno[0] = 109751) mri_label2vol --defects /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.nofix /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.defect_labels /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz 2000 1 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz mris_defects_pointset -s /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.nofix -d /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.defect_labels -o /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.defects.pointset --label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label Reading in surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.nofix Reading in defect segmentation /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.defect_labels Reading in label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 182732 mris_defects_pointset done Started at Thu May 28 02:27:07 AM CEST 2026 Ended at Thu May 28 02:28:05 AM CEST 2026 Defect2seg-Run-Time-Sec 58 Defect2seg-Run-Time-Min 1.16 Defect2seg-Run-Time-Hours 0.02 tkmeditfv sub-20_ses-0 brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2026:05:28:02:27:07 defect2seg N 3 e 58.22 S 1.08 U 57.10 P 99% M 392712 F 0 R 186831 W 0 c 85 w 977 I 22592 O 23208 L 12.01 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:28:05 defect2seg N 3 12.00 12.02 12.00 mris_remesh --remesh --iters 3 --input /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.premesh --output /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.708198 remeshing to edge length 0.708198 with 3 iterations avg qual before : 0.890371 after: 0.97114 Removing intersections Remeshed surface quality stats nv0 = 137487 nv = 143490 1.04366 Area 286976 0.30030 0.03356 0.089147 0.4552 Corner 860928 60.00000 8.80489 17.252839 144.4560 Edge 430464 0.84071 0.08220 0.443194 1.3074 Hinge 430464 9.42184 10.04914 0.000006 119.0942 mris_remesh done @#@FSTIME 2026:05:28:02:28:05 mris_remesh N 7 e 39.72 S 0.53 U 39.17 P 99% M 775700 F 0 R 133046 W 0 c 97 w 99 I 0 O 10096 L 12.00 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:28:45 mris_remesh N 7 12.00 12.01 12.00 mris_remesh --remesh --iters 3 --input /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.premesh --output /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.709931 remeshing to edge length 0.709931 with 3 iterations avg qual before : 0.891886 after: 0.971508 Removing intersections Remeshed surface quality stats nv0 = 138721 nv = 144808 1.04388 Area 289612 0.30206 0.03334 0.083080 0.4623 Corner 868836 60.00000 8.75040 17.861409 143.0944 Edge 434418 0.84309 0.08177 0.459822 1.2586 Hinge 434418 9.38788 10.09762 0.000034 131.3654 mris_remesh done @#@FSTIME 2026:05:28:02:28:45 mris_remesh N 7 e 41.18 S 0.53 U 40.62 P 99% M 779660 F 0 R 128436 W 0 c 57 w 145 I 0 O 10184 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:29:26 mris_remesh N 7 12.00 12.01 12.00 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/lh.orig @#@FSTIME 2026:05:28:02:29:26 mris_remove_intersection N 2 e 6.42 S 0.25 U 6.16 P 99% M 347548 F 0 R 67214 W 0 c 20 w 129 I 0 O 10096 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:29:33 mris_remove_intersection N 2 12.00 12.01 12.00 rm -f ../surf/lh.inflated /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/rh.orig @#@FSTIME 2026:05:28:02:29:33 mris_remove_intersection N 2 e 6.45 S 0.27 U 6.16 P 99% M 348344 F 0 R 66398 W 0 c 17 w 116 I 10184 O 10184 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:29:39 mris_remove_intersection N 2 12.00 12.01 12.00 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Thu May 28 02:29:39 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 252805 voxels (1.51%) border gray 288479 voxels (1.72%) 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=37474, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (104.0): 101.9 +- 8.2 [70.0 --> 110.0] CCS GM (72.0) : 73.0 +- 9.9 [30.0 --> 110.0] white_mean = 101.857 +/- 8.18857, gray_mean = 73.0038 +/- 9.88045 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=231 nbins=232 intensity peaks found at WM=107+-4.3, GM=68+-7.0 white_mode = 107, gray_mode = 68 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 58.1 (was 70.000000) setting MAX_BORDER_WHITE to 115.2 (was 105.000000) setting MIN_BORDER_WHITE to 68.0 (was 85.000000) setting MAX_CSF to 48.2 (was 40.000000) setting MAX_GRAY to 98.8 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 58.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 38.4 (was 40.000000) When placing the white surface white_border_hi = 115.189; white_border_low = 68; white_outside_low = 58.1195; white_inside_hi = 120; white_outside_hi = 115.189; When placing the pial surface pial_border_hi = 58.1195; pial_border_low = 38.3586; pial_outside_low = 10; pial_inside_hi = 98.8114; pial_outside_hi = 53.1793; #VMPC# mris_autodet_gwstats VmPeak 259988 mris_autodet_gwstats done @#@FSTIME 2026:05:28:02:29:39 mris_autodet_gwstats N 8 e 6.24 S 0.11 U 6.12 P 99% M 244652 F 0 R 29595 W 0 c 18 w 31 I 0 O 8 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:29:46 mris_autodet_gwstats N 8 12.00 12.01 12.00 #-------------------------------------------- #@# AutoDetGWStats rh Thu May 28 02:29:46 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 252805 voxels (1.51%) border gray 288479 voxels (1.72%) 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=37474, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (104.0): 101.9 +- 8.2 [70.0 --> 110.0] CCS GM (72.0) : 73.0 +- 9.9 [30.0 --> 110.0] white_mean = 101.857 +/- 8.18857, gray_mean = 73.0038 +/- 9.88045 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=231 nbins=232 intensity peaks found at WM=107+-4.3, GM=68+-7.0 white_mode = 107, gray_mode = 68 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 58.1 (was 70.000000) setting MAX_BORDER_WHITE to 115.2 (was 105.000000) setting MIN_BORDER_WHITE to 68.0 (was 85.000000) setting MAX_CSF to 48.2 (was 40.000000) setting MAX_GRAY to 98.8 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 58.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 38.4 (was 40.000000) When placing the white surface white_border_hi = 115.189; white_border_low = 68; white_outside_low = 58.1195; white_inside_hi = 120; white_outside_hi = 115.189; When placing the pial surface pial_border_hi = 58.1195; pial_border_low = 38.3586; pial_outside_low = 10; pial_inside_hi = 98.8114; pial_outside_hi = 53.1793; #VMPC# mris_autodet_gwstats VmPeak 261536 mris_autodet_gwstats done @#@FSTIME 2026:05:28:02:29:46 mris_autodet_gwstats N 8 e 6.28 S 0.14 U 6.13 P 99% M 245972 F 0 R 30666 W 0 c 15 w 26 I 0 O 8 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:29:52 mris_autodet_gwstats N 8 12.00 12.00 12.00 #-------------------------------------------- #@# WhitePreAparc lh Thu May 28 02:29:52 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 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 before ripping with 5 iterations Area 286976 0.26551 0.06241 0.007878 0.5574 Corner 860928 60.00000 9.63608 8.364761 154.6995 Edge 430464 0.78716 0.11364 0.113008 1.2769 Hinge 430464 6.36115 6.42005 0.000005 113.5258 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37474, wmmin=5, clip=110 MRIfindBrightNonWM(): 2840 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6374, nmarked2=4, nripped=6374 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 71745: xyz = (-31.2857,-8.93326,53.9901) oxyz = (-31.2857,-8.93326,53.9901) wxzy = (-31.2857,-8.93326,53.9901) pxyz = (0,0,0) CBVO Creating mask 143490 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=6374 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6374, nmarked2=4, nripped=6374 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=2 had to be increased for 91 vertices, nripped=6374 mean border=80.0, 53 (53) missing vertices, mean dist 0.4 [0.5 (%32.7)->0.8 (%67.3))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3731 min Finding expansion regions mean absolute distance = 0.68 +- 0.79 4955 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 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=silbe, 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=4423875.5, rms=12.476 001: dt: 0.5000, sse=2399648.0, rms=9.055 (27.426%) 002: dt: 0.5000, sse=1469576.6, rms=6.936 (23.399%) 003: dt: 0.5000, sse=979810.6, rms=5.498 (20.738%) 004: dt: 0.5000, sse=730737.2, rms=4.594 (16.434%) 005: dt: 0.5000, sse=609138.2, rms=4.077 (11.255%) 006: dt: 0.5000, sse=552339.2, rms=3.808 (6.586%) 007: dt: 0.5000, sse=528758.3, rms=3.687 (3.191%) 008: dt: 0.5000, sse=513953.9, rms=3.608 (2.141%) rms = 3.5846/3.6080, sse=510116.2/513953.9, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=510116.2, rms=3.585 (0.648%) 010: dt: 0.2500, sse=277047.3, rms=2.056 (42.649%) 011: dt: 0.2500, sse=233987.4, rms=1.628 (20.824%) 012: dt: 0.2500, sse=223877.5, rms=1.502 (7.694%) 013: dt: 0.2500, sse=217770.2, rms=1.416 (5.752%) rms = 1.3757/1.4161, sse=214743.4/217770.2, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=214743.4, rms=1.376 (2.850%) 015: dt: 0.1250, sse=207766.5, rms=1.287 (6.436%) rms = 1.2705/1.2871, sse=206723.2/207766.5, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=206723.2, rms=1.270 (1.297%) maximum number of reductions reached, breaking from loop positioning took 2.4 minutes done positioning surface 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=6374 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6625, nmarked2=4, nripped=6625 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=1 had to be increased for 60 vertices, nripped=6625 mean border=84.7, 25 (0) missing vertices, mean dist -0.3 [0.3 (%83.9)->0.2 (%16.1))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2464 min Finding expansion regions mean absolute distance = 0.32 +- 0.43 3905 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 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=silbe, 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=1202838.8, rms=6.011 017: dt: 0.5000, sse=608116.6, rms=3.800 (36.791%) rms = 3.8241/3.7996, sse=611366.0/608116.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=437817.8, rms=2.867 (24.540%) 019: dt: 0.2500, sse=329633.8, rms=2.066 (27.927%) 020: dt: 0.2500, sse=287556.0, rms=1.654 (19.955%) 021: dt: 0.2500, sse=269214.4, rms=1.436 (13.164%) 022: dt: 0.2500, sse=257780.5, rms=1.281 (10.831%) 023: dt: 0.2500, sse=250748.8, rms=1.173 (8.401%) 024: dt: 0.2500, sse=247518.5, rms=1.120 (4.495%) rms = 1.0872/1.1204, sse=245606.8/247518.5, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=245606.8, rms=1.087 (2.971%) 026: dt: 0.1250, sse=241951.5, rms=1.022 (6.014%) rms = 1.0139/1.0218, sse=241563.4/241951.5, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=241563.4, rms=1.014 (0.768%) maximum number of reductions reached, breaking from loop positioning took 1.7 minutes done positioning surface 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=6625 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6715, nmarked2=4, nripped=6715 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 60 vertices, nripped=6715 mean border=87.2, 16 (0) missing vertices, mean dist -0.1 [0.2 (%77.4)->0.2 (%22.6))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1377 min Finding expansion regions mean absolute distance = 0.18 +- 0.25 2831 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 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=silbe, 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=507675.4, rms=3.325 028: dt: 0.5000, sse=478578.1, rms=3.131 (5.852%) rms = 3.5193/3.1308, sse=543756.2/478578.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=303662.2, rms=1.866 (40.386%) 030: dt: 0.2500, sse=251801.9, rms=1.280 (31.420%) 031: dt: 0.2500, sse=238780.8, rms=1.083 (15.354%) rms = 1.0357/1.0834, sse=235808.9/238780.8, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=235808.9, rms=1.036 (4.406%) 033: dt: 0.1250, sse=229239.0, rms=0.913 (11.864%) rms = 0.8998/0.9128, sse=228528.7/229239.0, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=228528.7, rms=0.900 (1.423%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes done positioning surface 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=6715 removing 4 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 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=6780, nmarked2=4, nripped=6780 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 72 vertices, nripped=6780 mean border=87.9, 46 (0) missing vertices, mean dist -0.0 [0.1 (%57.8)->0.1 (%42.2))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0857 min Finding expansion regions mean absolute distance = 0.14 +- 0.20 3365 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 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=silbe, 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=247763.0, rms=1.269 rms = 1.7446/1.2691, sse=292759.9/247763.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=221357.1, rms=0.788 (37.942%) 036: dt: 0.2500, sse=217074.3, rms=0.653 (17.136%) rms = 0.6779/0.6526, sse=217582.5/217074.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.6497/0.6526, sse=216896.5/217074.3, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=216896.5, rms=0.650 (0.444%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Removing intersections #ET# mris_place_surface 6.78 minutes Writing output to ../surf/lh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2229928 mris_place_surface done @#@FSTIME 2026:05:28:02:29:52 mris_place_surface N 18 e 418.90 S 1.16 U 417.70 P 99% M 1977896 F 0 R 264354 W 0 c 403 w 149 I 0 O 10096 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:02:36:51 mris_place_surface N 18 12.16 12.06 12.02 #-------------------------------------------- #@# WhitePreAparc rh Thu May 28 02:36:51 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 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 before ripping with 5 iterations Area 289612 0.26702 0.06255 0.001541 0.5722 Corner 868836 60.00000 9.66117 10.253647 133.4471 Edge 434418 0.78943 0.11367 0.048108 1.3261 Hinge 434418 6.36377 6.51098 0.000004 147.3919 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37474, wmmin=5, clip=110 MRIfindBrightNonWM(): 2840 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6267, nmarked2=13, nripped=6267 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 72404: xyz = (28.0049,-12.9006,53.0456) oxyz = (28.0049,-12.9006,53.0456) wxzy = (28.0049,-12.9006,53.0456) pxyz = (0,0,0) CBVO Creating mask 144808 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=6267 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6267, nmarked2=13, nripped=6267 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=2 had to be increased for 79 vertices, nripped=6267 mean border=80.0, 49 (49) missing vertices, mean dist 0.4 [0.4 (%33.1)->0.8 (%66.9))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3718 min Finding expansion regions mean absolute distance = 0.67 +- 0.76 5106 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 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=silbe, 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=4619291.0, rms=12.689 001: dt: 0.5000, sse=2535996.8, rms=9.243 (27.156%) 002: dt: 0.5000, sse=1554612.6, rms=7.109 (23.091%) 003: dt: 0.5000, sse=1038226.6, rms=5.646 (20.578%) 004: dt: 0.5000, sse=767965.4, rms=4.694 (16.861%) 005: dt: 0.5000, sse=634902.8, rms=4.155 (11.493%) 006: dt: 0.5000, sse=573345.0, rms=3.865 (6.976%) 007: dt: 0.5000, sse=546518.6, rms=3.740 (3.236%) 008: dt: 0.5000, sse=530081.4, rms=3.652 (2.335%) rms = 3.6286/3.6524, sse=525705.5/530081.4, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=525705.5, rms=3.629 (0.651%) 010: dt: 0.2500, sse=284619.7, rms=2.083 (42.599%) 011: dt: 0.2500, sse=241349.6, rms=1.661 (20.233%) 012: dt: 0.2500, sse=231423.4, rms=1.536 (7.551%) 013: dt: 0.2500, sse=224657.1, rms=1.447 (5.790%) rms = 1.4010/1.4470, sse=220382.4/224657.1, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=220382.4, rms=1.401 (3.182%) 015: dt: 0.1250, sse=212524.2, rms=1.295 (7.536%) rms = 1.2745/1.2954, sse=210934.6/212524.2, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=210934.6, rms=1.275 (1.610%) maximum number of reductions reached, breaking from loop positioning took 2.5 minutes done positioning surface 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=6267 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 #FML# MRISripMidline(): nmarked=6514, nmarked2=14, nripped=6514 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=1 had to be increased for 44 vertices, nripped=6514 mean border=84.5, 42 (14) missing vertices, mean dist -0.2 [0.3 (%83.5)->0.2 (%16.5))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2470 min Finding expansion regions mean absolute distance = 0.31 +- 0.41 4481 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 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=silbe, 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=1212770.2, rms=5.998 017: dt: 0.5000, sse=617782.0, rms=3.809 (36.495%) rms = 3.8169/3.8089, sse=617970.1/617782.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=442035.8, rms=2.854 (25.066%) 019: dt: 0.2500, sse=331783.0, rms=2.043 (28.435%) 020: dt: 0.2500, sse=290145.8, rms=1.612 (21.074%) 021: dt: 0.2500, sse=270105.2, rms=1.383 (14.185%) 022: dt: 0.2500, sse=259254.8, rms=1.241 (10.317%) 023: dt: 0.2500, sse=254513.6, rms=1.156 (6.792%) rms = 1.1180/1.1565, sse=251355.3/254513.6, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=251355.3, rms=1.118 (3.323%) 025: dt: 0.1250, sse=246918.0, rms=1.038 (7.134%) rms = 1.0277/1.0383, sse=246549.5/246918.0, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=246549.5, rms=1.028 (1.022%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes done positioning surface 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=6514 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 #FML# MRISripMidline(): nmarked=6584, nmarked2=13, nripped=6584 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 101 vertices, nripped=6584 mean border=87.0, 61 (10) missing vertices, mean dist -0.1 [0.2 (%76.8)->0.2 (%23.2))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1357 min Finding expansion regions mean absolute distance = 0.18 +- 0.25 3434 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 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=silbe, 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=507288.0, rms=3.284 027: dt: 0.5000, sse=485680.1, rms=3.143 (4.320%) rms = 3.5287/3.1426, sse=552094.7/485680.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=309596.8, rms=1.889 (39.887%) 029: dt: 0.2500, sse=256705.8, rms=1.308 (30.760%) 030: dt: 0.2500, sse=243573.1, rms=1.108 (15.288%) rms = 1.0603/1.1080, sse=240722.7/243573.1, time step reduction 2 of 3 to 0.125 0 0 1 031: dt: 0.2500, sse=240722.7, rms=1.060 (4.310%) 032: dt: 0.1250, sse=232875.1, rms=0.930 (12.302%) rms = 0.9143/0.9299, sse=232157.7/232875.1, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=232157.7, rms=0.914 (1.669%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes done positioning surface 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=6584 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 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=6644, nmarked2=13, nripped=6644 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 106 vertices, nripped=6644 mean border=87.7, 70 (7) missing vertices, mean dist -0.0 [0.1 (%57.5)->0.1 (%42.5))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0866 min Finding expansion regions mean absolute distance = 0.15 +- 0.21 2530 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 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=silbe, 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=253388.5, rms=1.303 rms = 1.7218/1.3031, sse=292452.3/253388.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 034: dt: 0.2500, sse=226351.3, rms=0.840 (35.564%) 035: dt: 0.2500, sse=220532.1, rms=0.687 (18.149%) rms = 0.7102/0.6873, sse=220991.6/220532.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.6800/0.6873, sse=220182.5/220532.1, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=220182.5, rms=0.680 (1.056%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Removing intersections #ET# mris_place_surface 6.70 minutes Writing output to ../surf/rh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2216936 mris_place_surface done @#@FSTIME 2026:05:28:02:36:51 mris_place_surface N 18 e 413.64 S 0.99 U 412.62 P 99% M 1964968 F 0 R 252584 W 0 c 393 w 159 I 0 O 10184 L 12.16 12.06 12.02 @#@FSLOADPOST 2026:05:28:02:43:45 mris_place_surface N 18 12.00 12.02 12.00 #-------------------------------------------- #@# CortexLabel lh Thu May 28 02:43:45 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 11 non-cortical segments detected only using segment with 8191 vertices erasing segment 0 (vno[0] = 36388) erasing segment 1 (vno[0] = 39145) erasing segment 3 (vno[0] = 43075) erasing segment 4 (vno[0] = 48391) erasing segment 5 (vno[0] = 49370) erasing segment 6 (vno[0] = 81523) erasing segment 7 (vno[0] = 83260) erasing segment 8 (vno[0] = 83277) erasing segment 9 (vno[0] = 84868) erasing segment 10 (vno[0] = 102153) @#@FSTIME 2026:05:28:02:43:45 mri_label2label N 5 e 25.54 S 0.13 U 25.39 P 99% M 359764 F 0 R 37185 W 0 c 18 w 129 I 10096 O 11768 L 12.00 12.02 12.00 @#@FSLOADPOST 2026:05:28:02:44:10 mri_label2label N 5 12.00 12.01 12.00 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Thu May 28 02:44:10 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 17 non-cortical segments detected only using segment with 5922 vertices erasing segment 0 (vno[0] = 36388) erasing segment 1 (vno[0] = 39145) erasing segment 3 (vno[0] = 43075) erasing segment 4 (vno[0] = 43178) erasing segment 5 (vno[0] = 44950) erasing segment 6 (vno[0] = 47602) erasing segment 7 (vno[0] = 47625) erasing segment 8 (vno[0] = 48391) erasing segment 9 (vno[0] = 49370) erasing segment 10 (vno[0] = 52681) erasing segment 11 (vno[0] = 78703) erasing segment 12 (vno[0] = 83260) erasing segment 13 (vno[0] = 83277) erasing segment 14 (vno[0] = 84868) erasing segment 15 (vno[0] = 102153) erasing segment 16 (vno[0] = 128011) @#@FSTIME 2026:05:28:02:44:10 mri_label2label N 5 e 25.73 S 0.21 U 25.51 P 99% M 390240 F 0 R 39689 W 0 c 23 w 98 I 0 O 11960 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:44:36 mri_label2label N 5 12.00 12.01 12.00 #-------------------------------------------- #@# CortexLabel rh Thu May 28 02:44:36 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 11 non-cortical segments detected only using segment with 7972 vertices erasing segment 1 (vno[0] = 45026) erasing segment 2 (vno[0] = 84712) erasing segment 3 (vno[0] = 86446) erasing segment 4 (vno[0] = 86458) erasing segment 5 (vno[0] = 87348) erasing segment 6 (vno[0] = 87387) erasing segment 7 (vno[0] = 90493) erasing segment 8 (vno[0] = 90497) erasing segment 9 (vno[0] = 90500) erasing segment 10 (vno[0] = 121816) @#@FSTIME 2026:05:28:02:44:36 mri_label2label N 5 e 26.98 S 0.19 U 26.76 P 99% M 361764 F 0 R 37829 W 0 c 66 w 127 I 10184 O 11640 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:45:03 mri_label2label N 5 12.00 12.01 12.00 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Thu May 28 02:45:03 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 14 non-cortical segments detected only using segment with 5627 vertices erasing segment 1 (vno[0] = 45026) erasing segment 2 (vno[0] = 51998) erasing segment 3 (vno[0] = 52181) erasing segment 4 (vno[0] = 58989) erasing segment 5 (vno[0] = 84712) erasing segment 6 (vno[0] = 86446) erasing segment 7 (vno[0] = 86458) erasing segment 8 (vno[0] = 87348) erasing segment 9 (vno[0] = 87387) erasing segment 10 (vno[0] = 90493) erasing segment 11 (vno[0] = 90497) erasing segment 12 (vno[0] = 90500) erasing segment 13 (vno[0] = 121816) @#@FSTIME 2026:05:28:02:45:03 mri_label2label N 5 e 26.89 S 0.23 U 26.64 P 99% M 376868 F 0 R 38612 W 0 c 54 w 133 I 0 O 11832 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:45:30 mri_label2label N 5 12.00 12.01 12.00 #-------------------------------------------- #@# Smooth2 lh Thu May 28 02:45:30 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:02:45:30 mris_smooth N 7 e 4.94 S 0.14 U 4.77 P 99% M 221436 F 0 R 39180 W 0 c 11 w 80 I 0 O 10096 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:45:35 mris_smooth N 7 12.00 12.01 12.00 #-------------------------------------------- #@# Smooth2 rh Thu May 28 02:45:35 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:02:45:35 mris_smooth N 7 e 4.98 S 0.16 U 4.81 P 99% M 223448 F 0 R 39775 W 0 c 10 w 117 I 0 O 10192 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:45:40 mris_smooth N 7 12.00 12.01 12.00 #-------------------------------------------- #@# Inflation2 lh Thu May 28 02:45:40 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.1 mm, total surface area = 87311 mm^2 step 000: RMS=0.167 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.023 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.019 (target=0.015) step 060: RMS=0.018 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.6 minutes mris_inflate utimesec 33.454255 mris_inflate stimesec 0.787958 mris_inflate ru_maxrss 222296 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 239422 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10096 mris_inflate ru_oublock 11224 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 118 mris_inflate ru_nivcsw 91 @#@FSTIME 2026:05:28:02:45:40 mris_inflate N 2 e 34.27 S 0.79 U 33.45 P 99% M 222296 F 0 R 239427 W 0 c 92 w 119 I 10096 O 11224 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:02:46:15 mris_inflate N 2 12.00 12.00 12.00 #-------------------------------------------- #@# Inflation2 rh Thu May 28 02:46:15 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.7 mm, total surface area = 88700 mm^2 step 000: RMS=0.167 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.018 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.6 minutes mris_inflate utimesec 32.978328 mris_inflate stimesec 0.119993 mris_inflate ru_maxrss 225012 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34511 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11328 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 137 mris_inflate ru_nivcsw 31 @#@FSTIME 2026:05:28:02:46:15 mris_inflate N 2 e 33.13 S 0.13 U 32.97 P 99% M 225312 F 0 R 34516 W 0 c 31 w 137 I 0 O 11328 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:02:46:48 mris_inflate N 2 12.00 12.00 12.00 #-------------------------------------------- #@# Curv .H and .K lh Thu May 28 02:46:48 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 11.373*4pi (142.911) --> -10 handles ICI = 127.7, FI = 1464.3, variation=22474.996 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done. @#@FSTIME 2026:05:28:02:46:48 mris_curvature N 4 e 2.58 S 0.09 U 2.47 P 99% M 165540 F 0 R 19600 W 0 c 7 w 109 I 0 O 2256 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:02:46:50 mris_curvature N 4 12.00 12.00 12.00 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 250 vertices thresholded to be in k1 ~ [-0.22 0.28], k2 ~ [-0.08 0.05] total integrated curvature = 0.707*4pi (8.890) --> 0 handles ICI = 1.7, FI = 10.8, variation=181.411 132 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 = 0.001 157 vertices thresholded to be in [-0.12 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done. @#@FSTIME 2026:05:28:02:46:50 mris_curvature N 12 e 76.01 S 0.35 U 75.64 P 99% M 389804 F 0 R 74944 W 0 c 157 w 66 I 0 O 2256 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:02:48:06 mris_curvature N 12 12.00 12.00 12.00 #-------------------------------------------- #@# Curv .H and .K rh Thu May 28 02:48:06 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 11.310*4pi (142.124) --> -10 handles ICI = 130.5, FI = 1493.3, variation=22937.794 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done. @#@FSTIME 2026:05:28:02:48:07 mris_curvature N 4 e 2.61 S 0.10 U 2.50 P 99% M 166896 F 0 R 20500 W 0 c 9 w 79 I 0 O 2272 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:02:48:09 mris_curvature N 4 12.00 12.00 12.00 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 270 vertices thresholded to be in k1 ~ [-0.18 0.31], k2 ~ [-0.07 0.06] total integrated curvature = 0.700*4pi (8.796) --> 0 handles ICI = 1.8, FI = 10.5, variation=181.291 148 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 161 vertices thresholded to be in [-0.12 0.15] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.023 mris_curvature done. @#@FSTIME 2026:05:28:02:48:09 mris_curvature N 12 e 76.97 S 0.24 U 76.70 P 99% M 393120 F 0 R 76352 W 0 c 146 w 99 I 0 O 2272 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:02:49:26 mris_curvature N 12 12.00 12.00 12.00 #-------------------------------------------- #@# Sphere lh Thu May 28 02:49:26 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.280... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=silbe, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.28 pass 1: epoch 2 of 3 starting distance error %20.27 unfolding complete - removing small folds... starting distance error %20.27 removing remaining folds... final distance error %20.27 MRISunfold() return, current seed 1234 -01: dt=0.0000, 50 negative triangles VmPeak 549984 089: dt=0.9900, 50 negative triangles 090: dt=0.9900, 12 negative triangles 091: dt=0.9900, 5 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1893 hours FSRUNTIME@ mris_sphere 0.1893 hours 1 threads #VMPC# mris_sphere VmPeak 549984 mris_sphere done @#@FSTIME 2026:05:28:02:49:26 mris_sphere N 4 e 681.45 S 17.13 U 664.28 P 99% M 296680 F 0 R 5188347 W 0 c 1251 w 134 I 0 O 10096 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:03:00:48 mris_sphere N 4 12.03 12.02 12.00 #-------------------------------------------- #@# Sphere rh Thu May 28 03:00:48 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.279... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=silbe, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.53 pass 1: epoch 2 of 3 starting distance error %20.50 unfolding complete - removing small folds... starting distance error %20.50 removing remaining folds... final distance error %20.50 MRISunfold() return, current seed 1234 -01: dt=0.0000, 71 negative triangles VmPeak 552584 102: dt=0.9900, 71 negative triangles 103: dt=0.9900, 13 negative triangles 104: dt=0.9900, 3 negative triangles 105: dt=0.9900, 1 negative triangles 106: dt=0.9900, 1 negative triangles 107: dt=0.9900, 1 negative triangles 108: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.2233 hours FSRUNTIME@ mris_sphere 0.2233 hours 1 threads #VMPC# mris_sphere VmPeak 552584 mris_sphere done @#@FSTIME 2026:05:28:03:00:48 mris_sphere N 4 e 804.00 S 21.41 U 782.53 P 99% M 299468 F 0 R 6329939 W 0 c 1381 w 154 I 0 O 10192 L 12.03 12.02 12.00 @#@FSLOADPOST 2026:05:28:03:14:12 mris_sphere N 4 12.09 12.06 12.01 #-------------------------------------------- #@# Surf Reg lh Thu May 28 03:14:12 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_register -curv ../surf/lh.sphere /software/freesurfer/7.4.1/debian-bookworm-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts cmdline mris_register -curv ../surf/lh.sphere /software/freesurfer/7.4.1/debian-bookworm-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.4.1 7.4.1 reading surface from ../surf/lh.sphere... reading template parameterization from /software/freesurfer/7.4.1/debian-bookworm-amd64/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=silbe, 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=silbe, 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=silbe, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.517 curvature mean = 0.025, std = 0.816 curvature mean = 0.014, std = 0.863 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (2.00, -9.00, -3.50) sse = 270109.2, elapsed since starting=0.7204 min MRISrigidBodyAlignGlobal() done 0.72 min curvature mean = 0.021, std = 0.834 curvature mean = 0.007, std = 0.948 curvature mean = 0.021, std = 0.844 curvature mean = 0.003, std = 0.979 curvature mean = 0.021, std = 0.846 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.017, std = 0.273 curvature mean = 0.047, std = 0.247 curvature mean = 0.064, std = 0.346 curvature mean = 0.044, std = 0.304 curvature mean = 0.032, std = 0.552 curvature mean = 0.043, std = 0.332 curvature mean = 0.017, std = 0.695 curvature mean = 0.043, std = 0.344 curvature mean = 0.005, std = 0.804 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... -01: dt=0.0000, 0 negative triangles VmPeak 528888 registration took 0.20 hours #VMPC# mris_register VmPeak 528888 FSRUNTIME@ mris_register 0.2027 hours 1 threads @#@FSTIME 2026:05:28:03:14:12 mris_register N 4 e 729.80 S 19.19 U 710.57 P 99% M 276284 F 0 R 5549875 W 0 c 1036 w 161 I 0 O 10096 L 12.09 12.06 12.01 @#@FSLOADPOST 2026:05:28:03:26:22 mris_register N 4 12.10 12.07 12.01 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Thu May 28 03:26:22 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_register -curv ../surf/rh.sphere /software/freesurfer/7.4.1/debian-bookworm-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts cmdline mris_register -curv ../surf/rh.sphere /software/freesurfer/7.4.1/debian-bookworm-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.4.1 7.4.1 reading surface from ../surf/rh.sphere... reading template parameterization from /software/freesurfer/7.4.1/debian-bookworm-amd64/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=silbe, 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=silbe, 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=silbe, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.610 curvature mean = 0.028, std = 0.813 curvature mean = 0.012, std = 0.860 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (7.50, -6.50, -4.00) sse = 310937.2, elapsed since starting=0.7260 min MRISrigidBodyAlignGlobal() done 0.73 min curvature mean = 0.025, std = 0.827 curvature mean = 0.007, std = 0.946 curvature mean = 0.024, std = 0.834 curvature mean = 0.003, std = 0.978 curvature mean = 0.024, std = 0.835 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.018, std = 0.274 curvature mean = 0.040, std = 0.241 curvature mean = 0.060, std = 0.354 curvature mean = 0.038, std = 0.297 curvature mean = 0.031, std = 0.554 curvature mean = 0.038, std = 0.324 curvature mean = 0.016, std = 0.694 curvature mean = 0.037, std = 0.336 curvature mean = 0.004, std = 0.803 MRISregister() return, current seed 0 -01: dt=0.0000, 1 negative triangles VmPeak 532208 117: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.32 hours #VMPC# mris_register VmPeak 532208 FSRUNTIME@ mris_register 0.3150 hours 1 threads @#@FSTIME 2026:05:28:03:26:22 mris_register N 4 e 1134.17 S 22.88 U 1111.22 P 99% M 279536 F 0 R 6546923 W 0 c 1332 w 94 I 10192 O 10192 L 12.10 12.07 12.01 @#@FSLOADPOST 2026:05:28:03:45:16 mris_register N 4 12.04 12.02 12.00 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Thu May 28 03:45:16 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:03:45:16 mris_jacobian N 3 e 1.79 S 0.14 U 1.64 P 99% M 221068 F 0 R 38030 W 0 c 3 w 45 I 0 O 1128 L 12.04 12.02 12.00 @#@FSLOADPOST 2026:05:28:03:45:18 mris_jacobian N 3 12.04 12.02 12.00 #-------------------------------------------- #@# Jacobian white rh Thu May 28 03:45:18 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:03:45:18 mris_jacobian N 3 e 1.83 S 0.17 U 1.65 P 99% M 222976 F 0 R 38621 W 0 c 11 w 43 I 0 O 1136 L 12.04 12.02 12.00 @#@FSLOADPOST 2026:05:28:03:45:20 mris_jacobian N 3 12.04 12.02 12.00 #-------------------------------------------- #@# AvgCurv lh Thu May 28 03:45:20 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mrisp_paint -a 5 /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2026:05:28:03:45:20 mrisp_paint N 5 e 1.33 S 0.11 U 1.20 P 99% M 170272 F 0 R 19815 W 0 c 6 w 40 I 0 O 1128 L 12.04 12.02 12.00 @#@FSLOADPOST 2026:05:28:03:45:21 mrisp_paint N 5 12.04 12.02 12.00 #-------------------------------------------- #@# AvgCurv rh Thu May 28 03:45:21 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mrisp_paint -a 5 /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2026:05:28:03:45:21 mrisp_paint N 5 e 1.38 S 0.09 U 1.28 P 99% M 171728 F 0 R 21229 W 0 c 4 w 43 I 0 O 1136 L 12.04 12.02 12.00 @#@FSLOADPOST 2026:05:28:03:45:23 mrisp_paint N 5 12.03 12.02 12.00 #----------------------------------------- #@# Cortical Parc lh Thu May 28 03:45:23 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 lh ../surf/lh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1417 labels changed using aseg relabeling using gibbs priors... 000: 3277 changed, 143490 examined... 001: 754 changed, 13905 examined... 002: 187 changed, 4181 examined... 003: 53 changed, 1159 examined... 004: 18 changed, 324 examined... 005: 9 changed, 106 examined... 006: 4 changed, 49 examined... 007: 3 changed, 22 examined... 008: 2 changed, 18 examined... 009: 1 changed, 10 examined... 010: 1 changed, 7 examined... 011: 0 changed, 7 examined... 256 labels changed using aseg 000: 98 total segments, 56 labels (229 vertices) changed 001: 43 total segments, 3 labels (8 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1941 vertices marked for relabeling... 1941 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 16 seconds. @#@FSTIME 2026:05:28:03:45:23 mris_ca_label N 11 e 16.45 S 0.86 U 15.56 P 99% M 1176768 F 0 R 192921 W 0 c 29 w 87 I 11768 O 2248 L 12.03 12.02 12.00 @#@FSLOADPOST 2026:05:28:03:45:39 mris_ca_label N 11 12.03 12.02 12.00 #----------------------------------------- #@# Cortical Parc rh Thu May 28 03:45:39 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 rh ../surf/rh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1352 labels changed using aseg relabeling using gibbs priors... 000: 2903 changed, 144808 examined... 001: 682 changed, 12383 examined... 002: 152 changed, 3909 examined... 003: 56 changed, 944 examined... 004: 19 changed, 343 examined... 005: 9 changed, 122 examined... 006: 3 changed, 52 examined... 007: 4 changed, 19 examined... 008: 2 changed, 25 examined... 009: 2 changed, 10 examined... 010: 2 changed, 10 examined... 011: 2 changed, 13 examined... 012: 1 changed, 9 examined... 013: 1 changed, 7 examined... 014: 0 changed, 6 examined... 151 labels changed using aseg 000: 93 total segments, 56 labels (209 vertices) changed 001: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1736 vertices marked for relabeling... 1736 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 16 seconds. @#@FSTIME 2026:05:28:03:45:39 mris_ca_label N 11 e 15.92 S 0.78 U 15.12 P 99% M 1156432 F 0 R 168595 W 0 c 20 w 80 I 11640 O 2272 L 12.03 12.02 12.00 @#@FSLOADPOST 2026:05:28:03:45:55 mris_ca_label N 11 12.02 12.02 12.00 #-------------------------------------------- #@# WhiteSurfs lh Thu May 28 03:45:55 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 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 286976 0.33151 0.11733 0.000704 1.7938 Corner 860928 60.00000 14.18074 0.428179 178.4693 Edge 430464 0.88537 0.19632 0.019516 4.2884 Hinge 430464 9.85140 10.57774 0.000027 179.8366 Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37474, wmmin=5, clip=110 MRIfindBrightNonWM(): 2840 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label MRISripNotLabel() ripped 8398/143490 vertices (135092 unripped) Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 543 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 71745: xyz = (-31.0487,-9.17574,53.9706) oxyz = (-31.0487,-9.17574,53.9706) wxzy = (-31.0487,-9.17574,53.9706) pxyz = (0,0,0) CBVO Creating mask 143490 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=2 had to be increased for 116 vertices, nripped=8941 mean border=79.4, 58 (58) missing vertices, mean dist 0.4 [1.1 (%7.6)->0.6 (%92.4))] %69 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3416 min Finding expansion regions mean absolute distance = 0.61 +- 0.76 3317 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 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=silbe, 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=2760316.8, rms=9.753 001: dt: 0.5000, sse=948295.8, rms=5.285 (45.809%) 002: dt: 0.5000, sse=564527.6, rms=3.700 (29.996%) 003: dt: 0.5000, sse=515382.8, rms=3.443 (6.951%) 004: dt: 0.5000, sse=473835.2, rms=3.207 (6.839%) rms = 3.3651/3.2074, sse=502464.0/473835.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=313546.0, rms=2.064 (35.657%) 006: dt: 0.2500, sse=260808.2, rms=1.506 (27.016%) 007: dt: 0.2500, sse=243984.6, rms=1.278 (15.166%) rms = 1.2295/1.2778, sse=241074.3/243984.6, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=241074.3, rms=1.230 (3.773%) 009: dt: 0.1250, sse=236432.3, rms=1.154 (6.132%) rms = 1.1419/1.1542, sse=235827.1/236432.3, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=235827.1, rms=1.142 (1.059%) maximum number of reductions reached, breaking from loop positioning took 1.7 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=1 had to be increased for 46 vertices, nripped=8941 mean border=84.4, 60 (28) missing vertices, mean dist -0.3 [0.4 (%84.7)->0.2 (%15.3))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2449 min Finding expansion regions mean absolute distance = 0.34 +- 0.42 3473 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 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=silbe, 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=1226932.1, rms=6.129 011: dt: 0.5000, sse=610568.4, rms=3.828 (37.541%) 012: dt: 0.5000, sse=586631.7, rms=3.716 (2.925%) 013: dt: 0.5000, sse=572179.4, rms=3.646 (1.895%) rms = 3.7266/3.6458, sse=587594.5/572179.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 014: dt: 0.2500, sse=350796.1, rms=2.239 (38.581%) 015: dt: 0.2500, sse=274680.1, rms=1.477 (34.058%) 016: dt: 0.2500, sse=252042.2, rms=1.156 (21.715%) 017: dt: 0.2500, sse=246485.5, rms=1.063 (8.025%) rms = 1.0166/1.0632, sse=243966.7/246485.5, time step reduction 2 of 3 to 0.125 0 0 1 018: dt: 0.2500, sse=243966.7, rms=1.017 (4.382%) 019: dt: 0.1250, sse=239716.5, rms=0.933 (8.175%) rms = 0.9275/0.9335, sse=239411.0/239716.6, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=239411.0, rms=0.928 (0.640%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 43 vertices, nripped=8941 mean border=87.1, 56 (19) missing vertices, mean dist -0.1 [0.2 (%78.2)->0.2 (%21.8))] %90 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1356 min Finding expansion regions mean absolute distance = 0.18 +- 0.25 2738 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 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=silbe, 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=511817.7, rms=3.372 021: dt: 0.5000, sse=477596.2, rms=3.102 (7.999%) rms = 3.4588/3.1023, sse=529431.8/477596.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 022: dt: 0.2500, sse=303457.3, rms=1.833 (40.923%) 023: dt: 0.2500, sse=250116.9, rms=1.218 (33.531%) 024: dt: 0.2500, sse=237401.8, rms=1.012 (16.936%) rms = 0.9635/1.0119, sse=234518.7/237401.8, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=234518.7, rms=0.963 (4.783%) 026: dt: 0.1250, sse=228875.7, rms=0.850 (11.813%) rms = 0.8390/0.8497, sse=228226.4/228875.7, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=228226.4, rms=0.839 (1.251%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 61 vertices, nripped=8941 mean border=87.8, 78 (18) missing vertices, mean dist -0.0 [0.1 (%58.0)->0.1 (%42.0))] %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0846 min Finding expansion regions mean absolute distance = 0.14 +- 0.20 3327 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 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=silbe, 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=247674.5, rms=1.241 rms = 1.7196/1.2407, sse=303336.5/247674.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=223492.2, rms=0.752 (39.402%) 029: dt: 0.2500, sse=221955.5, rms=0.622 (17.213%) rms = 0.6407/0.6224, sse=221096.6/221955.6, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.6185/0.6224, sse=221448.8/221955.6, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=221448.8, rms=0.618 (0.634%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Removing intersections #ET# mris_place_surface 5.93 minutes Writing output to ../surf/lh.white #VMPC# mris_place_surfaces VmPeak 2118292 mris_place_surface done @#@FSTIME 2026:05:28:03:45:55 mris_place_surface N 25 e 368.78 S 1.15 U 367.61 P 99% M 1866416 F 0 R 261333 W 0 c 323 w 105 I 2248 O 10096 L 12.02 12.02 12.00 @#@FSLOADPOST 2026:05:28:03:52:04 mris_place_surface N 25 12.00 12.00 12.00 #-------------------------------------------- #@# WhiteSurfs rh Thu May 28 03:52:04 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 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 289612 0.33382 0.11647 0.001307 2.1087 Corner 868836 60.00000 13.96011 0.096198 179.5346 Edge 434418 0.88843 0.19455 0.010804 3.1409 Hinge 434418 9.80800 10.62746 0.000007 179.8049 Reading in aparc ../label/rh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37474, wmmin=5, clip=110 MRIfindBrightNonWM(): 2840 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label MRISripNotLabel() ripped 8276/144808 vertices (136532 unripped) Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 528 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 72404: xyz = (28.0538,-13.1566,53.0893) oxyz = (28.0538,-13.1566,53.0893) wxzy = (28.0538,-13.1566,53.0893) pxyz = (0,0,0) CBVO Creating mask 144808 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=2 had to be increased for 125 vertices, nripped=8804 mean border=79.4, 49 (49) missing vertices, mean dist 0.4 [0.9 (%8.1)->0.5 (%91.9))] %69 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3340 min Finding expansion regions mean absolute distance = 0.58 +- 0.71 2912 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 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=silbe, 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=2744801.8, rms=9.668 001: dt: 0.5000, sse=955626.4, rms=5.270 (45.490%) 002: dt: 0.5000, sse=571901.1, rms=3.698 (29.826%) 003: dt: 0.5000, sse=524678.8, rms=3.454 (6.606%) 004: dt: 0.5000, sse=486684.7, rms=3.242 (6.139%) rms = 3.3922/3.2419, sse=514304.7/486684.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=319754.3, rms=2.076 (35.951%) 006: dt: 0.2500, sse=264055.7, rms=1.495 (28.000%) 007: dt: 0.2500, sse=247318.8, rms=1.269 (15.121%) rms = 1.2206/1.2689, sse=244411.6/247318.8, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=244411.6, rms=1.221 (3.813%) 009: dt: 0.1250, sse=239045.3, rms=1.133 (7.156%) rms = 1.1170/1.1332, sse=238199.8/239045.3, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=238199.8, rms=1.117 (1.435%) maximum number of reductions reached, breaking from loop positioning took 1.7 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=1 had to be increased for 52 vertices, nripped=8804 mean border=84.2, 32 (1) missing vertices, mean dist -0.3 [0.3 (%84.3)->0.2 (%15.7))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2445 min Finding expansion regions mean absolute distance = 0.33 +- 0.41 4226 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 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=silbe, 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=1230086.9, rms=6.093 011: dt: 0.5000, sse=612078.7, rms=3.795 (37.714%) 012: dt: 0.5000, sse=596968.6, rms=3.729 (1.755%) 013: dt: 0.5000, sse=576516.8, rms=3.628 (2.695%) rms = 3.7524/3.6282, sse=600707.5/576516.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 014: dt: 0.2500, sse=352647.0, rms=2.212 (39.026%) 015: dt: 0.2500, sse=278931.2, rms=1.477 (33.255%) 016: dt: 0.2500, sse=257739.6, rms=1.181 (20.038%) 017: dt: 0.2500, sse=252206.7, rms=1.091 (7.613%) rms = 1.0566/1.0908, sse=250264.0/252206.7, time step reduction 2 of 3 to 0.125 0 0 1 018: dt: 0.2500, sse=250264.0, rms=1.057 (3.139%) 019: dt: 0.1250, sse=245124.9, rms=0.961 (9.044%) rms = 0.9535/0.9610, sse=244792.3/245124.9, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=244792.3, rms=0.954 (0.778%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 64 vertices, nripped=8804 mean border=86.9, 40 (1) missing vertices, mean dist -0.1 [0.2 (%77.7)->0.2 (%22.3))] %91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1361 min Finding expansion regions mean absolute distance = 0.19 +- 0.26 3360 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 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=silbe, 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=511851.0, rms=3.335 021: dt: 0.5000, sse=484816.6, rms=3.128 (6.194%) rms = 3.4804/3.1283, sse=539944.7/484816.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 022: dt: 0.2500, sse=310110.3, rms=1.869 (40.262%) 023: dt: 0.2500, sse=255486.9, rms=1.257 (32.746%) 024: dt: 0.2500, sse=241399.5, rms=1.036 (17.607%) rms = 1.0008/1.0355, sse=239193.5/241399.5, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=239193.5, rms=1.001 (3.356%) 026: dt: 0.1250, sse=232699.3, rms=0.879 (12.191%) rms = 0.8651/0.8788, sse=231957.9/232699.3, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=231957.9, rms=0.865 (1.562%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1885680; border_low = 68.0000000; outside_low = 58.1195450; outside_hi = 115.1885680; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 72 vertices, nripped=8804 mean border=87.5, 58 (1) missing vertices, mean dist -0.0 [0.1 (%57.7)->0.1 (%42.3))] %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0851 min Finding expansion regions mean absolute distance = 0.15 +- 0.21 2573 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 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=silbe, 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=252537.6, rms=1.271 rms = 1.7016/1.2708, sse=298812.4/252537.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=227010.7, rms=0.795 (37.435%) 029: dt: 0.2500, sse=223154.2, rms=0.643 (19.107%) rms = 0.6638/0.6432, sse=223280.8/223154.2, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.6375/0.6432, sse=222727.6/223154.2, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=222727.5, rms=0.638 (0.878%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface Removing intersections #ET# mris_place_surface 5.91 minutes Writing output to ../surf/rh.white #VMPC# mris_place_surfaces VmPeak 2125028 mris_place_surface done @#@FSTIME 2026:05:28:03:52:04 mris_place_surface N 25 e 367.65 S 1.09 U 366.52 P 99% M 1873152 F 0 R 267786 W 0 c 357 w 127 I 2272 O 10184 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:03:58:12 mris_place_surface N 25 12.48 12.36 12.15 #-------------------------------------------- #@# T1PialSurf lh Thu May 28 03:58:12 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 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 286976 0.33325 0.12820 0.001601 1.8227 Corner 860928 60.00000 15.42606 0.340450 178.7363 Edge 430464 0.88879 0.21127 0.012129 4.2884 Hinge 430464 9.92387 10.78586 0.000001 179.9583 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37474, wmmin=5, clip=110 MRIfindBrightNonWM(): 2840 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 68.585 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 6200/143490 vertices (137290 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 71745: xyz = (-31.0398,-9.14214,53.9855) oxyz = (-31.0398,-9.14214,53.9855) wxzy = (-31.0398,-9.14214,53.9855) pxyz = (-31.0398,-9.14214,53.9855) CBVO Creating mask 143490 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8114320; border_hi = 58.1195450; border_low = 38.3586430; outside_low = 10.0000000; outside_hi = 53.1793210; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=2 had to be increased for 172 vertices, nripped=6200 mean border=55.9, 106 (106) missing vertices, mean dist 1.8 [0.3 (%0.0)->2.8 (%100.0))] %14 local maxima, %50 large gradients and %32 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2756 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 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=silbe, 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=28903650.0, rms=32.342 001: dt: 0.5000, sse=18940220.0, rms=26.132 (19.202%) 002: dt: 0.5000, sse=12521229.0, rms=21.187 (18.924%) 003: dt: 0.5000, sse=8919176.0, rms=17.819 (15.896%) 004: dt: 0.5000, sse=6913211.5, rms=15.630 (12.283%) 005: dt: 0.5000, sse=5645169.5, rms=14.070 (9.981%) 006: dt: 0.5000, sse=4637561.5, rms=12.693 (9.786%) 007: dt: 0.5000, sse=3734750.5, rms=11.318 (10.839%) 008: dt: 0.5000, sse=2919627.2, rms=9.912 (12.417%) 009: dt: 0.5000, sse=2205803.0, rms=8.492 (14.325%) 010: dt: 0.5000, sse=1630778.2, rms=7.145 (15.863%) 011: dt: 0.5000, sse=1223489.9, rms=6.010 (15.887%) 012: dt: 0.5000, sse=975747.1, rms=5.198 (13.507%) 013: dt: 0.5000, sse=849176.5, rms=4.729 (9.036%) 014: dt: 0.5000, sse=783948.7, rms=4.466 (5.558%) 015: dt: 0.5000, sse=754132.0, rms=4.338 (2.861%) 016: dt: 0.5000, sse=736254.0, rms=4.259 (1.830%) rms = 4.2299/4.2586, sse=730409.4/736254.0, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=730409.4, rms=4.230 (0.675%) 018: dt: 0.2500, sse=533187.7, rms=3.242 (23.351%) 019: dt: 0.2500, sse=488585.6, rms=2.978 (8.161%) rms = 2.9282/2.9776, sse=481111.6/488585.6, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=481111.6, rms=2.928 (1.659%) 021: dt: 0.1250, sse=456671.9, rms=2.767 (5.489%) rms = 2.7395/2.7675, sse=452617.8/456671.9, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=452617.8, rms=2.740 (1.011%) maximum number of reductions reached, breaking from loop positioning took 3.2 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8114320; border_hi = 58.1195450; border_low = 38.3586430; outside_low = 10.0000000; outside_hi = 53.1793210; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=1 had to be increased for 8984 vertices, nripped=6200 mean border=54.2, 1354 (12) missing vertices, mean dist 0.1 [0.1 (%47.4)->0.4 (%52.6))] %31 local maxima, %36 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0744 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 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=silbe, 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=693136.9, rms=3.778 rms = 3.9296/3.7776, sse=726660.3/693136.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=590945.1, rms=3.243 (14.165%) 024: dt: 0.2500, sse=538395.3, rms=2.927 (9.733%) 025: dt: 0.2500, sse=522604.1, rms=2.830 (3.315%) rms = 2.7965/2.8299, sse=517522.4/522604.1, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=517522.4, rms=2.797 (1.178%) 027: dt: 0.1250, sse=497171.9, rms=2.657 (5.003%) rms = 2.6234/2.6566, sse=492391.4/497171.9, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=492391.4, rms=2.623 (1.252%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8114320; border_hi = 58.1195450; border_low = 38.3586430; outside_low = 10.0000000; outside_hi = 53.1793210; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 9673 vertices, nripped=6200 mean border=52.9, 1467 (2) missing vertices, mean dist 0.1 [0.1 (%40.3)->0.3 (%59.7))] %49 local maxima, %19 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0438 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 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=silbe, 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=607911.1, rms=3.312 rms = 4.0813/3.3120, sse=764695.8/607911.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=538439.2, rms=2.900 (12.437%) 030: dt: 0.2500, sse=525324.1, rms=2.816 (2.908%) rms = 2.8090/2.8158, sse=523729.1/525324.1, time step reduction 2 of 3 to 0.125 0 0 1 031: dt: 0.2500, sse=523729.1, rms=2.809 (0.239%) 032: dt: 0.1250, sse=505783.2, rms=2.687 (4.339%) rms = 2.6621/2.6871, sse=502038.3/505783.2, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=502038.3, rms=2.662 (0.934%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8114320; border_hi = 58.1195450; border_low = 38.3586430; outside_low = 10.0000000; outside_hi = 53.1793210; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143490 Gdiag_no=-1 vno start=0, stop=143490 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8443 vertices, nripped=6200 mean border=52.1, 3411 (1) missing vertices, mean dist 0.0 [0.1 (%44.4)->0.2 (%55.6))] %53 local maxima, %15 large gradients and %26 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0286 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 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=silbe, 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=535001.1, rms=2.876 rms = 3.5625/2.8756, sse=655218.2/535001.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 034: dt: 0.2500, sse=514010.4, rms=2.737 (4.824%) rms = 2.7124/2.7369, sse=509639.1/514010.4, time step reduction 2 of 3 to 0.125 0 0 1 035: dt: 0.2500, sse=509639.1, rms=2.712 (0.894%) 036: dt: 0.1250, sse=499292.8, rms=2.640 (2.654%) rms = 2.6121/2.6404, sse=494937.0/499292.8, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=494937.0, rms=2.612 (1.073%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 12 intersecting terminating search with 0 intersecting #ET# mris_place_surface 6.21 minutes Writing output to ../surf/lh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1380944 mris_place_surface done @#@FSTIME 2026:05:28:03:58:12 mris_place_surface N 28 e 384.90 S 0.86 U 383.98 P 99% M 1128864 F 0 R 209974 W 0 c 621 w 148 I 22056 O 10096 L 12.48 12.36 12.15 @#@FSLOADPOST 2026:05:28:04:04:37 mris_place_surface N 28 12.02 12.11 12.09 #-------------------------------------------- #@# T1PialSurf rh Thu May 28 04:04:37 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 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 289612 0.33574 0.12741 0.000924 2.0670 Corner 868836 60.00000 15.20735 0.297678 178.9439 Edge 434418 0.89213 0.20953 0.015391 3.5987 Hinge 434418 9.87295 10.70928 0.000007 179.9604 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37474, wmmin=5, clip=110 MRIfindBrightNonWM(): 2840 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 68.585 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 6078/144808 vertices (138730 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 72404: xyz = (28.0644,-13.145,53.0526) oxyz = (28.0644,-13.145,53.0526) wxzy = (28.0644,-13.145,53.0526) pxyz = (28.0644,-13.145,53.0526) CBVO Creating mask 144808 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8114320; border_hi = 58.1195450; border_low = 38.3586430; outside_low = 10.0000000; outside_hi = 53.1793210; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=2 had to be increased for 193 vertices, nripped=6078 mean border=56.1, 99 (99) missing vertices, mean dist 1.8 [0.6 (%0.0)->2.7 (%100.0))] %13 local maxima, %49 large gradients and %33 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2766 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 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=silbe, 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=28363010.0, rms=31.867 001: dt: 0.5000, sse=18395524.0, rms=25.612 (19.627%) 002: dt: 0.5000, sse=11990132.0, rms=20.613 (19.517%) 003: dt: 0.5000, sse=8418128.0, rms=17.205 (16.537%) 004: dt: 0.5000, sse=6443391.5, rms=14.989 (12.876%) 005: dt: 0.5000, sse=5191766.5, rms=13.395 (10.638%) 006: dt: 0.5000, sse=4181802.0, rms=11.953 (10.767%) 007: dt: 0.5000, sse=3272066.0, rms=10.484 (12.284%) 008: dt: 0.5000, sse=2479598.2, rms=9.012 (14.044%) 009: dt: 0.5000, sse=1833976.0, rms=7.603 (15.630%) 010: dt: 0.5000, sse=1357312.8, rms=6.365 (16.288%) 011: dt: 0.5000, sse=1054409.8, rms=5.432 (14.660%) 012: dt: 0.5000, sse=885646.6, rms=4.832 (11.046%) 013: dt: 0.5000, sse=804327.4, rms=4.513 (6.603%) 014: dt: 0.5000, sse=762470.2, rms=4.338 (3.882%) 015: dt: 0.5000, sse=741705.3, rms=4.247 (2.090%) 016: dt: 0.5000, sse=728681.1, rms=4.187 (1.407%) rms = 4.1418/4.1872, sse=718910.9/728681.1, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=718910.9, rms=4.142 (1.086%) 018: dt: 0.2500, sse=539919.7, rms=3.243 (21.711%) 019: dt: 0.2500, sse=500399.7, rms=3.012 (7.115%) rms = 2.9844/3.0118, sse=496347.8/500399.7, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=496347.8, rms=2.984 (0.910%) 021: dt: 0.1250, sse=474784.1, rms=2.847 (4.603%) rms = 2.8268/2.8471, sse=471723.4/474784.1, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=471723.4, rms=2.827 (0.714%) maximum number of reductions reached, breaking from loop positioning took 3.2 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8114320; border_hi = 58.1195450; border_low = 38.3586430; outside_low = 10.0000000; outside_hi = 53.1793210; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=1 had to be increased for 9935 vertices, nripped=6078 mean border=54.4, 1479 (18) missing vertices, mean dist 0.1 [0.1 (%46.3)->0.4 (%53.7))] %30 local maxima, %36 large gradients and %29 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0764 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 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=silbe, 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=733957.4, rms=3.933 rms = 3.9020/3.9328, sse=728842.1/733957.3, time step reduction 1 of 3 to 0.250 0 0 1 023: dt: 0.5000, sse=728842.1, rms=3.902 (0.784%) 024: dt: 0.2500, sse=571763.4, rms=3.094 (20.711%) 025: dt: 0.2500, sse=549613.5, rms=2.962 (4.274%) rms = 2.9859/2.9616, sse=553791.0/549613.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 026: dt: 0.1250, sse=540230.6, rms=2.902 (2.004%) 027: dt: 0.1250, sse=528860.4, rms=2.828 (2.570%) rms = 2.8241/2.8277, sse=528399.9/528860.5, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=528399.9, rms=2.824 (0.128%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8114320; border_hi = 58.1195450; border_low = 38.3586430; outside_low = 10.0000000; outside_hi = 53.1793210; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 10421 vertices, nripped=6078 mean border=53.0, 1675 (12) missing vertices, mean dist 0.1 [0.1 (%39.1)->0.3 (%60.9))] %48 local maxima, %18 large gradients and %29 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0441 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 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=silbe, 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=646466.1, rms=3.477 rms = 4.1301/3.4768, sse=785412.0/646466.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=576791.9, rms=3.090 (11.138%) 030: dt: 0.2500, sse=563371.9, rms=3.008 (2.637%) rms = 2.9935/3.0080, sse=560383.9/563371.9, time step reduction 2 of 3 to 0.125 0 0 1 031: dt: 0.2500, sse=560383.9, rms=2.994 (0.482%) 032: dt: 0.1250, sse=543443.1, rms=2.887 (3.560%) rms = 2.8639/2.8870, sse=539678.4/543443.1, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=539678.4, rms=2.864 (0.800%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8114320; border_hi = 58.1195450; border_low = 38.3586430; outside_low = 10.0000000; outside_hi = 53.1793210; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144808 Gdiag_no=-1 vno start=0, stop=144808 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8815 vertices, nripped=6078 mean border=52.2, 3863 (10) missing vertices, mean dist 0.0 [0.2 (%44.2)->0.2 (%55.8))] %52 local maxima, %14 large gradients and %28 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0289 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 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=silbe, 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=570979.2, rms=3.054 rms = 3.6047/3.0539, sse=671559.4/570979.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 034: dt: 0.2500, sse=548518.4, rms=2.916 (4.513%) 035: dt: 0.2500, sse=539140.6, rms=2.862 (1.861%) rms = 2.8439/2.8618, sse=535732.4/539140.6, time step reduction 2 of 3 to 0.125 0 0 1 036: dt: 0.2500, sse=535732.4, rms=2.844 (0.625%) 037: dt: 0.1250, sse=517831.6, rms=2.726 (4.131%) rms = 2.6946/2.7264, sse=512886.7/517831.6, time step reduction 3 of 3 to 0.062 0 0 1 038: dt: 0.1250, sse=512886.7, rms=2.695 (1.166%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 34 intersecting 001: 12 intersecting step 1 with no progress (num=18, old_num=12) 002: 18 intersecting terminating search with 0 intersecting #ET# mris_place_surface 6.55 minutes Writing output to ../surf/rh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1388160 mris_place_surface done @#@FSTIME 2026:05:28:04:04:37 mris_place_surface N 28 e 405.64 S 0.82 U 404.77 P 99% M 1136076 F 0 R 202340 W 0 c 472 w 136 I 11832 O 10184 L 12.02 12.11 12.09 @#@FSLOADPOST 2026:05:28:04:11:22 mris_place_surface N 28 12.00 12.03 12.06 #@# white curv lh Thu May 28 04:11:22 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:04:11:23 mris_place_surface N 5 e 3.15 S 0.09 U 3.05 P 99% M 199020 F 0 R 26495 W 0 c 7 w 41 I 0 O 1128 L 12.00 12.03 12.06 @#@FSLOADPOST 2026:05:28:04:11:26 mris_place_surface N 5 12.00 12.03 12.06 #@# white area lh Thu May 28 04:11:26 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2026:05:28:04:11:26 mris_place_surface N 3 e 1.46 S 0.10 U 1.35 P 99% M 199124 F 0 R 26462 W 0 c 3 w 58 I 0 O 1128 L 12.00 12.03 12.06 @#@FSLOADPOST 2026:05:28:04:11:27 mris_place_surface N 3 12.00 12.03 12.06 #@# pial curv lh Thu May 28 04:11:27 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:04:11:27 mris_place_surface N 5 e 3.22 S 0.10 U 3.11 P 99% M 199192 F 0 R 27010 W 0 c 10 w 48 I 10096 O 1128 L 12.00 12.03 12.06 @#@FSLOADPOST 2026:05:28:04:11:31 mris_place_surface N 5 12.00 12.03 12.06 #@# pial area lh Thu May 28 04:11:31 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2026:05:28:04:11:31 mris_place_surface N 3 e 1.47 S 0.12 U 1.34 P 99% M 199116 F 0 R 26462 W 0 c 4 w 61 I 0 O 1128 L 12.00 12.03 12.06 @#@FSLOADPOST 2026:05:28:04:11:32 mris_place_surface N 3 12.00 12.03 12.06 #@# thickness lh Thu May 28 04:11:32 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 143490 vertices processed 25000 of 143490 vertices processed 50000 of 143490 vertices processed 75000 of 143490 vertices processed 100000 of 143490 vertices processed 125000 of 143490 vertices processed 0 of 143490 vertices processed 25000 of 143490 vertices processed 50000 of 143490 vertices processed 75000 of 143490 vertices processed 100000 of 143490 vertices processed 125000 of 143490 vertices processed thickness calculation complete, 116:526 truncations. 62535 vertices at 0 distance 123496 vertices at 1 distance 68702 vertices at 2 distance 22177 vertices at 3 distance 6554 vertices at 4 distance 2164 vertices at 5 distance 804 vertices at 6 distance 282 vertices at 7 distance 104 vertices at 8 distance 53 vertices at 9 distance 26 vertices at 10 distance 10 vertices at 11 distance 15 vertices at 12 distance 8 vertices at 13 distance 7 vertices at 14 distance 10 vertices at 15 distance 9 vertices at 16 distance 8 vertices at 17 distance 6 vertices at 18 distance 7 vertices at 19 distance 3 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2026:05:28:04:11:32 mris_place_surface N 6 e 53.28 S 0.15 U 53.12 P 99% M 199112 F 0 R 33665 W 0 c 40 w 43 I 0 O 1128 L 12.00 12.03 12.06 @#@FSLOADPOST 2026:05:28:04:12:25 mris_place_surface N 6 12.00 12.02 12.05 #@# area and vertex vol lh Thu May 28 04:12:25 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 lh /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.volume masking with /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Total face volume 273211 Total vertex volume 273012 (mask=0) #@# sub-20_ses-0 lh 273012 vertexvol Done @#@FSTIME 2026:05:28:04:12:25 vertexvol N 4 e 2.86 S 0.26 U 2.57 P 99% M 329456 F 0 R 47315 W 0 c 25 w 235 I 0 O 3384 L 12.00 12.02 12.05 @#@FSLOADPOST 2026:05:28:04:12:28 vertexvol N 4 12.00 12.02 12.05 #@# white curv rh Thu May 28 04:12:28 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:04:12:28 mris_place_surface N 5 e 3.09 S 0.12 U 2.96 P 99% M 200892 F 0 R 27991 W 0 c 10 w 44 I 0 O 1136 L 12.00 12.02 12.05 @#@FSLOADPOST 2026:05:28:04:12:32 mris_place_surface N 5 12.00 12.02 12.05 #@# white area rh Thu May 28 04:12:32 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2026:05:28:04:12:32 mris_place_surface N 3 e 1.44 S 0.11 U 1.32 P 99% M 200900 F 0 R 27447 W 0 c 4 w 42 I 0 O 1136 L 12.00 12.02 12.05 @#@FSLOADPOST 2026:05:28:04:12:33 mris_place_surface N 3 12.00 12.02 12.05 #@# pial curv rh Thu May 28 04:12:33 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 2026:05:28:04:12:33 mris_place_surface N 5 e 3.18 S 0.11 U 3.05 P 99% M 201004 F 0 R 27994 W 0 c 21 w 58 I 0 O 1136 L 12.00 12.02 12.05 @#@FSLOADPOST 2026:05:28:04:12:36 mris_place_surface N 5 12.00 12.02 12.05 #@# pial area rh Thu May 28 04:12:36 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2026:05:28:04:12:36 mris_place_surface N 3 e 1.44 S 0.12 U 1.30 P 99% M 200744 F 0 R 26935 W 0 c 2 w 56 I 0 O 1136 L 12.00 12.02 12.05 @#@FSLOADPOST 2026:05:28:04:12:38 mris_place_surface N 3 12.00 12.02 12.05 #@# thickness rh Thu May 28 04:12:38 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 144808 vertices processed 25000 of 144808 vertices processed 50000 of 144808 vertices processed 75000 of 144808 vertices processed 100000 of 144808 vertices processed 125000 of 144808 vertices processed 0 of 144808 vertices processed 25000 of 144808 vertices processed 50000 of 144808 vertices processed 75000 of 144808 vertices processed 100000 of 144808 vertices processed 125000 of 144808 vertices processed thickness calculation complete, 124:556 truncations. 63588 vertices at 0 distance 128654 vertices at 1 distance 67398 vertices at 2 distance 20707 vertices at 3 distance 6050 vertices at 4 distance 1983 vertices at 5 distance 684 vertices at 6 distance 264 vertices at 7 distance 96 vertices at 8 distance 31 vertices at 9 distance 20 vertices at 10 distance 21 vertices at 11 distance 18 vertices at 12 distance 18 vertices at 13 distance 17 vertices at 14 distance 13 vertices at 15 distance 15 vertices at 16 distance 12 vertices at 17 distance 12 vertices at 18 distance 8 vertices at 19 distance 7 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2026:05:28:04:12:38 mris_place_surface N 6 e 53.22 S 0.13 U 53.06 P 99% M 201012 F 0 R 34209 W 0 c 341 w 59 I 0 O 1136 L 12.00 12.02 12.05 @#@FSLOADPOST 2026:05:28:04:13:31 mris_place_surface N 6 12.00 12.01 12.04 #@# area and vertex vol rh Thu May 28 04:13:31 AM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 rh /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.volume masking with /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Total face volume 273760 Total vertex volume 273547 (mask=0) #@# sub-20_ses-0 rh 273547 vertexvol Done @#@FSTIME 2026:05:28:04:13:31 vertexvol N 4 e 2.80 S 0.22 U 2.55 P 99% M 332344 F 0 R 48107 W 0 c 6 w 209 I 0 O 3408 L 12.00 12.01 12.04 @#@FSLOADPOST 2026:05:28:04:13:34 vertexvol N 4 12.00 12.01 12.04 #----------------------------------------- #@# Curvature Stats lh Thu May 28 04:13:34 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-20_ses-0 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 [ sub-20_ses-0/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 [ 276 ] Gb_filter = 0 WARN: S lookup min: -0.045168 WARN: S explicit min: 0.000000 vertex = 898 @#@FSTIME 2026:05:28:04:13:34 mris_curvature_stats N 11 e 4.24 S 0.09 U 4.09 P 98% M 198844 F 0 R 27155 W 0 c 8 w 324 I 0 O 9064 L 12.00 12.01 12.04 @#@FSLOADPOST 2026:05:28:04:13:38 mris_curvature_stats N 11 12.00 12.01 12.04 #----------------------------------------- #@# Curvature Stats rh Thu May 28 04:13:38 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-20_ses-0 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 [ sub-20_ses-0/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 [ 243 ] Gb_filter = 0 WARN: S lookup min: -0.276886 WARN: S explicit min: 0.000000 vertex = 725 @#@FSTIME 2026:05:28:04:13:38 mris_curvature_stats N 11 e 4.36 S 0.15 U 4.15 P 98% M 200712 F 0 R 28169 W 0 c 44 w 311 I 0 O 9128 L 12.00 12.01 12.04 @#@FSLOADPOST 2026:05:28:04:13:43 mris_curvature_stats N 11 12.00 12.01 12.04 #-------------------------------------------- #@# Cortical ribbon mask Thu May 28 04:13:43 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 SUBJECTS_DIR is /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 loading input data... Running hemis serially Processing left hemi computing distance to left white surface computing distance to left pial surface Processing right hemi computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 245 writing volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/ribbon.mgz mris_volmask took 18.21 minutes writing ribbon files @#@FSTIME 2026:05:28:04:13:43 mris_volmask N 12 e 1092.71 S 1.10 U 1091.59 P 99% M 1025608 F 0 R 223592 W 0 c 382 w 58 I 0 O 904 L 12.00 12.01 12.04 @#@FSLOADPOST 2026:05:28:04:31:55 mris_volmask N 12 12.00 12.00 12.00 #----------------------------------------- #@# Cortical Parc 2 lh Thu May 28 04:31:56 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 lh ../surf/lh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 7 labels changed using aseg relabeling using gibbs priors... 000: 9603 changed, 143490 examined... 001: 2219 changed, 37210 examined... 002: 688 changed, 11879 examined... 003: 289 changed, 3902 examined... 004: 114 changed, 1669 examined... 005: 54 changed, 681 examined... 006: 28 changed, 321 examined... 007: 13 changed, 160 examined... 008: 7 changed, 83 examined... 009: 5 changed, 40 examined... 010: 6 changed, 29 examined... 011: 2 changed, 25 examined... 012: 0 changed, 13 examined... 1 labels changed using aseg 000: 262 total segments, 173 labels (2034 vertices) changed 001: 104 total segments, 16 labels (58 vertices) changed 002: 89 total segments, 1 labels (1 vertices) changed 003: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1223 vertices marked for relabeling... 1223 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 23 seconds. @#@FSTIME 2026:05:28:04:31:56 mris_ca_label N 11 e 23.32 S 1.53 U 21.77 P 99% M 2022864 F 0 R 373150 W 0 c 47 w 77 I 0 O 2256 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:32:19 mris_ca_label N 11 12.00 12.00 12.00 #----------------------------------------- #@# Cortical Parc 2 rh Thu May 28 04:32:19 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 rh ../surf/rh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1 labels changed using aseg relabeling using gibbs priors... 000: 9478 changed, 144808 examined... 001: 2165 changed, 37168 examined... 002: 656 changed, 11550 examined... 003: 318 changed, 3806 examined... 004: 134 changed, 1818 examined... 005: 68 changed, 784 examined... 006: 41 changed, 400 examined... 007: 14 changed, 241 examined... 008: 8 changed, 79 examined... 009: 8 changed, 55 examined... 010: 5 changed, 49 examined... 011: 0 changed, 26 examined... 1 labels changed using aseg 000: 248 total segments, 162 labels (2133 vertices) changed 001: 96 total segments, 12 labels (59 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1350 vertices marked for relabeling... 1350 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 23 seconds. @#@FSTIME 2026:05:28:04:32:19 mris_ca_label N 11 e 22.84 S 1.50 U 21.31 P 99% M 1966188 F 0 R 319669 W 0 c 212 w 88 I 0 O 2272 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:32:42 mris_ca_label N 11 12.00 12.00 12.00 #----------------------------------------- #@# Cortical Parc 3 lh Thu May 28 04:32:42 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 lh ../surf/lh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1665 labels changed using aseg relabeling using gibbs priors... 000: 2066 changed, 143490 examined... 001: 460 changed, 9589 examined... 002: 155 changed, 2637 examined... 003: 59 changed, 898 examined... 004: 29 changed, 340 examined... 005: 12 changed, 170 examined... 006: 7 changed, 67 examined... 007: 3 changed, 43 examined... 008: 2 changed, 21 examined... 009: 0 changed, 13 examined... 220 labels changed using aseg 000: 48 total segments, 15 labels (84 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 865 vertices marked for relabeling... 865 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. @#@FSTIME 2026:05:28:04:32:42 mris_ca_label N 11 e 16.61 S 0.62 U 15.97 P 99% M 936656 F 0 R 148632 W 0 c 31 w 69 I 0 O 2248 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:32:58 mris_ca_label N 11 12.00 12.00 12.00 #----------------------------------------- #@# Cortical Parc 3 rh Thu May 28 04:32:59 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 rh ../surf/rh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1600 labels changed using aseg relabeling using gibbs priors... 000: 2027 changed, 144808 examined... 001: 475 changed, 9575 examined... 002: 138 changed, 2711 examined... 003: 61 changed, 807 examined... 004: 40 changed, 347 examined... 005: 20 changed, 213 examined... 006: 7 changed, 104 examined... 007: 3 changed, 45 examined... 008: 2 changed, 18 examined... 009: 1 changed, 15 examined... 010: 0 changed, 7 examined... 163 labels changed using aseg 000: 58 total segments, 25 labels (146 vertices) changed 001: 34 total segments, 1 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1049 vertices marked for relabeling... 1049 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. @#@FSTIME 2026:05:28:04:32:59 mris_ca_label N 11 e 17.30 S 0.78 U 16.50 P 99% M 991200 F 0 R 170692 W 0 c 37 w 85 I 0 O 2272 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:33:16 mris_ca_label N 11 12.00 12.00 12.00 #----------------------------------------- #@# WM/GM Contrast lh Thu May 28 04:33:16 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts pctsurfcon --s sub-20_ses-0 --lh-only Log file is /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts/pctsurfcon.log Thu May 28 04:33:16 AM CEST 2026 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/pctsurfcon pctsurfcon 7.4.1 Linux silbermond 6.1.0-45-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.170-1 (2026-04-30) x86_64 GNU/Linux FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 mri_vol2surf --mov /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.27910/lh.wm.mgh --regheader sub-20_ses-0 --cortex srcvol = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Reading surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 82778 Masking with /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.27910/lh.wm.mgh Dim: 143490 1 1 mri_vol2surf done mri_vol2surf --mov /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.27910/lh.gm.mgh --projfrac 0.3 --regheader sub-20_ses-0 --cortex srcvol = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Reading surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Done reading source surface Reading thickness /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 99203 Masking with /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.27910/lh.gm.mgh Dim: 143490 1 1 mri_vol2surf done mri_concat /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.27910/lh.wm.mgh /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.27910/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh mri_segstats --in /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh --annot sub-20_ses-0 lh aparc --sum /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/stats/lh.w-g.pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh --annot sub-20_ses-0 lh aparc --sum /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/stats/lh.w-g.pct.stats --snr sysname Linux hostname silbermond machine x86_64 user flores whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot Seg base 1000 MRISannot2seg(): nhits = 135092 Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh Vertex Area is 0.666481 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 2026:05:28:04:33:16 pctsurfcon N 3 e 5.39 S 0.38 U 4.96 P 99% M 278064 F 0 R 72004 W 0 c 48 w 329 I 0 O 3552 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:33:21 pctsurfcon N 3 12.00 12.00 12.00 #----------------------------------------- #@# WM/GM Contrast rh Thu May 28 04:33:21 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts pctsurfcon --s sub-20_ses-0 --rh-only Log file is /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts/pctsurfcon.log Thu May 28 04:33:21 AM CEST 2026 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/scripts /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/pctsurfcon pctsurfcon 7.4.1 Linux silbermond 6.1.0-45-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.170-1 (2026-04-30) x86_64 GNU/Linux FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 mri_vol2surf --mov /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.28068/rh.wm.mgh --regheader sub-20_ses-0 --cortex srcvol = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Reading surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 83651 Masking with /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.28068/rh.wm.mgh Dim: 144808 1 1 mri_vol2surf done mri_vol2surf --mov /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.28068/rh.gm.mgh --projfrac 0.3 --regheader sub-20_ses-0 --cortex srcvol = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Reading surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Done reading source surface Reading thickness /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 100413 Masking with /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.28068/rh.gm.mgh Dim: 144808 1 1 mri_vol2surf done mri_concat /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.28068/rh.wm.mgh /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.28068/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh mri_segstats --in /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh --annot sub-20_ses-0 rh aparc --sum /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/stats/rh.w-g.pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh --annot sub-20_ses-0 rh aparc --sum /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/stats/rh.w-g.pct.stats --snr sysname Linux hostname silbermond machine x86_64 user flores whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.annot Seg base 2000 MRISannot2seg(): nhits = 136532 Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh Vertex Area is 0.67147 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 2026:05:28:04:33:21 pctsurfcon N 3 e 5.73 S 0.40 U 5.30 P 99% M 279400 F 0 R 75513 W 0 c 24 w 310 I 0 O 3576 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:33:27 pctsurfcon N 3 12.00 12.00 12.00 #----------------------------------------- #@# Relabel Hypointensities Thu May 28 04:33:27 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 788 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 677 voxels changed to hypointensity... 1472 hypointense voxels neighboring cortex changed @#@FSTIME 2026:05:28:04:33:27 mri_relabel_hypointensities N 3 e 26.96 S 0.50 U 26.45 P 99% M 510956 F 0 R 72035 W 0 c 40 w 25 I 0 O 696 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:33:54 mri_relabel_hypointensities N 3 12.06 12.01 12.00 #----------------------------------------- #@# APas-to-ASeg Thu May 28 04:33:54 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/ribbon.mgz --threads 1 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 outvol aseg.mgz 32 avail.processors, using 1 Loading aseg.presurf.hypos.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/ribbon.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 nrelabeled = 0 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 955580 mri_surf2volseg done @#@FSTIME 2026:05:28:04:33:54 mri_surf2volseg N 20 e 15.98 S 0.44 U 15.52 P 99% M 935668 F 0 R 96607 W 0 c 26 w 70 I 0 O 728 L 12.06 12.01 12.00 @#@FSLOADPOST 2026:05:28:04:34:10 mri_surf2volseg N 20 12.04 12.01 12.00 mri_brainvol_stats --subject sub-20_ses-0 ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1681891.0 #CBVS2 BrainSegVol 1215721.0 #CBVS2 BrainSegVolNotVent 1200623.0 #CBVS2 SupraTentVol 1074159.0 #CBVS2 SupraTentVolNotVent 1059061.0 #CBVS2 lhCtxGM 273705.0 #CBVS2 rhCtxGM 274096.3 #CBVS2 lhCerebralWM 224260.5 #CBVS2 rhCerebralWM 226174.5 #CBVS2 SubCortGMVol 61921.0 #CBVS2 CerebellumVol 141562.0 #CBVS2 CerebellumGMVol 110424.0 #CBVS2 VentChorVol 12286.0 #CBVS2 3rd4th5thCSF 2812.0 #CBVS2 AllCSF 15098.0 #CBVS2 CCVol 3655.0 @#@FSTIME 2026:05:28:04:34:10 mri_brainvol_stats N 2 e 6.84 S 0.18 U 6.66 P 99% M 232396 F 0 R 30245 W 0 c 16 w 48 I 0 O 8 L 12.04 12.01 12.00 @#@FSLOADPOST 2026:05:28:04:34:17 mri_brainvol_stats N 2 12.04 12.01 12.00 #----------------------------------------- #@# AParc-to-ASeg aparc Thu May 28 04:34:17 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot 1000 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-annot /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.annot 2000 --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 outvol aparc+aseg.mgz 32 avail.processors, using 1 Loading aseg.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8398 vertices from lh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8276 vertices from rh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 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/data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-annot /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 outvol aparc.a2009s+aseg.mgz 32 avail.processors, using 1 Loading aseg.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8398 vertices from lh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.a2009s.annot Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8276 vertices from rh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 nrelabeled = 0 ndotcheck = 25443 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 938804 mri_surf2volseg done @#@FSTIME 2026:05:28:04:38:21 mri_surf2volseg N 25 e 245.86 S 0.57 U 245.25 P 99% M 919300 F 0 R 100479 W 0 c 166 w 88 I 4528 O 920 L 12.00 12.01 12.00 @#@FSLOADPOST 2026:05:28:04:42:27 mri_surf2volseg N 25 12.00 12.00 12.00 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Thu May 28 04:42:27 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-annot /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 outvol aparc.DKTatlas+aseg.mgz 32 avail.processors, using 1 Loading aseg.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8398 vertices from lh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.DKTatlas.annot Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8276 vertices from rh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 nrelabeled = 0 ndotcheck = 25443 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 938828 mri_surf2volseg done @#@FSTIME 2026:05:28:04:42:27 mri_surf2volseg N 25 e 238.74 S 0.52 U 238.17 P 99% M 918992 F 0 R 97150 W 0 c 144 w 96 I 4520 O 840 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:46:26 mri_surf2volseg N 25 12.04 12.03 12.01 #----------------------------------------- #@# WMParc Thu May 28 04:46:26 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 1 --lh-annot /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot 3000 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-annot /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.annot 4000 --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 outvol wmparc.mgz 32 avail.processors, using 1 Loading aparc+aseg.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8398 vertices from lh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8276 vertices from rh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 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--surf-wm-vol --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 7.4.1 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 sub-20_ses-0 --surf-wm-vol --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/WMParcStatsLUT.txt --etiv sysname Linux hostname silbermond machine x86_64 user flores whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1572797 mm^3 (det: 1.238625 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2026:05:28:04:47:34 mri_segstats N 24 e 432.63 S 0.33 U 432.27 P 99% M 239840 F 0 R 43026 W 0 c 695 w 47 I 0 O 24 L 12.01 12.02 12.00 @#@FSLOADPOST 2026:05:28:04:54:47 mri_segstats N 24 11.93 11.97 11.99 #----------------------------------------- #@# Parcellation Stats lh Thu May 28 04:54:47 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 273211 Total vertex volume 273012 (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) = 1572797 mm^3 (det: 1.238625 ) 1768 1122 3031 2.688 0.483 0.084 0.015 10 1.1 bankssts 1000 641 1887 2.477 0.813 0.115 0.017 12 0.7 caudalanteriorcingulate 3366 2133 6727 2.785 0.473 0.096 0.016 23 2.2 caudalmiddlefrontal 2735 1880 4354 2.168 0.488 0.142 0.029 36 3.5 cuneus 651 466 1955 3.304 0.733 0.122 0.029 6 0.7 entorhinal 5278 3563 11611 2.744 0.582 0.116 0.021 63 4.6 fusiform 6225 4250 12726 2.632 0.513 0.106 0.017 61 4.5 inferiorparietal 5593 3763 12203 2.773 0.608 0.102 0.018 49 4.2 inferiortemporal 1565 1055 2800 2.332 0.838 0.129 0.031 22 1.8 isthmuscingulate 8659 5820 14583 2.203 0.513 0.125 0.024 106 8.8 lateraloccipital 4205 2884 8637 2.769 0.650 0.117 0.024 44 4.0 lateralorbitofrontal 5631 3960 9574 2.248 0.592 0.130 0.031 73 7.0 lingual 2975 2066 5570 2.495 0.603 0.110 0.026 39 2.7 medialorbitofrontal 4957 3338 12843 3.127 0.618 0.107 0.019 47 3.8 middletemporal 1096 742 2515 2.882 0.610 0.104 0.021 10 0.9 parahippocampal 2260 1448 4366 2.725 0.577 0.102 0.016 17 1.6 paracentral 2400 1626 5136 2.769 0.449 0.112 0.020 27 1.9 parsopercularis 1084 739 2781 2.865 0.564 0.127 0.024 13 1.1 parsorbitalis 2004 1312 4211 2.775 0.494 0.116 0.019 20 1.7 parstriangularis 2511 1716 3005 1.951 0.434 0.111 0.022 21 2.5 pericalcarine 6346 4074 11309 2.376 0.617 0.106 0.019 56 5.2 postcentral 2037 1409 4065 2.521 0.722 0.120 0.023 25 2.1 posteriorcingulate 6751 4211 13742 2.879 0.628 0.095 0.015 45 4.3 precentral 6054 4053 10765 2.454 0.496 0.112 0.020 61 4.9 precuneus 1487 1042 3683 2.910 0.591 0.110 0.023 18 1.4 rostralanteriorcingulate 8768 5984 18029 2.607 0.486 0.120 0.023 106 7.8 rostralmiddlefrontal 12023 8106 26533 2.833 0.542 0.114 0.021 111 10.3 superiorfrontal 8048 5329 14355 2.416 0.464 0.115 0.019 86 6.3 superiorparietal 6351 4127 14928 3.079 0.630 0.091 0.015 43 4.1 superiortemporal 5804 3894 12345 2.753 0.518 0.113 0.021 57 5.0 supramarginal 360 268 1075 2.934 0.374 0.144 0.033 8 0.4 frontalpole 726 571 2782 3.625 0.716 0.127 0.027 11 0.7 temporalpole 707 452 1344 2.722 0.349 0.115 0.018 7 0.5 transversetemporal 3667 2489 7542 3.053 0.674 0.113 0.029 36 3.9 insula @#@FSTIME 2026:05:28:04:54:47 mris_anatomical_stats N 14 e 24.11 S 0.34 U 23.72 P 99% M 508412 F 0 R 72035 W 0 c 54 w 179 I 0 O 296 L 11.93 11.97 11.99 @#@FSLOADPOST 2026:05:28:04:55:11 mris_anatomical_stats N 14 12.01 11.99 12.00 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 sub-20_ses-0 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 273211 Total vertex volume 273012 (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) = 1572797 mm^3 (det: 1.238625 ) 1768 1098 3031 2.688 0.483 0.111 0.028 21 2.0 bankssts 1000 843 1887 2.477 0.813 0.165 0.045 40 2.0 caudalanteriorcingulate 3366 2571 6727 2.785 0.473 0.116 0.024 39 3.2 caudalmiddlefrontal 2735 2266 4354 2.168 0.488 0.150 0.038 48 4.2 cuneus 651 772 1955 3.304 0.733 0.288 0.083 23 3.0 entorhinal 5278 4822 11611 2.744 0.582 0.158 0.041 119 8.5 fusiform 6225 5244 12726 2.632 0.513 0.137 0.028 77 7.4 inferiorparietal 5593 4786 12203 2.773 0.608 0.143 0.037 117 8.0 inferiortemporal 1565 1370 2800 2.332 0.838 0.194 0.059 69 3.8 isthmuscingulate 8659 7343 14583 2.203 0.513 0.144 0.035 161 11.7 lateraloccipital 4205 3318 8637 2.769 0.650 0.144 0.038 90 6.3 lateralorbitofrontal 5631 4880 9574 2.248 0.592 0.156 0.043 162 9.4 lingual 2975 2464 5570 2.495 0.603 0.154 0.040 52 4.9 medialorbitofrontal 4957 4670 12843 3.127 0.618 0.150 0.034 97 7.0 middletemporal 1096 1070 2515 2.882 0.610 0.212 0.066 35 3.4 parahippocampal 2260 1724 4366 2.725 0.577 0.117 0.026 24 2.3 paracentral 2400 2075 5136 2.769 0.449 0.152 0.031 31 3.2 parsopercularis 1084 1164 2781 2.865 0.564 0.172 0.043 18 2.0 parsorbitalis 2004 1697 4211 2.775 0.494 0.146 0.034 32 2.7 parstriangularis 2511 1417 3005 1.951 0.434 0.110 0.027 102 2.6 pericalcarine 6346 5314 11309 2.376 0.617 0.136 0.027 80 7.6 postcentral 2037 1801 4065 2.521 0.722 0.174 0.047 66 4.3 posteriorcingulate 6751 5129 13742 2.879 0.628 0.109 0.023 81 6.4 precentral 6054 4608 10765 2.454 0.496 0.138 0.032 108 7.9 precuneus 1487 1539 3683 2.910 0.591 0.185 0.051 34 3.1 rostralanteriorcingulate 8768 7563 18029 2.607 0.486 0.155 0.038 199 12.7 rostralmiddlefrontal 12023 10179 26533 2.833 0.542 0.141 0.033 203 16.0 superiorfrontal 8048 6415 14355 2.416 0.464 0.130 0.028 122 8.7 superiorparietal 6351 5353 14928 3.079 0.630 0.140 0.032 99 8.7 superiortemporal 5804 4883 12345 2.753 0.518 0.147 0.037 105 8.8 supramarginal 360 478 1075 2.934 0.374 0.186 0.040 4 0.5 frontalpole 726 979 2782 3.625 0.716 0.208 0.045 15 1.4 temporalpole 707 549 1344 2.722 0.349 0.118 0.034 7 0.9 transversetemporal 3667 2414 7542 3.053 0.674 0.152 0.044 130 6.2 insula @#@FSTIME 2026:05:28:04:55:11 mris_anatomical_stats N 14 e 23.56 S 0.29 U 23.23 P 99% M 508292 F 0 R 72543 W 0 c 27 w 164 I 0 O 296 L 12.01 11.99 12.00 @#@FSLOADPOST 2026:05:28:04:55:35 mris_anatomical_stats N 14 12.01 11.99 12.00 #----------------------------------------- #@# Parcellation Stats rh Thu May 28 04:55:35 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 273760 Total vertex volume 273547 (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) = 1572797 mm^3 (det: 1.238625 ) 1633 1037 2786 2.806 0.350 0.083 0.013 7 0.9 bankssts 1020 647 1754 2.234 0.817 0.103 0.014 10 0.7 caudalanteriorcingulate 3012 2029 5816 2.616 0.440 0.104 0.017 24 2.3 caudalmiddlefrontal 2934 1957 4892 2.219 0.427 0.137 0.031 36 3.7 cuneus 544 366 1951 3.783 0.634 0.103 0.024 3 0.5 entorhinal 5253 3506 11842 2.865 0.586 0.109 0.021 57 4.3 fusiform 8662 5762 17086 2.606 0.483 0.104 0.018 81 6.5 inferiorparietal 4519 3079 10002 2.861 0.580 0.113 0.019 49 3.6 inferiortemporal 1658 1162 3094 2.326 0.759 0.123 0.027 27 1.6 isthmuscingulate 8570 5752 15624 2.395 0.478 0.123 0.022 98 7.6 lateraloccipital 4237 2939 8644 2.695 0.563 0.123 0.024 56 4.3 lateralorbitofrontal 6597 4680 11342 2.265 0.548 0.131 0.031 84 8.0 lingual 3195 2306 6773 2.541 0.685 0.125 0.030 48 3.7 medialorbitofrontal 5200 3527 13115 3.017 0.571 0.108 0.019 52 4.1 middletemporal 1189 757 2321 2.708 0.533 0.087 0.017 7 0.7 parahippocampal 2666 1710 5060 2.682 0.518 0.112 0.018 22 2.1 paracentral 1802 1310 3644 2.557 0.451 0.123 0.022 22 1.7 parsopercularis 1376 948 2953 2.560 0.570 0.125 0.020 16 1.1 parsorbitalis 2219 1537 4560 2.506 0.490 0.112 0.019 26 1.8 parstriangularis 2926 2015 3575 1.977 0.583 0.120 0.024 26 3.0 pericalcarine 6027 3905 10417 2.345 0.581 0.102 0.016 53 4.3 postcentral 2125 1484 4121 2.438 0.795 0.123 0.025 27 2.2 posteriorcingulate 6538 4193 13181 2.805 0.552 0.098 0.016 43 4.6 precentral 6331 4284 11278 2.487 0.520 0.113 0.020 61 5.3 precuneus 1107 772 2506 2.904 0.623 0.126 0.026 20 1.2 rostralanteriorcingulate 8934 6275 18123 2.484 0.508 0.124 0.023 111 8.2 rostralmiddlefrontal 11814 7883 25801 2.783 0.540 0.108 0.019 105 9.0 superiorfrontal 8289 5459 15023 2.411 0.478 0.110 0.019 77 6.5 superiorparietal 5535 3602 12187 2.927 0.530 0.090 0.014 40 3.3 superiortemporal 5604 3807 11506 2.662 0.514 0.118 0.022 57 5.3 supramarginal 434 366 1327 2.808 0.454 0.187 0.056 10 1.2 frontalpole 592 448 2851 4.285 0.517 0.134 0.031 6 0.8 temporalpole 531 331 1133 2.812 0.362 0.115 0.019 5 0.4 transversetemporal 3459 2340 7260 3.065 0.797 0.113 0.029 33 4.0 insula @#@FSTIME 2026:05:28:04:55:35 mris_anatomical_stats N 14 e 23.50 S 0.33 U 23.12 P 99% M 512692 F 0 R 69571 W 0 c 49 w 175 I 0 O 296 L 12.01 11.99 12.00 @#@FSLOADPOST 2026:05:28:04:55:58 mris_anatomical_stats N 14 12.00 11.99 12.00 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 sub-20_ses-0 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 273760 Total vertex volume 273547 (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) = 1572797 mm^3 (det: 1.238625 ) 1633 926 2786 2.806 0.350 0.107 0.033 25 2.1 bankssts 1020 853 1754 2.234 0.817 0.162 0.044 35 2.0 caudalanteriorcingulate 3012 2344 5816 2.616 0.440 0.126 0.027 43 3.3 caudalmiddlefrontal 2934 2575 4892 2.219 0.427 0.153 0.037 55 4.4 cuneus 544 706 1951 3.783 0.634 0.274 0.072 18 2.0 entorhinal 5253 4757 11842 2.865 0.586 0.154 0.038 110 8.2 fusiform 8662 7062 17086 2.606 0.483 0.132 0.028 185 10.7 inferiorparietal 4519 3735 10002 2.861 0.580 0.146 0.038 89 6.5 inferiortemporal 1658 1550 3094 2.326 0.759 0.188 0.056 42 3.5 isthmuscingulate 8570 7318 15624 2.395 0.478 0.143 0.032 148 11.4 lateraloccipital 4237 3532 8644 2.695 0.563 0.163 0.045 111 7.6 lateralorbitofrontal 6597 5648 11342 2.265 0.548 0.153 0.042 164 11.1 lingual 3195 2998 6773 2.541 0.685 0.169 0.043 62 5.3 medialorbitofrontal 5200 4948 13115 3.017 0.571 0.152 0.032 68 6.9 middletemporal 1189 1040 2321 2.708 0.533 0.183 0.046 20 3.0 parahippocampal 2666 2026 5060 2.682 0.518 0.126 0.032 39 3.2 paracentral 1802 1552 3644 2.557 0.451 0.154 0.037 41 2.7 parsopercularis 1376 1288 2953 2.560 0.570 0.155 0.037 21 1.9 parsorbitalis 2219 2058 4560 2.506 0.490 0.150 0.032 28 3.2 parstriangularis 2926 1738 3575 1.977 0.583 0.114 0.030 98 3.0 pericalcarine 6027 4985 10417 2.345 0.581 0.128 0.025 58 6.6 postcentral 2125 1889 4121 2.438 0.795 0.181 0.048 95 4.0 posteriorcingulate 6538 4950 13181 2.805 0.552 0.114 0.025 79 6.5 precentral 6331 4712 11278 2.487 0.520 0.133 0.034 132 8.3 precuneus 1107 956 2506 2.904 0.623 0.159 0.042 35 1.9 rostralanteriorcingulate 8934 7955 18123 2.484 0.508 0.157 0.033 153 11.9 rostralmiddlefrontal 11814 10204 25801 2.783 0.540 0.143 0.032 185 15.9 superiorfrontal 8289 6806 15023 2.411 0.478 0.131 0.026 119 9.2 superiorparietal 5535 4606 12187 2.927 0.530 0.133 0.029 68 6.7 superiortemporal 5604 4611 11506 2.662 0.514 0.144 0.038 114 8.0 supramarginal 434 578 1327 2.808 0.454 0.221 0.056 7 0.9 frontalpole 592 890 2851 4.285 0.517 0.223 0.054 13 1.6 temporalpole 531 471 1133 2.812 0.362 0.141 0.040 15 0.8 transversetemporal 3459 2387 7260 3.065 0.797 0.170 0.055 138 7.6 insula @#@FSTIME 2026:05:28:04:55:58 mris_anatomical_stats N 14 e 23.95 S 0.31 U 23.60 P 99% M 512712 F 0 R 69061 W 0 c 30 w 167 I 0 O 296 L 12.00 11.99 12.00 @#@FSLOADPOST 2026:05:28:04:56:22 mris_anatomical_stats N 14 12.00 12.00 12.00 #----------------------------------------- #@# Parcellation Stats 2 lh Thu May 28 04:56:22 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 273211 Total vertex volume 273012 (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) = 1572797 mm^3 (det: 1.238625 ) 1455 1053 3026 2.493 0.489 0.134 0.027 21 1.6 G_and_S_frontomargin 1532 1026 3045 2.370 0.524 0.122 0.023 17 1.5 G_and_S_occipital_inf 1671 1051 3459 2.704 0.619 0.105 0.018 16 1.3 G_and_S_paracentral 1487 1001 3621 2.964 0.521 0.126 0.025 17 1.5 G_and_S_subcentral 955 717 2436 2.677 0.449 0.136 0.021 16 0.9 G_and_S_transv_frontopol 2759 1961 5818 2.794 0.442 0.111 0.021 24 2.5 G_and_S_cingul-Ant 1391 914 2671 2.790 0.477 0.104 0.017 10 1.0 G_and_S_cingul-Mid-Ant 1544 1064 2999 2.699 0.440 0.109 0.023 12 1.4 G_and_S_cingul-Mid-Post 751 510 1982 2.931 0.407 0.140 0.028 12 0.9 G_cingul-Post-dorsal 372 246 877 2.719 0.540 0.147 0.041 7 0.5 G_cingul-Post-ventral 2436 1684 4174 2.146 0.560 0.157 0.037 43 3.8 G_cuneus 1316 902 3599 2.969 0.439 0.123 0.024 22 1.1 G_front_inf-Opercular 445 286 1096 2.862 0.519 0.130 0.030 7 0.4 G_front_inf-Orbital 1104 717 2909 2.932 0.423 0.121 0.021 14 1.0 G_front_inf-Triangul 4851 3194 12503 2.888 0.496 0.121 0.023 68 4.3 G_front_middle 8079 5418 20777 2.968 0.572 0.121 0.023 96 7.3 G_front_sup 686 473 1557 3.135 0.669 0.124 0.034 11 0.8 G_Ins_lg_and_S_cent_ins 807 577 2690 3.559 0.686 0.125 0.032 11 0.9 G_insular_short 2059 1438 4809 2.549 0.544 0.129 0.027 40 2.1 G_occipital_middle 1547 1047 2582 2.200 0.468 0.131 0.024 18 1.6 G_occipital_sup 2311 1528 5491 2.813 0.500 0.121 0.024 38 2.2 G_oc-temp_lat-fusifor 3859 2737 7008 2.208 0.624 0.141 0.037 62 5.4 G_oc-temp_med-Lingual 1214 829 3386 3.157 0.757 0.111 0.026 12 1.1 G_oc-temp_med-Parahip 2526 1803 6950 2.905 0.707 0.128 0.027 37 2.6 G_orbital 2268 1589 6487 2.993 0.467 0.129 0.023 40 2.1 G_pariet_inf-Angular 2764 1894 7097 2.908 0.529 0.121 0.023 34 2.6 G_pariet_inf-Supramar 2736 1856 6282 2.597 0.514 0.124 0.020 41 2.2 G_parietal_sup 2408 1481 4971 2.546 0.543 0.112 0.021 28 2.0 G_postcentral 2372 1364 6316 3.297 0.576 0.096 0.017 20 1.6 G_precentral 2687 1828 6278 2.626 0.489 0.116 0.023 37 2.4 G_precuneus 1071 790 2727 2.624 0.535 0.129 0.032 26 1.3 G_rectus 779 533 1283 2.490 0.963 0.124 0.047 10 1.3 G_subcallosal 457 281 1073 2.903 0.321 0.111 0.019 5 0.3 G_temp_sup-G_T_transv 2349 1537 7320 3.279 0.589 0.112 0.020 28 2.0 G_temp_sup-Lateral 728 474 2121 3.977 0.458 0.081 0.014 3 0.4 G_temp_sup-Plan_polar 858 567 1914 2.736 0.602 0.091 0.014 7 0.5 G_temp_sup-Plan_tempo 2672 1842 7281 2.914 0.624 0.110 0.020 31 2.3 G_temporal_inf 2506 1744 8334 3.345 0.591 0.115 0.021 32 2.1 G_temporal_middle 184 135 338 2.662 0.805 0.119 0.012 1 0.1 Lat_Fis-ant-Horizont 430 281 646 2.619 0.447 0.092 0.014 2 0.3 Lat_Fis-ant-Vertical 1060 679 1374 2.504 0.354 0.098 0.016 5 0.8 Lat_Fis-post 2378 1613 4228 2.218 0.539 0.147 0.033 38 3.1 Pole_occipital 2066 1556 7305 3.306 0.657 0.139 0.030 31 2.3 Pole_temporal 3401 2301 4416 2.161 0.524 0.103 0.018 22 2.6 S_calcarine 2761 1815 3388 2.105 0.553 0.090 0.014 11 1.8 S_central 1288 831 1787 2.404 0.440 0.091 0.012 6 0.7 S_cingul-Marginalis 619 394 822 2.735 0.524 0.092 0.016 3 0.4 S_circular_insula_ant 1711 1082 2629 2.931 0.510 0.073 0.013 5 0.9 S_circular_insula_inf 1851 1223 2657 2.665 0.433 0.099 0.016 8 1.4 S_circular_insula_sup 1159 761 2112 2.704 0.581 0.099 0.013 8 0.7 S_collat_transv_ant 635 443 790 2.031 0.392 0.135 0.022 6 0.7 S_collat_transv_post 2049 1331 3163 2.532 0.413 0.099 0.017 12 1.5 S_front_inf 1800 1186 2536 2.405 0.381 0.108 0.019 12 1.5 S_front_middle 2884 1946 4680 2.558 0.379 0.100 0.018 15 2.0 S_front_sup 325 219 466 2.563 0.386 0.107 0.019 2 0.3 S_interm_prim-Jensen 2841 1862 3844 2.323 0.370 0.095 0.014 14 1.9 S_intrapariet_and_P_trans 1725 1130 2059 1.959 0.365 0.102 0.015 12 1.2 S_oc_middle_and_Lunatus 1304 856 1720 2.168 0.381 0.099 0.013 9 0.8 S_oc_sup_and_transversal 957 625 1337 2.269 0.421 0.093 0.013 5 0.5 S_occipital_ant 1496 958 2021 2.353 0.369 0.082 0.011 7 0.7 S_oc-temp_lat 2554 1761 4049 2.551 0.441 0.115 0.022 19 2.5 S_oc-temp_med_and_Lingual 451 306 599 2.389 0.332 0.106 0.017 2 0.4 S_orbital_lateral 784 539 1094 2.382 0.460 0.118 0.023 7 0.7 S_orbital_med-olfact 1566 1069 2959 2.787 0.537 0.112 0.021 11 1.5 S_orbital-H_Shaped 2797 1848 3884 2.277 0.444 0.111 0.017 22 2.1 S_parieto_occipital 1376 869 1267 1.588 0.741 0.110 0.020 20 1.0 S_pericallosal 3623 2373 5137 2.325 0.385 0.101 0.017 22 2.8 S_postcentral 1681 1067 2438 2.588 0.423 0.084 0.010 6 0.8 S_precentral-inf-part 1181 767 1696 2.584 0.413 0.090 0.014 5 0.7 S_precentral-sup-part 651 420 797 2.328 0.386 0.084 0.011 2 0.3 S_suborbital 863 590 1127 2.245 0.359 0.115 0.023 5 0.9 S_subparietal 1700 1106 2564 2.688 0.560 0.094 0.014 8 1.2 S_temporal_inf 6658 4325 11365 2.742 0.499 0.088 0.014 31 4.1 S_temporal_sup 471 311 770 2.824 0.406 0.104 0.012 3 0.3 S_temporal_transverse @#@FSTIME 2026:05:28:04:56:22 mris_anatomical_stats N 14 e 24.61 S 0.32 U 24.23 P 99% M 508412 F 0 R 69486 W 0 c 22 w 290 I 0 O 632 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:04:56:47 mris_anatomical_stats N 14 12.06 12.01 12.00 #----------------------------------------- #@# Parcellation Stats 2 rh Thu May 28 04:56:47 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 273760 Total vertex volume 273547 (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) = 1572797 mm^3 (det: 1.238625 ) 928 689 1908 2.494 0.541 0.129 0.025 12 1.0 G_and_S_frontomargin 1653 1129 3247 2.436 0.499 0.113 0.019 20 1.2 G_and_S_occipital_inf 1531 970 3167 2.632 0.504 0.116 0.019 15 1.2 G_and_S_paracentral 1266 859 2986 3.007 0.431 0.126 0.021 13 1.2 G_and_S_subcentral 1533 1163 3691 2.583 0.494 0.136 0.026 25 1.6 G_and_S_transv_frontopol 3451 2447 7193 2.772 0.586 0.123 0.025 43 3.6 G_and_S_cingul-Ant 1700 1075 3416 2.783 0.520 0.101 0.015 12 1.1 G_and_S_cingul-Mid-Ant 1728 1171 3168 2.637 0.499 0.114 0.022 14 1.5 G_and_S_cingul-Mid-Post 697 481 2003 3.011 0.441 0.148 0.033 18 0.8 G_cingul-Post-dorsal 430 311 1013 2.599 0.391 0.135 0.036 8 0.5 G_cingul-Post-ventral 2765 1869 4489 2.137 0.483 0.142 0.034 36 3.8 G_cuneus 1179 884 2941 2.756 0.479 0.130 0.026 19 1.2 G_front_inf-Opercular 573 378 1410 2.780 0.307 0.115 0.019 9 0.4 G_front_inf-Orbital 868 636 2271 2.717 0.434 0.131 0.026 15 0.9 G_front_inf-Triangul 4006 2859 11067 2.790 0.465 0.134 0.025 66 4.2 G_front_middle 6769 4579 17789 2.949 0.547 0.115 0.021 74 5.7 G_front_sup 710 511 1834 3.435 0.900 0.119 0.035 9 0.9 G_Ins_lg_and_S_cent_ins 755 538 2379 3.466 0.780 0.133 0.036 10 1.2 G_insular_short 2596 1758 6451 2.780 0.467 0.130 0.027 40 2.8 G_occipital_middle 1597 1049 3251 2.410 0.451 0.128 0.026 19 1.7 G_occipital_sup 2530 1692 6735 2.986 0.589 0.117 0.024 38 2.3 G_oc-temp_lat-fusifor 3887 2778 7420 2.274 0.628 0.137 0.034 55 5.3 G_oc-temp_med-Lingual 1102 702 3240 3.228 0.805 0.098 0.025 8 0.9 G_oc-temp_med-Parahip 3012 2148 8009 2.824 0.609 0.134 0.027 53 3.3 G_orbital 2827 1951 7425 2.863 0.496 0.125 0.021 43 2.4 G_pariet_inf-Angular 2946 2015 7297 2.838 0.515 0.132 0.025 41 3.2 G_pariet_inf-Supramar 2308 1564 5433 2.620 0.571 0.121 0.022 29 2.0 G_parietal_sup 2098 1323 4342 2.474 0.506 0.107 0.018 23 1.6 G_postcentral 2488 1537 6703 3.177 0.450 0.099 0.016 21 1.7 G_precentral 2697 1865 6058 2.593 0.504 0.117 0.022 34 2.5 G_precuneus 976 692 2589 2.687 0.707 0.135 0.038 23 1.4 G_rectus 513 343 843 2.461 0.834 0.115 0.049 9 0.8 G_subcallosal 397 238 996 2.965 0.267 0.116 0.020 4 0.3 G_temp_sup-G_T_transv 1812 1210 5513 3.244 0.446 0.118 0.022 24 1.6 G_temp_sup-Lateral 937 610 2295 3.397 0.646 0.074 0.013 3 0.5 G_temp_sup-Plan_polar 856 554 1694 2.679 0.539 0.092 0.014 7 0.5 G_temp_sup-Plan_tempo 2109 1475 6102 3.054 0.593 0.121 0.022 34 1.8 G_temporal_inf 2987 2066 9583 3.261 0.493 0.124 0.022 43 2.7 G_temporal_middle 417 273 485 2.038 0.314 0.082 0.009 1 0.2 Lat_Fis-ant-Horizont 133 92 210 2.488 0.456 0.096 0.019 0 0.1 Lat_Fis-ant-Vertical 1281 831 1714 2.505 0.363 0.092 0.015 5 0.8 Lat_Fis-post 3797 2566 6611 2.231 0.510 0.139 0.029 54 4.3 Pole_occipital 1561 1142 5920 3.537 0.762 0.129 0.028 19 1.9 Pole_temporal 3907 2710 5299 2.188 0.598 0.123 0.024 40 4.0 S_calcarine 2709 1785 3343 2.146 0.573 0.094 0.015 14 1.8 S_central 1591 1065 2352 2.453 0.463 0.100 0.016 10 1.2 S_cingul-Marginalis 940 617 1325 2.578 0.601 0.091 0.014 4 0.6 S_circular_insula_ant 1149 731 1647 2.808 0.471 0.076 0.011 3 0.6 S_circular_insula_inf 1282 815 1787 2.626 0.460 0.097 0.017 5 1.0 S_circular_insula_sup 1019 663 1908 2.802 0.502 0.081 0.010 4 0.4 S_collat_transv_ant 470 325 648 2.448 0.373 0.114 0.018 3 0.3 S_collat_transv_post 1992 1303 2707 2.311 0.338 0.102 0.017 12 1.4 S_front_inf 2289 1579 3337 2.260 0.409 0.115 0.020 18 1.9 S_front_middle 3009 1982 4474 2.455 0.372 0.098 0.016 18 2.0 S_front_sup 520 366 751 2.387 0.270 0.124 0.021 3 0.6 S_interm_prim-Jensen 3787 2488 5782 2.326 0.419 0.099 0.015 24 2.5 S_intrapariet_and_P_trans 959 639 1179 2.218 0.283 0.092 0.014 4 0.6 S_oc_middle_and_Lunatus 1700 1105 2245 2.305 0.355 0.100 0.016 9 1.2 S_oc_sup_and_transversal 803 544 1126 2.411 0.331 0.099 0.016 4 0.5 S_occipital_ant 1356 905 1994 2.614 0.461 0.109 0.020 9 1.2 S_oc-temp_lat 2977 1995 4434 2.511 0.396 0.097 0.016 17 1.8 S_oc-temp_med_and_Lingual 454 336 678 2.253 0.429 0.140 0.022 6 0.5 S_orbital_lateral 866 592 1179 2.207 0.574 0.122 0.026 8 0.9 S_orbital_med-olfact 1624 1098 2759 2.601 0.433 0.110 0.019 15 1.3 S_orbital-H_Shaped 2882 1909 4274 2.382 0.462 0.111 0.018 21 2.1 S_parieto_occipital 1617 1053 1409 1.525 0.633 0.104 0.021 19 1.3 S_pericallosal 3076 2006 4225 2.231 0.378 0.100 0.017 19 2.3 S_postcentral 1589 1052 2489 2.433 0.405 0.097 0.013 11 0.9 S_precentral-inf-part 1347 866 1809 2.550 0.322 0.093 0.016 6 1.0 S_precentral-sup-part 415 284 659 2.218 0.621 0.091 0.016 2 0.2 S_suborbital 874 602 1391 2.489 0.388 0.110 0.020 5 0.7 S_subparietal 1367 894 2004 2.671 0.456 0.098 0.015 7 1.0 S_temporal_inf 7330 4676 11077 2.572 0.419 0.080 0.012 29 3.8 S_temporal_sup 226 167 368 2.398 0.439 0.111 0.014 1 0.1 S_temporal_transverse @#@FSTIME 2026:05:28:04:56:47 mris_anatomical_stats N 14 e 26.28 S 0.51 U 25.68 P 99% M 512680 F 0 R 93879 W 0 c 74 w 293 I 0 O 632 L 12.06 12.01 12.00 @#@FSLOADPOST 2026:05:28:04:57:13 mris_anatomical_stats N 14 12.04 12.01 12.00 #----------------------------------------- #@# Parcellation Stats 3 lh Thu May 28 04:57:13 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 273211 Total vertex volume 273012 (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) = 1572797 mm^3 (det: 1.238625 ) 1843 1189 3555 2.639 0.710 0.113 0.018 20 1.4 caudalanteriorcingulate 3649 2311 7282 2.784 0.475 0.096 0.015 25 2.3 caudalmiddlefrontal 3785 2564 6046 2.197 0.489 0.139 0.028 51 4.5 cuneus 589 410 1702 3.416 0.662 0.120 0.030 5 0.6 entorhinal 5009 3336 10021 2.652 0.538 0.113 0.020 55 4.2 fusiform 6161 4219 12874 2.651 0.524 0.108 0.017 64 4.5 inferiorparietal 5597 3833 13381 2.826 0.648 0.108 0.019 58 4.5 inferiortemporal 1548 1045 2789 2.364 0.820 0.130 0.031 22 1.8 isthmuscingulate 8674 5821 14744 2.216 0.506 0.126 0.024 108 8.8 lateraloccipital 4710 3307 10099 2.736 0.652 0.126 0.029 59 5.3 lateralorbitofrontal 5738 4035 9610 2.225 0.591 0.130 0.031 75 7.2 lingual 2331 1647 4745 2.512 0.607 0.109 0.027 34 2.1 medialorbitofrontal 6717 4474 16020 3.021 0.626 0.101 0.018 54 4.9 middletemporal 1140 772 2605 2.867 0.617 0.103 0.021 10 0.9 parahippocampal 2675 1708 5180 2.742 0.566 0.101 0.016 20 1.8 paracentral 2260 1532 4809 2.774 0.446 0.115 0.020 26 1.8 parsopercularis 1052 700 2154 2.663 0.590 0.114 0.020 10 0.9 parsorbitalis 2335 1516 4688 2.733 0.470 0.110 0.018 21 1.8 parstriangularis 2413 1651 2876 1.960 0.434 0.109 0.021 18 2.2 pericalcarine 7205 4654 12581 2.369 0.600 0.107 0.020 64 5.8 postcentral 2187 1507 4188 2.504 0.712 0.119 0.023 26 2.1 posteriorcingulate 6683 4167 13597 2.887 0.623 0.096 0.016 45 4.3 precentral 5759 3879 10520 2.467 0.494 0.112 0.020 59 4.8 precuneus 2107 1443 4550 2.819 0.598 0.113 0.023 24 1.9 rostralanteriorcingulate 6214 4179 13073 2.659 0.499 0.118 0.023 71 5.5 rostralmiddlefrontal 12938 8861 28940 2.788 0.554 0.118 0.021 132 11.4 superiorfrontal 6296 4157 11341 2.445 0.460 0.112 0.018 63 4.7 superiorparietal 8349 5501 19854 3.073 0.654 0.094 0.016 62 5.7 superiortemporal 5351 3587 11259 2.739 0.517 0.113 0.021 52 4.7 supramarginal 669 427 1282 2.722 0.354 0.117 0.019 6 0.5 transversetemporal 3108 2098 6643 3.127 0.641 0.107 0.024 28 2.7 insula @#@FSTIME 2026:05:28:04:57:13 mris_anatomical_stats N 14 e 24.82 S 0.29 U 24.48 P 99% M 508248 F 0 R 69589 W 0 c 89 w 157 I 0 O 272 L 12.04 12.01 12.00 @#@FSLOADPOST 2026:05:28:04:57:38 mris_anatomical_stats N 14 12.02 12.01 12.00 #----------------------------------------- #@# Parcellation Stats 3 rh Thu May 28 04:57:38 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 273760 Total vertex volume 273547 (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) = 1572797 mm^3 (det: 1.238625 ) 1105 699 1872 2.237 0.815 0.103 0.014 11 0.7 caudalanteriorcingulate 3213 2161 6143 2.613 0.437 0.104 0.017 25 2.4 caudalmiddlefrontal 3545 2354 5794 2.218 0.430 0.134 0.029 42 4.2 cuneus 483 325 1683 3.713 0.633 0.102 0.024 3 0.4 entorhinal 4847 3250 10342 2.809 0.550 0.105 0.020 48 3.7 fusiform 8588 5712 16912 2.607 0.483 0.107 0.019 83 6.7 inferiorparietal 4962 3389 11820 2.926 0.621 0.115 0.020 57 4.2 inferiortemporal 1647 1152 3064 2.336 0.748 0.123 0.027 26 1.6 isthmuscingulate 8655 5795 15788 2.386 0.482 0.123 0.023 100 7.7 lateraloccipital 4641 3277 9972 2.701 0.579 0.129 0.027 66 5.3 lateralorbitofrontal 6515 4622 11159 2.262 0.544 0.131 0.031 84 8.0 lingual 2428 1698 4950 2.479 0.710 0.123 0.035 41 3.4 medialorbitofrontal 6421 4293 15125 2.964 0.555 0.103 0.018 57 4.7 middletemporal 1257 801 2443 2.721 0.540 0.087 0.017 8 0.8 parahippocampal 2733 1754 5318 2.706 0.542 0.111 0.018 22 2.1 paracentral 2092 1505 4196 2.567 0.437 0.123 0.023 27 2.0 parsopercularis 1526 994 2898 2.486 0.538 0.109 0.017 15 1.1 parsorbitalis 1952 1371 3826 2.442 0.485 0.112 0.018 22 1.4 parstriangularis 2834 1954 3519 2.004 0.577 0.119 0.025 24 2.9 pericalcarine 6695 4345 11233 2.320 0.567 0.106 0.018 60 5.1 postcentral 2204 1539 4229 2.450 0.784 0.124 0.025 27 2.3 posteriorcingulate 6279 4032 12896 2.814 0.560 0.098 0.016 41 4.4 precentral 6451 4373 11757 2.493 0.526 0.110 0.020 62 5.3 precuneus 1466 1057 3487 2.922 0.670 0.135 0.029 26 1.8 rostralanteriorcingulate 5902 4130 11688 2.469 0.486 0.127 0.024 74 5.6 rostralmiddlefrontal 15186 10355 33107 2.720 0.547 0.113 0.020 152 12.5 superiorfrontal 6768 4461 12410 2.421 0.492 0.108 0.018 61 5.2 superiorparietal 7133 4696 16798 3.028 0.644 0.094 0.016 52 4.8 superiortemporal 5421 3685 11292 2.684 0.510 0.117 0.021 54 5.0 supramarginal 514 321 1101 2.823 0.366 0.115 0.019 4 0.4 transversetemporal 3069 2074 6725 3.182 0.698 0.103 0.022 23 2.6 insula @#@FSTIME 2026:05:28:04:57:38 mris_anatomical_stats N 14 e 24.91 S 0.33 U 24.54 P 99% M 512852 F 0 R 70273 W 0 c 30 w 157 I 0 O 272 L 12.02 12.01 12.00 @#@FSLOADPOST 2026:05:28:04:58:03 mris_anatomical_stats N 14 12.01 12.00 12.00 #-------------------------------------------- #@# ASeg Stats Thu May 28 04:58:03 AM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0 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 /software/freesurfer/7.4.1/debian-bookworm-amd64/ASegStatsLUT.txt --subject sub-20_ses-0 setting seed for random number genererator to 1234 7.4.1 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 /software/freesurfer/7.4.1/debian-bookworm-amd64/ASegStatsLUT.txt --subject sub-20_ses-0 sysname Linux hostname silbermond machine x86_64 user flores whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1572797 mm^3 (det: 1.238625 ) Computing euler number orig.nofix lheno = -14, rheno = -18 orig.nofix lhholes = 8, rhholes = 10 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2026:05:28:04:58:03 mri_segstats N 32 e 230.95 S 0.33 U 230.59 P 99% M 269148 F 0 R 52803 W 0 c 439 w 63 I 0 O 24 L 12.01 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:01:54 mri_segstats N 32 12.02 12.02 12.00 /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0; ln -s /software/freesurfer/7.4.1/debian-bookworm-amd64/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Thu May 28 05:01:54 AM CEST 2026 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 207 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4336 mri_label2label: Done @#@FSTIME 2026:05:28:05:01:54 mri_label2label N 12 e 8.10 S 0.32 U 7.77 P 99% M 573568 F 0 R 77697 W 0 c 45 w 48 I 0 O 280 L 12.02 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:02:02 mri_label2label N 12 12.02 12.02 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 423 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8332 mri_label2label: Done @#@FSTIME 2026:05:28:05:02:03 mri_label2label N 12 e 9.02 S 0.41 U 8.60 P 99% M 573940 F 0 R 78311 W 0 c 17 w 35 I 0 O 552 L 12.02 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:02:12 mri_label2label N 12 12.02 12.02 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4095 mri_label2label: Done @#@FSTIME 2026:05:28:05:02:12 mri_label2label N 12 e 8.02 S 0.37 U 7.64 P 99% M 573620 F 0 R 77183 W 0 c 13 w 27 I 0 O 216 L 12.02 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:02:20 mri_label2label N 12 12.02 12.02 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6102 mri_label2label: Done @#@FSTIME 2026:05:28:05:02:20 mri_label2label N 12 e 8.55 S 0.37 U 8.16 P 99% M 573808 F 0 R 77220 W 0 c 26 w 35 I 0 O 352 L 12.02 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:02:28 mri_label2label N 12 12.01 12.02 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5842 mri_label2label: Done @#@FSTIME 2026:05:28:05:02:28 mri_label2label N 12 e 8.49 S 0.34 U 8.15 P 99% M 573752 F 0 R 77214 W 0 c 35 w 35 I 0 O 328 L 12.01 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:02:37 mri_label2label N 12 12.01 12.02 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4096 mri_label2label: Done @#@FSTIME 2026:05:28:05:02:37 mri_label2label N 12 e 7.80 S 0.30 U 7.49 P 99% M 573672 F 0 R 76675 W 0 c 13 w 25 I 0 O 216 L 12.01 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:02:45 mri_label2label N 12 12.01 12.02 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 605 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14194 mri_label2label: Done @#@FSTIME 2026:05:28:05:02:45 mri_label2label N 12 e 12.60 S 0.34 U 12.26 P 99% M 574332 F 0 R 77427 W 0 c 22 w 46 I 0 O 872 L 12.01 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:02:57 mri_label2label N 12 11.93 12.00 11.99 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4308 mri_label2label: Done @#@FSTIME 2026:05:28:05:02:57 mri_label2label N 12 e 8.03 S 0.35 U 7.68 P 99% M 573652 F 0 R 77189 W 0 c 19 w 27 I 0 O 272 L 11.93 12.00 11.99 @#@FSLOADPOST 2026:05:28:05:03:05 mri_label2label N 12 11.94 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 333 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3755 mri_label2label: Done @#@FSTIME 2026:05:28:05:03:05 mri_label2label N 12 e 7.79 S 0.32 U 7.46 P 99% M 573644 F 0 R 77439 W 0 c 14 w 30 I 0 O 280 L 11.94 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:03:13 mri_label2label N 12 11.94 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 1696 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6337 mri_label2label: Done @#@FSTIME 2026:05:28:05:03:13 mri_label2label N 12 e 8.25 S 0.37 U 7.87 P 99% M 573712 F 0 R 77715 W 0 c 20 w 36 I 0 O 528 L 11.94 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:03:22 mri_label2label N 12 11.95 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 3947 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 12061 mri_label2label: Done @#@FSTIME 2026:05:28:05:03:22 mri_label2label N 12 e 9.94 S 0.30 U 9.63 P 99% M 574088 F 0 R 76309 W 0 c 23 w 49 I 0 O 1008 L 11.95 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:03:32 mri_label2label N 12 11.96 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 427 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2445 mri_label2label: Done @#@FSTIME 2026:05:28:05:03:32 mri_label2label N 12 e 7.47 S 0.40 U 7.06 P 99% M 573496 F 0 R 77155 W 0 c 20 w 29 I 0 O 200 L 11.96 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:03:39 mri_label2label N 12 11.96 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1362 mri_label2label: Done @#@FSTIME 2026:05:28:05:03:39 mri_label2label N 12 e 7.16 S 0.33 U 6.82 P 99% M 573436 F 0 R 77136 W 0 c 17 w 25 I 0 O 96 L 11.96 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:03:46 mri_label2label N 12 11.97 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1272 mri_label2label: Done @#@FSTIME 2026:05:28:05:03:46 mri_label2label N 12 e 7.14 S 0.30 U 6.83 P 99% M 573388 F 0 R 76630 W 0 c 23 w 27 I 0 O 88 L 11.97 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:03:53 mri_label2label N 12 11.97 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 227 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 641 mri_label2label: Done @#@FSTIME 2026:05:28:05:03:53 mri_label2label N 12 e 7.04 S 0.32 U 6.70 P 99% M 573384 F 0 R 77366 W 0 c 19 w 26 I 0 O 64 L 11.97 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:04:01 mri_label2label N 12 11.98 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 943 mri_label2label: Done @#@FSTIME 2026:05:28:05:04:01 mri_label2label N 12 e 6.98 S 0.40 U 6.57 P 99% M 573392 F 0 R 78124 W 0 c 15 w 30 I 0 O 88 L 11.98 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:04:08 mri_label2label N 12 12.06 12.02 12.01 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 177 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 2050 mri_label2label: Done @#@FSTIME 2026:05:28:05:04:08 mri_label2label N 12 e 7.11 S 0.32 U 6.78 P 99% M 573476 F 0 R 77146 W 0 c 17 w 28 I 0 O 160 L 12.06 12.02 12.01 @#@FSLOADPOST 2026:05:28:05:04:15 mri_label2label N 12 12.05 12.02 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 832 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2933 mri_label2label: Done @#@FSTIME 2026:05:28:05:04:15 mri_label2label N 12 e 7.20 S 0.37 U 6.82 P 99% M 573524 F 0 R 77406 W 0 c 19 w 28 I 0 O 256 L 12.05 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:04:22 mri_label2label N 12 12.05 12.02 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 1344 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 5221 mri_label2label: Done @#@FSTIME 2026:05:28:05:04:22 mri_label2label N 12 e 7.68 S 0.32 U 7.35 P 99% M 573676 F 0 R 76684 W 0 c 19 w 31 I 0 O 432 L 12.05 12.02 12.00 @#@FSLOADPOST 2026:05:28:05:04:30 mri_label2label N 12 12.04 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 1443 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 4362 mri_label2label: Done @#@FSTIME 2026:05:28:05:04:30 mri_label2label N 12 e 7.50 S 0.32 U 7.17 P 99% M 573600 F 0 R 78198 W 0 c 43 w 36 I 0 O 368 L 12.04 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:04:37 mri_label2label N 12 12.03 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 899 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 2185 mri_label2label: Done @#@FSTIME 2026:05:28:05:04:37 mri_label2label N 12 e 7.11 S 0.38 U 6.72 P 99% M 573500 F 0 R 77133 W 0 c 19 w 27 I 0 O 192 L 12.03 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:04:44 mri_label2label N 12 12.03 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 633 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1639 mri_label2label: Done @#@FSTIME 2026:05:28:05:04:44 mri_label2label N 12 e 7.08 S 0.32 U 6.76 P 99% M 573424 F 0 R 77904 W 0 c 47 w 26 I 0 O 144 L 12.03 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:04:52 mri_label2label N 12 12.03 12.01 12.00 mris_label2annot --s sub-20_ses-0 --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 silbermond machine x86_64 user flores subject sub-20_ses-0 hemi lh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig Index Offset 0 0 reading lh.FG1.mpm.vpnl.label 1 1376057 FG1 1 reading lh.FG2.mpm.vpnl.label 2 16711935 FG2 2 reading lh.FG3.mpm.vpnl.label 3 16711680 FG3 3 reading lh.FG4.mpm.vpnl.label 4 1705837 FG4 4 reading lh.hOc1.mpm.vpnl.label 5 25600 hOc1 5 reading lh.hOc2.mpm.vpnl.label 6 255 hOc2 6 reading lh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v 7 reading lh.hOc4v.mpm.vpnl.label 8 65535 hOc4v Mapping unhit to unknown Found 124467 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.mpm.vpnl.annot @#@FSTIME 2026:05:28:05:04:52 mris_label2annot N 26 e 1.18 S 0.09 U 1.07 P 98% M 166080 F 0 R 21375 W 0 c 2 w 147 I 0 O 2248 L 12.03 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:04:53 mris_label2annot N 26 12.03 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1039 mri_label2label: Done @#@FSTIME 2026:05:28:05:04:53 mri_label2label N 12 e 7.04 S 0.31 U 6.72 P 99% M 573372 F 0 R 76597 W 0 c 19 w 26 I 0 O 72 L 12.03 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:05:00 mri_label2label N 12 12.02 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2287 mri_label2label: Done @#@FSTIME 2026:05:28:05:05:00 mri_label2label N 12 e 7.20 S 0.32 U 6.87 P 99% M 573420 F 0 R 77927 W 0 c 13 w 34 I 0 O 168 L 12.02 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:05:07 mri_label2label N 12 12.02 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 5 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1509 mri_label2label: Done @#@FSTIME 2026:05:28:05:05:07 mri_label2label N 12 e 7.07 S 0.33 U 6.73 P 99% M 573456 F 0 R 76627 W 0 c 15 w 27 I 0 O 80 L 12.02 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:05:14 mri_label2label N 12 12.02 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2005 mri_label2label: Done @#@FSTIME 2026:05:28:05:05:14 mri_label2label N 12 e 7.66 S 0.64 U 7.01 P 99% M 573472 F 0 R 121655 W 0 c 40 w 30 I 0 O 112 L 12.02 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:05:22 mri_label2label N 12 12.02 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2334 mri_label2label: Done @#@FSTIME 2026:05:28:05:05:22 mri_label2label N 12 e 7.56 S 0.33 U 7.22 P 99% M 573508 F 0 R 76646 W 0 c 14 w 25 I 0 O 136 L 12.02 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:05:30 mri_label2label N 12 12.01 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1565 mri_label2label: Done @#@FSTIME 2026:05:28:05:05:30 mri_label2label N 12 e 7.14 S 0.35 U 6.79 P 99% M 573436 F 0 R 77657 W 0 c 19 w 25 I 0 O 88 L 12.01 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:05:37 mri_label2label N 12 12.01 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 125 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7160 mri_label2label: Done @#@FSTIME 2026:05:28:05:05:37 mri_label2label N 12 e 8.91 S 0.29 U 8.61 P 99% M 573856 F 0 R 76767 W 0 c 19 w 40 I 0 O 416 L 12.01 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:05:46 mri_label2label N 12 12.01 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1967 mri_label2label: Done @#@FSTIME 2026:05:28:05:05:46 mri_label2label N 12 e 7.22 S 0.33 U 6.88 P 99% M 573456 F 0 R 77149 W 0 c 17 w 31 I 0 O 128 L 12.01 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:05:53 mri_label2label N 12 12.01 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 145 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1296 mri_label2label: Done @#@FSTIME 2026:05:28:05:05:53 mri_label2label N 12 e 6.99 S 0.31 U 6.68 P 99% M 573432 F 0 R 77102 W 0 c 14 w 24 I 0 O 104 L 12.01 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:06:00 mri_label2label N 12 12.01 12.01 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 1236 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4641 mri_label2label: Done @#@FSTIME 2026:05:28:05:06:00 mri_label2label N 12 e 7.68 S 0.34 U 7.34 P 99% M 573644 F 0 R 77188 W 0 c 51 w 40 I 0 O 392 L 12.01 12.01 12.00 @#@FSLOADPOST 2026:05:28:05:06:08 mri_label2label N 12 12.01 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 1489 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4823 mri_label2label: Done @#@FSTIME 2026:05:28:05:06:08 mri_label2label N 12 e 7.75 S 0.32 U 7.41 P 99% M 573608 F 0 R 77186 W 0 c 53 w 36 I 0 O 408 L 12.01 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:06:16 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 587 mri_label2label: Done @#@FSTIME 2026:05:28:05:06:16 mri_label2label N 12 e 7.02 S 0.38 U 6.63 P 99% M 573372 F 0 R 77108 W 0 c 9 w 23 I 0 O 48 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:06:23 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 490 mri_label2label: Done @#@FSTIME 2026:05:28:05:06:23 mri_label2label N 12 e 6.87 S 0.30 U 6.56 P 99% M 573360 F 0 R 78119 W 0 c 12 w 25 I 0 O 40 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:06:30 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 143490 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 486 mri_label2label: Done @#@FSTIME 2026:05:28:05:06:30 mri_label2label N 12 e 6.83 S 0.28 U 6.55 P 99% M 573300 F 0 R 76587 W 0 c 18 w 24 I 0 O 40 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:06:36 mri_label2label N 12 12.00 12.00 12.00 mris_label2annot --s sub-20_ses-0 --hemi lh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --hemi lh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 silbermond machine x86_64 user flores subject sub-20_ses-0 hemi lh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig Index Offset 0 0 reading lh.BA1_exvivo.label 1 1530880 BA1_exvivo 1 reading lh.BA2_exvivo.label 2 16749699 BA2_exvivo 2 reading lh.BA3a_exvivo.label 3 16711680 BA3a_exvivo 3 reading lh.BA3b_exvivo.label 4 3368703 BA3b_exvivo 4 reading lh.BA4a_exvivo.label 5 1376196 BA4a_exvivo 5 reading lh.BA4p_exvivo.label 6 13382655 BA4p_exvivo 6 reading lh.BA6_exvivo.label 7 10036737 BA6_exvivo 7 reading lh.BA44_exvivo.label 8 2490521 BA44_exvivo 8 reading lh.BA45_exvivo.label 9 39283 BA45_exvivo 9 reading lh.V1_exvivo.label 10 3993 V1_exvivo 10 reading lh.V2_exvivo.label 11 8508928 V2_exvivo 11 reading lh.MT_exvivo.label 12 10027163 MT_exvivo 12 reading lh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo 13 reading lh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 99926 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.BA_exvivo.annot @#@FSTIME 2026:05:28:05:06:36 mris_label2annot N 38 e 1.44 S 0.08 U 1.34 P 98% M 166572 F 0 R 20476 W 0 c 7 w 164 I 0 O 2248 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:06:38 mris_label2annot N 38 12.00 12.00 12.00 mris_label2annot --s sub-20_ses-0 --hemi lh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --hemi lh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 silbermond machine x86_64 user flores subject sub-20_ses-0 hemi lh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.orig Index Offset 0 0 reading lh.BA1_exvivo.thresh.label 1 1530880 BA1_exvivo 1 reading lh.BA2_exvivo.thresh.label 2 16749699 BA2_exvivo 2 reading lh.BA3a_exvivo.thresh.label 3 16711680 BA3a_exvivo 3 reading lh.BA3b_exvivo.thresh.label 4 3368703 BA3b_exvivo 4 reading lh.BA4a_exvivo.thresh.label 5 1376196 BA4a_exvivo 5 reading lh.BA4p_exvivo.thresh.label 6 13382655 BA4p_exvivo 6 reading lh.BA6_exvivo.thresh.label 7 10036737 BA6_exvivo 7 reading lh.BA44_exvivo.thresh.label 8 2490521 BA44_exvivo 8 reading lh.BA45_exvivo.thresh.label 9 39283 BA45_exvivo 9 reading lh.V1_exvivo.thresh.label 10 3993 V1_exvivo 10 reading lh.V2_exvivo.thresh.label 11 8508928 V2_exvivo 11 reading lh.MT_exvivo.thresh.label 12 10027163 MT_exvivo 12 reading lh.perirhinal_exvivo.thresh.label 13 16422433 perirhinal_exvivo 13 reading lh.entorhinal_exvivo.thresh.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 118807 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2026:05:28:05:06:38 mris_label2annot N 38 e 1.21 S 0.08 U 1.11 P 98% M 166236 F 0 R 20392 W 0 c 3 w 190 I 0 O 2248 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:06:39 mris_label2annot N 38 12.00 12.00 12.00 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-20_ses-0 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 273211 Total vertex volume 273012 (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) = 1572797 mm^3 (det: 1.238625 ) 1105 662 2435 2.655 0.571 0.109 0.024 14 0.9 BA1_exvivo 4567 2975 7481 2.420 0.459 0.106 0.019 35 3.6 BA2_exvivo 963 630 957 1.887 0.383 0.120 0.020 7 0.8 BA3a_exvivo 2237 1446 3765 2.243 0.676 0.106 0.019 19 2.0 BA3b_exvivo 1518 930 3547 3.165 0.502 0.091 0.014 10 0.9 BA4a_exvivo 1138 696 1921 2.859 0.518 0.072 0.011 4 0.5 BA4p_exvivo 9155 5893 20852 2.917 0.582 0.104 0.017 72 6.8 BA6_exvivo 2279 1522 4950 2.808 0.491 0.107 0.019 24 1.6 BA44_exvivo 2828 1858 6207 2.744 0.461 0.109 0.019 29 2.2 BA45_exvivo 4220 2929 5708 1.924 0.465 0.115 0.026 41 4.3 V1_exvivo 10013 6883 16567 2.226 0.536 0.141 0.031 133 13.0 V2_exvivo 2226 1513 3806 2.317 0.475 0.111 0.018 26 1.7 MT_exvivo 713 530 1648 2.903 0.561 0.128 0.025 7 0.8 perirhinal_exvivo 602 410 1968 3.259 1.137 0.108 0.031 6 0.6 entorhinal_exvivo @#@FSTIME 2026:05:28:05:06:39 mris_anatomical_stats N 12 e 7.37 S 0.28 U 7.06 P 99% M 503608 F 0 R 68710 W 0 c 11 w 112 I 2248 O 136 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:06:47 mris_anatomical_stats N 12 12.00 12.00 12.00 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-20_ses-0 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 273211 Total vertex volume 273012 (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) = 1572797 mm^3 (det: 1.238625 ) 714 410 1636 2.706 0.522 0.122 0.026 10 0.7 BA1_exvivo 1843 1192 3211 2.435 0.459 0.104 0.017 15 1.3 BA2_exvivo 787 514 710 1.851 0.335 0.125 0.022 6 0.7 BA3a_exvivo 1261 827 1651 1.840 0.430 0.082 0.014 6 0.7 BA3b_exvivo 1410 869 3204 3.191 0.478 0.083 0.012 6 0.8 BA4a_exvivo 948 581 1482 2.719 0.507 0.077 0.012 4 0.5 BA4p_exvivo 4735 2996 11197 2.994 0.605 0.104 0.018 38 3.5 BA6_exvivo 1450 986 3039 2.688 0.460 0.114 0.019 18 1.0 BA44_exvivo 1158 762 2995 2.880 0.479 0.117 0.021 13 1.0 BA45_exvivo 4471 3108 6226 1.947 0.461 0.114 0.026 41 4.6 V1_exvivo 4676 3321 7381 2.114 0.556 0.153 0.035 73 6.9 V2_exvivo 536 366 1033 2.497 0.559 0.117 0.018 7 0.4 MT_exvivo 320 229 578 2.834 0.499 0.128 0.028 3 0.4 perirhinal_exvivo 374 256 1320 3.656 0.664 0.087 0.018 2 0.3 entorhinal_exvivo @#@FSTIME 2026:05:28:05:06:47 mris_anatomical_stats N 12 e 7.43 S 0.31 U 7.09 P 99% M 503668 F 0 R 71775 W 0 c 15 w 105 I 2248 O 136 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:06:54 mris_anatomical_stats N 12 12.00 12.00 12.00 #-------------------------------------------- #@# BA_exvivo Labels rh Thu May 28 05:06:54 AM CEST 2026 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4076 mri_label2label: Done @#@FSTIME 2026:05:28:05:06:54 mri_label2label N 12 e 7.77 S 0.38 U 7.38 P 99% M 576468 F 0 R 77526 W 0 c 16 w 31 I 0 O 248 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:07:02 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6881 mri_label2label: Done @#@FSTIME 2026:05:28:05:07:02 mri_label2label N 12 e 8.53 S 0.33 U 8.18 P 99% M 576680 F 0 R 78083 W 0 c 20 w 40 I 0 O 416 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:07:11 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 3991 mri_label2label: Done @#@FSTIME 2026:05:28:05:07:11 mri_label2label N 12 e 7.86 S 0.31 U 7.54 P 99% M 576476 F 0 R 77012 W 0 c 15 w 29 I 0 O 192 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:07:18 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4623 mri_label2label: Done @#@FSTIME 2026:05:28:05:07:18 mri_label2label N 12 e 8.63 S 0.60 U 8.02 P 99% M 576564 F 0 R 128192 W 0 c 28 w 33 I 0 O 256 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:07:27 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5823 mri_label2label: Done @#@FSTIME 2026:05:28:05:07:27 mri_label2label N 12 e 8.32 S 0.31 U 8.01 P 99% M 576616 F 0 R 78065 W 0 c 17 w 36 I 0 O 320 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:07:35 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4504 mri_label2label: Done @#@FSTIME 2026:05:28:05:07:36 mri_label2label N 12 e 7.96 S 0.33 U 7.62 P 99% M 576484 F 0 R 77025 W 0 c 10 w 28 I 0 O 224 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:07:43 mri_label2label N 12 12.00 12.00 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 504 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12760 mri_label2label: Done @#@FSTIME 2026:05:28:05:07:44 mri_label2label N 12 e 11.16 S 0.34 U 10.81 P 99% M 577072 F 0 R 77236 W 0 c 25 w 53 I 0 O 784 L 12.00 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:07:55 mri_label2label N 12 11.93 11.98 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 320 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7232 mri_label2label: Done @#@FSTIME 2026:05:28:05:07:55 mri_label2label N 12 e 8.35 S 0.30 U 8.04 P 99% M 576692 F 0 R 76545 W 0 c 13 w 32 I 0 O 440 L 11.93 11.98 12.00 @#@FSLOADPOST 2026:05:28:05:08:03 mri_label2label N 12 11.94 11.98 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 670 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6025 mri_label2label: Done @#@FSTIME 2026:05:28:05:08:03 mri_label2label N 12 e 7.95 S 0.35 U 7.60 P 99% M 576572 F 0 R 78062 W 0 c 19 w 34 I 0 O 416 L 11.94 11.98 12.00 @#@FSLOADPOST 2026:05:28:05:08:11 mri_label2label N 12 11.95 11.99 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 2351 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 7078 mri_label2label: Done @#@FSTIME 2026:05:28:05:08:11 mri_label2label N 12 e 8.07 S 0.34 U 7.72 P 99% M 576628 F 0 R 77558 W 0 c 20 w 38 I 0 O 592 L 11.95 11.99 12.00 @#@FSLOADPOST 2026:05:28:05:08:19 mri_label2label N 12 11.95 11.99 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 4272 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 12288 mri_label2label: Done @#@FSTIME 2026:05:28:05:08:19 mri_label2label N 12 e 10.61 S 0.55 U 10.05 P 99% M 576940 F 0 R 102975 W 0 c 26 w 50 I 0 O 1024 L 11.95 11.99 12.00 @#@FSLOADPOST 2026:05:28:05:08:30 mri_label2label N 12 11.96 11.99 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 611 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2543 mri_label2label: Done @#@FSTIME 2026:05:28:05:08:30 mri_label2label N 12 e 7.42 S 0.30 U 7.11 P 99% M 576380 F 0 R 77752 W 0 c 17 w 31 I 0 O 208 L 11.96 11.99 12.00 @#@FSLOADPOST 2026:05:28:05:08:37 mri_label2label N 12 11.97 11.99 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1065 mri_label2label: Done @#@FSTIME 2026:05:28:05:08:37 mri_label2label N 12 e 7.06 S 0.34 U 6.71 P 99% M 576316 F 0 R 77737 W 0 c 16 w 28 I 0 O 72 L 11.97 11.99 12.00 @#@FSLOADPOST 2026:05:28:05:08:44 mri_label2label N 12 11.97 11.99 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 773 mri_label2label: Done @#@FSTIME 2026:05:28:05:08:45 mri_label2label N 12 e 6.92 S 0.28 U 6.63 P 99% M 576184 F 0 R 76931 W 0 c 12 w 25 I 0 O 56 L 11.97 11.99 12.00 @#@FSLOADPOST 2026:05:28:05:08:51 mri_label2label N 12 11.97 11.99 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 385 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 926 mri_label2label: Done @#@FSTIME 2026:05:28:05:08:51 mri_label2label N 12 e 7.01 S 0.36 U 6.65 P 99% M 576272 F 0 R 77445 W 0 c 11 w 25 I 0 O 88 L 11.97 11.99 12.00 @#@FSLOADPOST 2026:05:28:05:08:59 mri_label2label N 12 11.90 11.97 11.99 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 511 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 1232 mri_label2label: Done @#@FSTIME 2026:05:28:05:08:59 mri_label2label N 12 e 7.07 S 0.34 U 6.73 P 99% M 576276 F 0 R 76963 W 0 c 15 w 28 I 0 O 112 L 11.90 11.97 11.99 @#@FSLOADPOST 2026:05:28:05:09:06 mri_label2label N 12 11.91 11.97 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 429 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1952 mri_label2label: Done @#@FSTIME 2026:05:28:05:09:06 mri_label2label N 12 e 7.24 S 0.28 U 6.95 P 99% M 576248 F 0 R 77232 W 0 c 12 w 30 I 0 O 160 L 11.91 11.97 12.00 @#@FSLOADPOST 2026:05:28:05:09:13 mri_label2label N 12 11.92 11.97 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 527 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 2113 mri_label2label: Done @#@FSTIME 2026:05:28:05:09:13 mri_label2label N 12 e 7.22 S 0.31 U 6.90 P 99% M 576368 F 0 R 76462 W 0 c 18 w 32 I 0 O 184 L 11.92 11.97 12.00 @#@FSLOADPOST 2026:05:28:05:09:20 mri_label2label N 12 11.93 11.97 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 1849 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 5516 mri_label2label: Done @#@FSTIME 2026:05:28:05:09:20 mri_label2label N 12 e 7.84 S 0.31 U 7.52 P 99% M 576520 F 0 R 77025 W 0 c 15 w 39 I 0 O 464 L 11.93 11.97 12.00 @#@FSLOADPOST 2026:05:28:05:09:28 mri_label2label N 12 11.94 11.98 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 1480 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 4199 mri_label2label: Done @#@FSTIME 2026:05:28:05:09:28 mri_label2label N 12 e 7.72 S 0.30 U 7.41 P 99% M 576432 F 0 R 78022 W 0 c 15 w 33 I 0 O 352 L 11.94 11.98 12.00 @#@FSLOADPOST 2026:05:28:05:09:36 mri_label2label N 12 11.95 11.98 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 838 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 2066 mri_label2label: Done @#@FSTIME 2026:05:28:05:09:36 mri_label2label N 12 e 7.38 S 0.31 U 7.06 P 99% M 576316 F 0 R 78758 W 0 c 12 w 34 I 0 O 184 L 11.95 11.98 12.00 @#@FSLOADPOST 2026:05:28:05:09:43 mri_label2label N 12 11.95 11.98 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 709 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1734 mri_label2label: Done @#@FSTIME 2026:05:28:05:09:43 mri_label2label N 12 e 7.37 S 0.31 U 7.05 P 99% M 576220 F 0 R 76960 W 0 c 13 w 27 I 0 O 152 L 11.95 11.98 12.00 @#@FSLOADPOST 2026:05:28:05:09:51 mri_label2label N 12 11.96 11.98 12.00 mris_label2annot --s sub-20_ses-0 --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 silbermond machine x86_64 user flores subject sub-20_ses-0 hemi rh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig Index Offset 0 0 reading rh.FG1.mpm.vpnl.label 1 1376057 FG1 1 reading rh.FG2.mpm.vpnl.label 2 16711935 FG2 2 reading rh.FG3.mpm.vpnl.label 3 16711680 FG3 3 reading rh.FG4.mpm.vpnl.label 4 1705837 FG4 4 reading rh.hOc1.mpm.vpnl.label 5 25600 hOc1 5 reading rh.hOc2.mpm.vpnl.label 6 255 hOc2 6 reading rh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v 7 reading rh.hOc4v.mpm.vpnl.label 8 65535 hOc4v Mapping unhit to unknown Found 125523 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.mpm.vpnl.annot @#@FSTIME 2026:05:28:05:09:51 mris_label2annot N 26 e 1.23 S 0.10 U 1.12 P 98% M 167392 F 0 R 21285 W 0 c 3 w 104 I 0 O 2264 L 11.96 11.98 12.00 @#@FSLOADPOST 2026:05:28:05:09:52 mris_label2annot N 26 11.96 11.98 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 909 mri_label2label: Done @#@FSTIME 2026:05:28:05:09:52 mri_label2label N 12 e 7.27 S 0.31 U 6.95 P 99% M 576304 F 0 R 77729 W 0 c 16 w 25 I 0 O 64 L 11.96 11.98 12.00 @#@FSLOADPOST 2026:05:28:05:09:59 mri_label2label N 12 11.96 11.98 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2722 mri_label2label: Done @#@FSTIME 2026:05:28:05:09:59 mri_label2label N 12 e 7.35 S 0.32 U 7.03 P 99% M 576376 F 0 R 78008 W 0 c 10 w 27 I 0 O 160 L 11.96 11.98 12.00 @#@FSLOADPOST 2026:05:28:05:10:07 mri_label2label N 12 11.89 11.96 11.99 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1702 mri_label2label: Done @#@FSTIME 2026:05:28:05:10:07 mri_label2label N 12 e 7.00 S 0.31 U 6.68 P 99% M 576312 F 0 R 76945 W 0 c 13 w 29 I 0 O 80 L 11.89 11.96 11.99 @#@FSLOADPOST 2026:05:28:05:10:14 mri_label2label N 12 11.90 11.96 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2226 mri_label2label: Done @#@FSTIME 2026:05:28:05:10:14 mri_label2label N 12 e 7.18 S 0.32 U 6.85 P 99% M 576356 F 0 R 76980 W 0 c 21 w 32 I 0 O 128 L 11.90 11.96 12.00 @#@FSLOADPOST 2026:05:28:05:10:21 mri_label2label N 12 11.91 11.97 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1413 mri_label2label: Done @#@FSTIME 2026:05:28:05:10:21 mri_label2label N 12 e 7.09 S 0.30 U 6.79 P 99% M 576316 F 0 R 77229 W 0 c 14 w 28 I 0 O 88 L 11.91 11.97 12.00 @#@FSLOADPOST 2026:05:28:05:10:28 mri_label2label N 12 11.92 11.97 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1495 mri_label2label: Done @#@FSTIME 2026:05:28:05:10:28 mri_label2label N 12 e 7.04 S 0.35 U 6.68 P 99% M 576292 F 0 R 77453 W 0 c 15 w 26 I 0 O 80 L 11.92 11.97 12.00 @#@FSLOADPOST 2026:05:28:05:10:35 mri_label2label N 12 11.93 11.97 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 229 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7188 mri_label2label: Done @#@FSTIME 2026:05:28:05:10:35 mri_label2label N 12 e 8.61 S 0.35 U 8.25 P 99% M 576696 F 0 R 77579 W 0 c 15 w 34 I 0 O 432 L 11.93 11.97 12.00 @#@FSLOADPOST 2026:05:28:05:10:44 mri_label2label N 12 12.01 11.99 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1124 mri_label2label: Done @#@FSTIME 2026:05:28:05:10:44 mri_label2label N 12 e 6.95 S 0.36 U 6.58 P 99% M 576296 F 0 R 76938 W 0 c 16 w 25 I 0 O 80 L 12.01 11.99 12.00 @#@FSLOADPOST 2026:05:28:05:10:51 mri_label2label N 12 11.93 11.97 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1222 mri_label2label: Done @#@FSTIME 2026:05:28:05:10:51 mri_label2label N 12 e 7.00 S 0.35 U 6.64 P 99% M 576292 F 0 R 76942 W 0 c 19 w 27 I 0 O 80 L 11.93 11.97 12.00 @#@FSLOADPOST 2026:05:28:05:10:58 mri_label2label N 12 11.94 11.97 12.00 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 1582 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4814 mri_label2label: Done @#@FSTIME 2026:05:28:05:10:58 mri_label2label N 12 e 7.56 S 0.37 U 7.18 P 99% M 576528 F 0 R 77524 W 0 c 17 w 38 I 0 O 400 L 11.94 11.97 12.00 @#@FSLOADPOST 2026:05:28:05:11:06 mri_label2label N 12 12.09 12.00 12.01 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 1997 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5434 mri_label2label: Done @#@FSTIME 2026:05:28:05:11:06 mri_label2label N 12 e 7.65 S 0.36 U 7.28 P 99% M 576520 F 0 R 78042 W 0 c 19 w 42 I 0 O 456 L 12.09 12.00 12.01 @#@FSLOADPOST 2026:05:28:05:11:13 mri_label2label N 12 12.09 12.00 12.01 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 339 mri_label2label: Done @#@FSTIME 2026:05:28:05:11:13 mri_label2label N 12 e 6.79 S 0.33 U 6.45 P 99% M 576208 F 0 R 77184 W 0 c 18 w 26 I 0 O 32 L 12.09 12.00 12.01 @#@FSLOADPOST 2026:05:28:05:11:20 mri_label2label N 12 12.08 12.00 12.01 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 710 mri_label2label: Done @#@FSTIME 2026:05:28:05:11:20 mri_label2label N 12 e 6.83 S 0.34 U 6.48 P 99% M 576208 F 0 R 77942 W 0 c 12 w 26 I 0 O 48 L 12.08 12.00 12.01 @#@FSLOADPOST 2026:05:28:05:11:27 mri_label2label N 12 12.07 12.00 12.01 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/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 144808 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 301 mri_label2label: Done @#@FSTIME 2026:05:28:05:11:27 mri_label2label N 12 e 6.85 S 0.33 U 6.51 P 99% M 576164 F 0 R 77439 W 0 c 18 w 28 I 0 O 24 L 12.07 12.00 12.01 @#@FSLOADPOST 2026:05:28:05:11:34 mri_label2label N 12 12.06 12.00 12.00 mris_label2annot --s sub-20_ses-0 --hemi rh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --hemi rh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 silbermond machine x86_64 user flores subject sub-20_ses-0 hemi rh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig Index Offset 0 0 reading rh.BA1_exvivo.label 1 1530880 BA1_exvivo 1 reading rh.BA2_exvivo.label 2 16749699 BA2_exvivo 2 reading rh.BA3a_exvivo.label 3 16711680 BA3a_exvivo 3 reading rh.BA3b_exvivo.label 4 3368703 BA3b_exvivo 4 reading rh.BA4a_exvivo.label 5 1376196 BA4a_exvivo 5 reading rh.BA4p_exvivo.label 6 13382655 BA4p_exvivo 6 reading rh.BA6_exvivo.label 7 10036737 BA6_exvivo 7 reading rh.BA44_exvivo.label 8 2490521 BA44_exvivo 8 reading rh.BA45_exvivo.label 9 39283 BA45_exvivo 9 reading rh.V1_exvivo.label 10 3993 V1_exvivo 10 reading rh.V2_exvivo.label 11 8508928 V2_exvivo 11 reading rh.MT_exvivo.label 12 10027163 MT_exvivo 12 reading rh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo 13 reading rh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 101079 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.BA_exvivo.annot @#@FSTIME 2026:05:28:05:11:34 mris_label2annot N 38 e 1.24 S 0.09 U 1.13 P 98% M 167992 F 0 R 21473 W 0 c 5 w 159 I 0 O 2264 L 12.06 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:11:35 mris_label2annot N 38 12.06 12.00 12.00 mris_label2annot --s sub-20_ses-0 --hemi rh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --hemi rh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 silbermond machine x86_64 user flores subject sub-20_ses-0 hemi rh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.orig Index Offset 0 0 reading rh.BA1_exvivo.thresh.label 1 1530880 BA1_exvivo 1 reading rh.BA2_exvivo.thresh.label 2 16749699 BA2_exvivo 2 reading rh.BA3a_exvivo.thresh.label 3 16711680 BA3a_exvivo 3 reading rh.BA3b_exvivo.thresh.label 4 3368703 BA3b_exvivo 4 reading rh.BA4a_exvivo.thresh.label 5 1376196 BA4a_exvivo 5 reading rh.BA4p_exvivo.thresh.label 6 13382655 BA4p_exvivo 6 reading rh.BA6_exvivo.thresh.label 7 10036737 BA6_exvivo 7 reading rh.BA44_exvivo.thresh.label 8 2490521 BA44_exvivo 8 reading rh.BA45_exvivo.thresh.label 9 39283 BA45_exvivo 9 reading rh.V1_exvivo.thresh.label 10 3993 V1_exvivo 10 reading rh.V2_exvivo.thresh.label 11 8508928 V2_exvivo 11 reading rh.MT_exvivo.thresh.label 12 10027163 MT_exvivo 12 reading rh.perirhinal_exvivo.thresh.label 13 16422433 perirhinal_exvivo 13 reading rh.entorhinal_exvivo.thresh.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 120557 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2026:05:28:05:11:35 mris_label2annot N 38 e 1.24 S 0.10 U 1.12 P 98% M 167664 F 0 R 21380 W 0 c 3 w 161 I 0 O 2264 L 12.06 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:11:36 mris_label2annot N 38 12.06 12.00 12.00 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-20_ses-0 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 273760 Total vertex volume 273547 (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) = 1572797 mm^3 (det: 1.238625 ) 951 569 2221 2.647 0.448 0.130 0.024 15 0.9 BA1_exvivo 3450 2247 5175 2.290 0.408 0.098 0.016 22 2.5 BA2_exvivo 909 607 943 2.017 0.443 0.119 0.023 7 0.8 BA3a_exvivo 1881 1231 2863 2.055 0.547 0.094 0.014 14 1.2 BA3b_exvivo 1485 886 3231 2.957 0.529 0.094 0.015 9 1.0 BA4a_exvivo 1111 713 1884 2.689 0.390 0.087 0.014 5 0.7 BA4p_exvivo 8117 5300 18261 2.863 0.537 0.103 0.018 63 6.1 BA6_exvivo 3360 2353 6671 2.563 0.480 0.116 0.019 37 2.8 BA44_exvivo 4055 2772 8060 2.501 0.499 0.114 0.020 47 3.2 BA45_exvivo 4918 3444 7238 2.062 0.553 0.132 0.031 56 6.4 V1_exvivo 10196 7009 17017 2.220 0.515 0.134 0.030 132 11.7 V2_exvivo 2407 1601 4425 2.521 0.357 0.109 0.018 25 1.8 MT_exvivo 364 246 856 3.313 0.518 0.087 0.017 1 0.3 perirhinal_exvivo 525 349 1932 3.617 0.797 0.096 0.023 3 0.4 entorhinal_exvivo @#@FSTIME 2026:05:28:05:11:36 mris_anatomical_stats N 12 e 7.16 S 0.31 U 6.83 P 99% M 507868 F 0 R 68953 W 0 c 16 w 111 I 0 O 136 L 12.06 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:11:44 mris_anatomical_stats N 12 12.05 12.00 12.00 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-20_ses-0 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/output/sub-20/ses-0/sub-20_ses-0/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 273760 Total vertex volume 273547 (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) = 1572797 mm^3 (det: 1.238625 ) 645 383 1475 2.592 0.477 0.124 0.026 10 0.7 BA1_exvivo 1790 1171 2969 2.314 0.452 0.086 0.012 10 1.0 BA2_exvivo 805 542 769 1.965 0.419 0.127 0.024 6 0.8 BA3a_exvivo 1438 969 1844 1.845 0.401 0.084 0.012 7 0.7 BA3b_exvivo 939 563 2160 2.960 0.499 0.110 0.019 9 0.8 BA4a_exvivo 873 566 1450 2.708 0.401 0.077 0.012 3 0.5 BA4p_exvivo 5024 3273 11597 2.888 0.559 0.105 0.017 41 3.7 BA6_exvivo 900 709 2255 2.583 0.471 0.143 0.026 18 1.1 BA44_exvivo 866 629 2086 2.684 0.468 0.123 0.026 10 0.8 BA45_exvivo 4723 3296 6865 2.062 0.559 0.128 0.029 51 5.6 V1_exvivo 5352 3718 8335 2.087 0.540 0.141 0.033 71 7.2 V2_exvivo 330 208 737 2.724 0.315 0.118 0.020 4 0.2 MT_exvivo 34 21 54 3.290 0.277 0.080 0.014 0 0.0 perirhinal_exvivo 532 351 1702 3.604 0.627 0.092 0.018 2 0.4 entorhinal_exvivo @#@FSTIME 2026:05:28:05:11:44 mris_anatomical_stats N 12 e 7.13 S 0.28 U 6.82 P 99% M 507856 F 0 R 68759 W 0 c 17 w 109 I 2264 O 136 L 12.05 12.00 12.00 @#@FSLOADPOST 2026:05:28:05:11:51 mris_anatomical_stats N 12 12.04 12.00 12.00 Started at Wed May 27 09:19:06 PM CEST 2026 Ended at Thu May 28 05:11:51 AM CEST 2026 #@#%# recon-all-run-time-hours 7.879 recon-all -s sub-20_ses-0 finished without error at Thu May 28 05:11:51 AM CEST 2026 #New# invocation of recon-all Wed Jul 8 04:56:56 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/recon-all -s sub-20_ses-0 -autorecon2 -autorecon3 subjid sub-20_ses-0 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Actual FREESURFER_HOME /software/freesurfer/7.4.1/debian-bullseye-amd64 build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 Linux comps10h04 6.1.0-49-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.174-1 (2026-05-26) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 12382665 maxlocks unlimited maxsignal 12382665 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 3.0Ti 300Gi 1.7Ti 421Mi 1.0Ti 2.7Ti Swap: 9.3Gi 0B 9.3Gi ######################################## program versions used 7.4.1 (freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:56-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.4.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 7.4.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/07/08-14:56:57-GMT BuildTime: Jun 14 2023 04:28:01 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 User: asmolova Machine: comps10h04 Platform: Linux PlatformVersion: 6.1.0-49-amd64 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 /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Wed Jul 8 04:56:58 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /software/freesurfer/7.4.1/debian-bookworm-amd64/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 '/software/freesurfer/7.4.1/debian-bookworm-amd64/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (60, 52, 26) --> (195, 197, 192) finding center of left hemi white matter using (105, 100, 109) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (88,82,89) --> (121, 117,129) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 108 +- 4.6 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -3.955 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.923901 @ (0.000, 0.000, 0.000) max log p = -3.798784 @ (-5.263, 5.263, -5.263) max log p = -3.678796 @ (2.632, 2.632, 2.632) max log p = -3.660171 @ (3.947, -1.316, -1.316) max log p = -3.660171 @ (0.000, 0.000, 0.000) max log p = -3.660171 @ (0.000, 0.000, 0.000) max log p = -3.660171 @ (0.000, 0.000, 0.000) max log p = -3.660171 @ (0.000, 0.000, 0.000) Found translation: (1.3, 6.6, -3.9): log p = -3.660 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.573, old_max_log_p =-3.660 (thresh=-3.7) 1.00000 0.00000 0.00000 1.31579; 0.00000 1.04996 0.15634 -16.15105; 0.00000 -0.11161 0.99651 9.01428; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 55 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.559, old_max_log_p =-3.573 (thresh=-3.6) 1.07500 0.00000 0.00000 -8.09570; 0.00000 1.12871 0.16807 -26.30916; 0.00000 -0.10324 0.92177 16.24477; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 57 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.559, old_max_log_p =-3.559 (thresh=-3.6) 1.07500 0.00000 0.00000 -8.09570; 0.00000 1.12871 0.16807 -26.30916; 0.00000 -0.10324 0.92177 16.24477; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 58 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.401, old_max_log_p =-3.559 (thresh=-3.6) 1.07442 -0.03524 -0.00733 -5.12306; 0.03517 1.07647 0.22385 -31.05856; 0.00000 -0.17794 0.94371 24.13932; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 55 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.401, old_max_log_p =-3.401 (thresh=-3.4) 1.07442 -0.03524 -0.00733 -5.12306; 0.03517 1.07647 0.22385 -31.05856; 0.00000 -0.17794 0.94371 24.13932; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 54 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.359, old_max_log_p =-3.401 (thresh=-3.4) 1.07820 -0.03536 -0.00735 -6.52581; 0.03504 1.07545 0.20764 -28.24871; 0.00058 -0.16030 0.94725 21.69023; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 52 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.359, old_max_log_p =-3.359 (thresh=-3.4) 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 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: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.359 (old=-3.955) transform before final EM align: 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 771616 FSRUNTIME@ mri_em_register 0.1212 hours 1 threads registration took 7 minutes and 16 seconds. @#@FSTIME 2026:07:08:16:56:58 mri_em_register N 7 e 436.40 S 0.76 U 435.54 P 99% M 618160 F 10 R 115033 W 0 c 1240 w 67 I 153032 O 32 L 1.14 5.87 7.18 @#@FSLOADPOST 2026:07:08:17:04:14 mri_em_register N 7 32.78 13.08 9.23 #-------------------------------------- #@# CA Normalize Wed Jul 8 05:04:14 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /software/freesurfer/7.4.1/debian-bookworm-amd64/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 '/software/freesurfer/7.4.1/debian-bookworm-amd64/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=22.0 skull bounding box = (60, 52, 26) --> (195, 197, 192) finding center of left hemi white matter using (105, 100, 109) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (88,82,89) --> (121, 117,129) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 108 +- 4.6 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246437 sample points... INFO: compute sample coordinates transform 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24871; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 50, 27) --> (189, 157, 200) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 3659 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 52, 26) --> (129, 157, 200) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 6 of 3381 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 131, 55) --> (175, 174, 111) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 37 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 131, 52) --> (129, 174, 112) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 13 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 122, 92) --> (145, 187, 123) Brain_Stem: limiting intensities to 94.0 --> 132.0 0 of 14 (0.0%) samples deleted using 7104 total control points for intensity normalization... bias field = 0.985 +- 0.038 54 of 7098 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 50, 27) --> (189, 157, 200) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 3967 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 52, 26) --> (129, 157, 200) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 9 of 3670 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 131, 55) --> (175, 174, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 67 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 131, 52) --> (129, 174, 112) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 85 (0.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 122, 92) --> (145, 187, 123) Brain_Stem: limiting intensities to 88.0 --> 132.0 3 of 106 (2.8%) samples deleted using 7895 total control points for intensity normalization... bias field = 1.024 +- 0.044 88 of 7825 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (127, 50, 27) --> (189, 157, 200) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 3942 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 52, 26) --> (129, 157, 200) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 12 of 3681 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (130, 131, 55) --> (175, 174, 111) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 94 (6.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 131, 52) --> (129, 174, 112) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 21 of 120 (17.5%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (113, 122, 92) --> (145, 187, 123) Brain_Stem: limiting intensities to 88.0 --> 132.0 40 of 187 (21.4%) samples deleted using 8024 total control points for intensity normalization... bias field = 1.024 +- 0.041 60 of 7796 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 1 seconds. @#@FSTIME 2026:07:08:17:04:14 mri_ca_normalize N 8 e 61.03 S 0.52 U 60.48 P 99% M 919416 F 8 R 138547 W 0 c 109 w 90 I 1416 O 3952 L 32.78 13.08 9.23 @#@FSLOADPOST 2026:07:08:17:05:15 mri_ca_normalize N 8 13.35 11.08 8.78 #-------------------------------------- #@# CA Reg Wed Jul 8 05:05:15 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /software/freesurfer/7.4.1/debian-bookworm-amd64/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 '/software/freesurfer/7.4.1/debian-bookworm-amd64/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 0.902753 #GCAMreg# pass 0 level1 5 level2 1 tsec 413.94 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 0.691271 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 0.702749 #GCAMreg# pass 0 level1 4 level2 1 tsec 167.064 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 0.674767 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 0.714859 #GCAMreg# pass 0 level1 3 level2 1 tsec 44.037 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 0.714829 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 0.827384 #GCAMreg# pass 0 level1 2 level2 1 tsec 67.66 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 0.790979 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 0.886848 #GCAMreg# pass 0 level1 1 level2 1 tsec 158.24 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 0.852198 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 0.800603 #GCAMreg# pass 0 level1 0 level2 1 tsec 46.044 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 0.795059 GCAMregister done in 20.6502 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.13293 (21) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (1257 voxels, overlap=0.743) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (1257 voxels, peak = 16), gca=15.6 gca peak = 0.17690 (16) mri peak = 0.12371 (21) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (594 voxels, overlap=0.905) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (594 voxels, peak = 18), gca=17.5 gca peak = 0.28275 (96) mri peak = 0.10800 (77) Right_Pallidum (52): linear fit = 0.80 x + 0.0 (638 voxels, overlap=0.096) Right_Pallidum (52): linear fit = 0.80 x + 0.0 (638 voxels, peak = 76), gca=76.3 gca peak = 0.18948 (93) mri peak = 0.08786 (98) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (640 voxels, overlap=0.953) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (640 voxels, peak = 96), gca=96.3 gca peak = 0.20755 (55) mri peak = 0.09273 (63) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (550 voxels, overlap=0.234) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (550 voxels, peak = 62), gca=62.4 gca peak = 0.31831 (58) mri peak = 0.08154 (66) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (608 voxels, overlap=0.623) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (608 voxels, peak = 65), gca=64.7 gca peak = 0.11957 (102) mri peak = 0.14035 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57671 voxels, overlap=0.576) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57671 voxels, peak = 106), gca=105.6 gca peak = 0.11429 (102) mri peak = 0.14837 (105) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (59735 voxels, overlap=0.597) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (59735 voxels, peak = 105), gca=104.5 gca peak = 0.14521 (59) mri peak = 0.04831 (63) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (17877 voxels, overlap=0.976) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (17877 voxels, peak = 63), gca=63.4 gca peak = 0.14336 (58) mri peak = 0.05774 (63) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (16047 voxels, overlap=0.956) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (16047 voxels, peak = 62), gca=62.4 gca peak = 0.13305 (70) mri peak = 0.09834 (74) Right_Caudate (50): linear fit = 1.12 x + 0.0 (856 voxels, overlap=0.457) Right_Caudate (50): linear fit = 1.12 x + 0.0 (856 voxels, peak = 78), gca=78.1 gca peak = 0.15761 (71) mri peak = 0.18831 (79) Left_Caudate (11): linear fit = 1.05 x + 0.0 (1038 voxels, overlap=0.643) Left_Caudate (11): linear fit = 1.05 x + 0.0 (1038 voxels, peak = 75), gca=74.9 gca peak = 0.13537 (57) mri peak = 0.03724 (57) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (15387 voxels, overlap=0.941) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (15387 voxels, peak = 60), gca=59.6 gca peak = 0.13487 (56) mri peak = 0.04347 (62) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (19828 voxels, overlap=0.847) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (19828 voxels, peak = 62), gca=62.4 gca peak = 0.19040 (84) mri peak = 0.08288 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7352 voxels, overlap=0.306) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7352 voxels, peak = 91), gca=91.1 gca peak = 0.18871 (83) mri peak = 0.08852 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7402 voxels, overlap=0.193) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7402 voxels, peak = 90), gca=90.1 gca peak = 0.24248 (57) mri peak = 0.08093 (73) Left_Amygdala (18): linear fit = 1.21 x + 0.0 (427 voxels, overlap=0.257) Left_Amygdala (18): linear fit = 1.21 x + 0.0 (427 voxels, peak = 69), gca=68.7 gca peak = 0.35833 (56) mri peak = 0.06557 (68) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (522 voxels, overlap=0.305) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (522 voxels, peak = 67), gca=67.5 gca peak = 0.12897 (85) mri peak = 0.05802 (98) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (5346 voxels, overlap=0.783) Left_Thalamus (10): linear fit = 1.07 x + 0.0 (5346 voxels, peak = 91), gca=90.5 gca peak = 0.13127 (83) mri peak = 0.06017 (98) Right_Thalamus (49): linear fit = 1.17 x + 0.0 (4346 voxels, overlap=0.545) Right_Thalamus (49): linear fit = 1.17 x + 0.0 (4346 voxels, peak = 98), gca=97.5 gca peak = 0.12974 (78) mri peak = 0.08193 (84) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2340 voxels, overlap=0.770) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2340 voxels, peak = 85), gca=85.4 gca peak = 0.17796 (79) mri peak = 0.06924 (79) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2056 voxels, overlap=0.862) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2056 voxels, peak = 83), gca=82.6 gca peak = 0.10999 (80) mri peak = 0.06917 (91) Brain_Stem (16): linear fit = 1.14 x + 0.0 (11743 voxels, overlap=0.210) Brain_Stem (16): linear fit = 1.14 x + 0.0 (11743 voxels, peak = 92), gca=91.6 gca peak = 0.13215 (88) mri peak = 0.09827 (95) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (885 voxels, overlap=0.246) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (885 voxels, peak = 100), gca=99.9 gca peak = 0.11941 (89) mri peak = 0.07630 (95) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1075 voxels, overlap=0.364) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1075 voxels, peak = 97), gca=97.5 gca peak = 0.20775 (25) mri peak = 0.09528 (20) gca peak = 0.13297 (21) mri peak = 0.12807 (22) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (203 voxels, overlap=0.827) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (203 voxels, peak = 24), gca=24.0 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means estimating mean gm scale to be 1.13 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.07 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 2.73257 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 0.810023 #GCAMreg# pass 0 level1 5 level2 1 tsec 1036.68 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.653847 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 0.650444 #GCAMreg# pass 0 level1 4 level2 1 tsec 1615.28 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 0.551144 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 0.555266 #GCAMreg# pass 0 level1 3 level2 1 tsec 723.184 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 0.514341 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 0.53465 #GCAMreg# pass 0 level1 2 level2 1 tsec 49.877 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 0.53465 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 0.590751 #GCAMreg# pass 0 level1 1 level2 1 tsec 51.594 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 0.588292 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 0.5129 #GCAMreg# pass 0 level1 0 level2 1 tsec 336.026 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 0.486275 GCAMregister done in 79.413 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 0.477688 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 5 level2 1 tsec 69.311 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 0.477676 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_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 0.476613 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 4 level2 1 tsec 59.655 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 0.476392 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_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 0.470523 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 12 after 12 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 6 after 12 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 14 after 8 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 11 after 10 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 8 after 5 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 10 after 13 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 5 after 11 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 8 after 14 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 377.824 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 0.45301 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.449359 #GCAMreg# pass 0 level1 2 level2 1 tsec 46.84 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 0.449359 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.457855 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 1 level2 1 tsec 53.825 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 0.457751 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 0.448455 iter 0, gcam->neg = 882 after 14 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 58.07 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 0.415596 label assignment complete, 0 changed (0.00%) GCAMregister done in 20.3738 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 0.398894 #GCAMreg# pass 0 level1 5 level2 1 tsec 27.545 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 0.398894 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 0.39908 #GCAMreg# pass 0 level1 4 level2 1 tsec 26.647 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 0.39908 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 0.399459 #GCAMreg# pass 0 level1 3 level2 1 tsec 51.181 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 0.39934 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_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 0.393779 #GCAMreg# pass 0 level1 2 level2 1 tsec 48.55 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 0.393779 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.401771 #GCAMreg# pass 0 level1 1 level2 1 tsec 28.298 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 0.401771 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 0.388273 iter 0, gcam->neg = 541 after 14 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 59.158 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 0.380731 GCAMregister done in 11.5356 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4884 tmin = 19.016 Calls to gcamLabelEnergy 4384 tmin = 1.87852 Calls to gcamJacobianEnergy 4884 tmin = 14.3086 Calls to gcamSmoothnessEnergy 4884 tmin = 15.0169 Calls to gcamLogLikelihoodTerm 644 tmin = 4.87752 Calls to gcamLabelTerm 591 tmin = 8.59193 Calls to gcamJacobianTerm 644 tmin = 9.23045 Calls to gcamSmoothnessTerm 644 tmin = 3.50563 Calls to gcamComputeGradient 644 tmin = 50.5712 Calls to gcamComputeMetricProperties 6877 tmin = 20.9233 mri_ca_register took 2 hours, 14 minutes and 55 seconds. #VMPC# mri_ca_register VmPeak 2013404 FSRUNTIME@ mri_ca_register 2.2486 hours 1 threads @#@FSTIME 2026:07:08:17:05:15 mri_ca_register N 9 e 8095.17 S 3.58 U 8090.74 P 99% M 1336332 F 14 R 518230 W 0 c 17604 w 202 I 1768 O 63408 L 13.35 11.08 8.78 @#@FSLOADPOST 2026:07:08:19:20:10 mri_ca_register N 9 2.13 5.43 7.44 #-------------------------------------- #@# SubCort Seg Wed Jul 8 07:20:10 PM CEST 2026 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz sysname Linux hostname comps10h04 machine x86_64 user asmolova Seg1 aseg.auto.mgz Seg2 aseg.presurf.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /software/freesurfer/7.4.1/debian-bookworm-amd64/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname comps10h04 machine x86_64 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.05 Atlas used for the 3D morph was /software/freesurfer/7.4.1/debian-bookworm-amd64/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 = 0.11479 (21) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (904 voxels, overlap=0.888) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (904 voxels, peak = 19), gca=18.7 gca peak = 0.20380 (13) mri peak = 0.12188 (16) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (497 voxels, overlap=0.686) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (497 voxels, peak = 15), gca=15.4 gca peak = 0.26283 (96) mri peak = 0.08287 (85) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (544 voxels, overlap=0.381) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (544 voxels, peak = 84), gca=84.0 gca peak = 0.15814 (97) mri peak = 0.14761 (98) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (691 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (691 voxels, peak = 100), gca=100.4 gca peak = 0.27624 (56) mri peak = 0.09249 (68) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (689 voxels, overlap=0.292) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (689 voxels, peak = 64), gca=63.6 gca peak = 0.28723 (59) mri peak = 0.08874 (63) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (728 voxels, overlap=0.551) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (728 voxels, peak = 65), gca=64.6 gca peak = 0.07623 (103) mri peak = 0.15220 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38134 voxels, overlap=0.569) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38134 voxels, peak = 105), gca=104.5 gca peak = 0.07837 (105) mri peak = 0.15711 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39899 voxels, overlap=0.572) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39899 voxels, peak = 105), gca=105.0 gca peak = 0.10165 (58) mri peak = 0.05481 (63) Left_Cerebral_Cortex (3): linear fit = 1.07 x + 0.0 (23344 voxels, overlap=0.948) Left_Cerebral_Cortex (3): linear fit = 1.07 x + 0.0 (23344 voxels, peak = 62), gca=61.8 gca peak = 0.11113 (58) mri peak = 0.05866 (61) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22229 voxels, overlap=0.917) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22229 voxels, peak = 59), gca=59.4 gca peak = 0.27796 (67) mri peak = 0.13407 (79) Right_Caudate (50): linear fit = 1.14 x + 0.0 (910 voxels, overlap=0.059) Right_Caudate (50): linear fit = 1.14 x + 0.0 (910 voxels, peak = 77), gca=76.7 gca peak = 0.14473 (69) mri peak = 0.19819 (79) Left_Caudate (11): linear fit = 1.04 x + 0.0 (993 voxels, overlap=0.679) Left_Caudate (11): linear fit = 1.04 x + 0.0 (993 voxels, peak = 72), gca=72.1 gca peak = 0.14301 (56) mri peak = 0.05023 (60) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (14261 voxels, overlap=0.981) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (14261 voxels, peak = 59), gca=58.5 gca peak = 0.14610 (55) mri peak = 0.05314 (64) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (17290 voxels, overlap=0.746) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (17290 voxels, peak = 62), gca=62.4 gca peak = 0.16309 (85) mri peak = 0.10801 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6273 voxels, overlap=0.427) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6273 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.10534 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5968 voxels, overlap=0.366) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5968 voxels, peak = 89), gca=89.5 gca peak = 0.30461 (58) mri peak = 0.08315 (71) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (682 voxels, overlap=0.064) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (682 voxels, peak = 70), gca=70.5 gca peak = 0.32293 (57) mri peak = 0.08817 (70) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (640 voxels, overlap=0.050) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (640 voxels, peak = 70), gca=69.8 gca peak = 0.11083 (90) mri peak = 0.06429 (87) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (4012 voxels, overlap=0.979) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (4012 voxels, peak = 91), gca=91.3 gca peak = 0.11393 (83) mri peak = 0.05888 (98) Right_Thalamus (49): linear fit = 1.12 x + 0.0 (4874 voxels, overlap=0.523) Right_Thalamus (49): linear fit = 1.12 x + 0.0 (4874 voxels, peak = 93), gca=93.4 gca peak = 0.08575 (81) mri peak = 0.09167 (84) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2269 voxels, overlap=0.655) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2269 voxels, peak = 86), gca=86.3 gca peak = 0.08618 (78) mri peak = 0.08112 (79) Right_Putamen (51): linear fit = 1.04 x + 0.0 (959 voxels, overlap=0.761) Right_Putamen (51): linear fit = 1.04 x + 0.0 (959 voxels, peak = 82), gca=81.5 gca peak = 0.08005 (78) mri peak = 0.06932 (91) Brain_Stem (16): linear fit = 1.13 x + 0.0 (12661 voxels, overlap=0.367) Brain_Stem (16): linear fit = 1.13 x + 0.0 (12661 voxels, peak = 89), gca=88.5 gca peak = 0.12854 (88) mri peak = 0.08895 (100) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1392 voxels, overlap=0.346) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1392 voxels, peak = 97), gca=97.2 gca peak = 0.15703 (87) mri peak = 0.07339 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1391 voxels, overlap=0.491) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1391 voxels, peak = 96), gca=96.1 gca peak = 0.17522 (25) mri peak = 0.25000 (20) gca peak = 0.17113 (14) mri peak = 0.15603 (24) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (140 voxels, overlap=0.851) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (140 voxels, peak = 21), gca=20.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) 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 1.13 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.20 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17693 (19) mri peak = 0.11479 (21) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (904 voxels, overlap=0.927) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (904 voxels, peak = 20), gca=20.4 gca peak = 0.18351 (15) mri peak = 0.12188 (16) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (497 voxels, overlap=0.799) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (497 voxels, peak = 15), gca=14.6 gca peak = 0.28564 (84) mri peak = 0.08287 (85) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (544 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (544 voxels, peak = 84), gca=83.6 gca peak = 0.16762 (98) mri peak = 0.14761 (98) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (691 voxels, overlap=0.997) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (691 voxels, peak = 98), gca=98.0 gca peak = 0.24486 (63) mri peak = 0.09249 (68) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (689 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (689 voxels, peak = 62), gca=62.1 gca peak = 0.30464 (62) mri peak = 0.08874 (63) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (728 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (728 voxels, peak = 61), gca=61.1 gca peak = 0.07884 (105) mri peak = 0.15220 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38134 voxels, overlap=0.627) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38134 voxels, peak = 104), gca=104.5 gca peak = 0.07837 (105) mri peak = 0.15711 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39899 voxels, overlap=0.572) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39899 voxels, peak = 105), gca=105.0 gca peak = 0.09431 (62) mri peak = 0.05481 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23344 voxels, overlap=0.988) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23344 voxels, peak = 64), gca=63.5 gca peak = 0.11127 (60) mri peak = 0.05866 (61) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22229 voxels, overlap=0.952) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22229 voxels, peak = 62), gca=61.5 gca peak = 0.21856 (76) mri peak = 0.13407 (79) Right_Caudate (50): linear fit = 1.00 x + 0.0 (910 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (910 voxels, peak = 76), gca=76.0 gca peak = 0.16719 (81) mri peak = 0.19819 (79) Left_Caudate (11): linear fit = 0.99 x + 0.0 (993 voxels, overlap=0.997) Left_Caudate (11): linear fit = 0.99 x + 0.0 (993 voxels, peak = 80), gca=79.8 gca peak = 0.13133 (58) mri peak = 0.05023 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (14261 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (14261 voxels, peak = 59), gca=59.4 gca peak = 0.14016 (63) mri peak = 0.05314 (64) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (17290 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (17290 voxels, peak = 62), gca=62.1 gca peak = 0.15236 (90) mri peak = 0.10801 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6273 voxels, overlap=0.881) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6273 voxels, peak = 91), gca=91.3 gca peak = 0.16794 (90) mri peak = 0.10534 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5968 voxels, overlap=0.841) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5968 voxels, peak = 91), gca=91.3 gca peak = 0.22728 (69) mri peak = 0.08315 (71) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (682 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (682 voxels, peak = 68), gca=68.0 gca peak = 0.23727 (70) mri peak = 0.08817 (70) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (640 voxels, overlap=1.002) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (640 voxels, peak = 70), gca=70.0 gca peak = 0.10534 (91) mri peak = 0.06429 (87) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4012 voxels, overlap=0.976) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4012 voxels, peak = 91), gca=90.5 gca peak = 0.10675 (91) mri peak = 0.05888 (98) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4874 voxels, overlap=0.993) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4874 voxels, peak = 91), gca=91.5 gca peak = 0.07448 (88) mri peak = 0.09167 (84) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2269 voxels, overlap=0.868) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2269 voxels, peak = 88), gca=88.0 gca peak = 0.11252 (79) mri peak = 0.08112 (79) Right_Putamen (51): linear fit = 0.99 x + 0.0 (959 voxels, overlap=0.877) Right_Putamen (51): linear fit = 0.99 x + 0.0 (959 voxels, peak = 78), gca=77.8 gca peak = 0.07817 (89) mri peak = 0.06932 (91) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12661 voxels, overlap=0.861) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12661 voxels, peak = 90), gca=90.3 gca peak = 0.11659 (97) mri peak = 0.08895 (100) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1392 voxels, overlap=0.810) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1392 voxels, peak = 98), gca=98.5 gca peak = 0.14494 (96) mri peak = 0.07339 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1391 voxels, overlap=0.925) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1391 voxels, peak = 96), gca=96.5 gca peak = 0.13281 (32) mri peak = 0.25000 (20) gca peak = 0.12908 (21) mri peak = 0.15603 (24) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (140 voxels, overlap=0.710) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (140 voxels, peak = 21), gca=21.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.17186 (31) gca peak Third_Ventricle = 0.13281 (32) gca peak CSF = 0.18178 (43) gca peak Left_Accumbens_area = 0.74301 (65) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.10623 (35) gca peak Right_Inf_Lat_Vent = 0.23431 (26) gca peak Right_Accumbens_area = 0.29441 (74) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13278 (38) gca peak Fifth_Ventricle = 0.59466 (39) gca peak WM_hypointensities = 0.10795 (77) gca peak non_WM_hypointensities = 0.14635 (41) gca peak Optic_Chiasm = 0.61279 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 67709 voxels changed in iteration 0 of unlikely voxel relabeling 202 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 31043 gm and wm labels changed (%31 to gray, %69 to white out of all changed labels) 312 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 68610 changed. image ll: -2.102, PF=0.500 pass 2: 18445 changed. image ll: -2.102, PF=0.500 pass 3: 4819 changed. 41699 voxels changed in iteration 0 of unlikely voxel relabeling 190 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6427 voxels changed in iteration 0 of unlikely voxel relabeling 67 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5671 voxels changed in iteration 0 of unlikely voxel relabeling 47 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4384 voxels changed in iteration 0 of unlikely voxel relabeling 40 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 5883 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 691 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 4078 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 665 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1684.911585 mri_ca_label stimesec 1.999714 mri_ca_label ru_maxrss 2107144 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 470497 mri_ca_label ru_majflt 12 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1952 mri_ca_label ru_oublock 712 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 75 mri_ca_label ru_nivcsw 5384 mri_ca_label took 28 minutes and 7 seconds. mri_ca_label done @#@FSTIME 2026:07:08:19:20:13 mri_ca_label N 10 e 1687.27 S 2.08 U 1684.91 P 99% M 2107144 F 12 R 470509 W 0 c 5384 w 76 I 1952 O 720 L 2.13 5.43 7.44 @#@FSLOADPOST 2026:07:08:19:48:21 mri_ca_label N 10 1.00 1.26 3.82 #-------------------------------------- #@# CC Seg Wed Jul 8 07:48:21 PM CEST 2026 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/transforms/cc_up.lta sub-20_ses-0 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/transforms/cc_up.lta reading aseg from /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/aseg.auto_noCCseg.mgz reading norm from /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/norm.mgz 22367 voxels in left wm, 37695 in right wm, xrange [123, 130] searching rotation angles z=[-7 7], y=[-6 8] searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 global minimum found at slice 127.0, rotations (1.45, -0.74) final transformation (x=127.0, yr=1.453, zr=-0.744): 0.99959 0.01298 0.02536 -2.97058; -0.01298 0.99992 -0.00033 34.69205; -0.02536 -0.00000 0.99968 21.25576; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 131] in xformed coordinates best xformed slice 128 min_x_fornix = 135 min_x_fornix = 140 min_x_fornix = 144 min_x_fornix = 148 min_x_fornix = 136 cc center is found at 128 95 110 eigenvectors: 0.00242 -0.00555 0.99998; -0.11034 -0.99388 -0.00525; 0.99389 -0.11033 -0.00301; writing aseg with callosum to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #VMPC# mri_cc VmPeak 434228 mri_cc done @#@FSTIME 2026:07:08:19:48:21 mri_cc N 7 e 36.15 S 0.19 U 35.94 P 99% M 344552 F 6 R 12991 W 0 c 107 w 76 I 984 O 704 L 1.00 1.26 3.82 @#@FSLOADPOST 2026:07:08:19:48:57 mri_cc N 7 1.00 1.23 3.71 #-------------------------------------- #@# Merge ASeg Wed Jul 8 07:48:57 PM CEST 2026 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Jul 8 07:48:57 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz aseg read with width 256 (src width 256) ************** resampling aseg to account for mismatch with source image *************** normalizing image... NOT doing gentle normalization with control points/label processing with aseg removing outliers in the aseg WM... 705 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 68 (68), valley at 43 (43) csf peak at 16, 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 68 (68), valley at 43 (43) csf peak at 16, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 4 seconds. @#@FSTIME 2026:07:08:19:48:57 mri_normalize N 9 e 128.54 S 0.74 U 127.76 P 99% M 1233924 F 10 R 234440 W 0 c 536 w 73 I 1736 O 2720 L 1.00 1.23 3.71 @#@FSLOADPOST 2026:07:08:19:51:06 mri_normalize N 9 1.20 1.20 3.37 #-------------------------------------------- #@# Mask BFS Wed Jul 8 07:51:06 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1628562 voxels in mask (pct= 9.71) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2026:07:08:19:51:06 mri_mask N 5 e 0.78 S 0.02 U 0.74 P 98% M 74304 F 6 R 2449 W 0 c 2 w 110 I 3624 O 2648 L 1.20 1.20 3.37 @#@FSLOADPOST 2026:07:08:19:51:07 mri_mask N 5 1.20 1.20 3.37 mri_mask -transfer 255 -keep_mask_deletion_edits brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz brain.finalsurfs.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 maskval=255, outval=255 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2026:07:08:19:51:07 mri_mask N 6 e 0.90 S 0.03 U 0.81 P 93% M 90744 F 0 R 3038 W 0 c 3 w 53 I 5296 O 2648 L 1.20 1.20 3.37 @#@FSLOADPOST 2026:07:08:19:51:08 mri_mask N 6 1.20 1.20 3.37 #-------------------------------------------- #@# WM Segmentation Wed Jul 8 07:51:08 PM CEST 2026 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname comps10h04 machine x86_64 user asmolova input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Writing output to wm255.mgz Count: -1 -1.000000 16777216 -0.000006 mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname comps10h04 machine x86_64 user asmolova input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Writing output to wm1.mgz Count: -1 -1.000000 16777216 -0.000006 mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: -1 deletes, -1 fills cp wm.mgz wm.seg.mgz AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2026:07:08:19:51:13 AntsDenoiseImageFs N 4 e 40.43 S 0.10 U 40.30 P 99% M 351068 F 25 R 4022 W 0 c 84 w 70 I 4520 O 2720 L 1.18 1.20 3.36 @#@FSLOADPOST 2026:07:08:19:51:53 AntsDenoiseImageFs N 4 1.09 1.17 3.26 mri_segment -wsizemm 13 -keep -mprage antsdn.brain.mgz wm.seg.mgz preserving editing changes in output volume... wsizemm = 13, voxres = 1, wsize = 13 Widening wm low from 89 to 79 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm mean: 110 wsize: 13 wm low: 79 wm hi: 125 gray low: 30 gray hi: 99 Doing initial trinary intensity segmentation MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99 white = 414056, nonwhite = 16095030, ambig = 268130, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (105.0): 104.3 +- 5.4 [79.0 --> 125.0] CCS GM (73.0) : 72.1 +- 10.0 [30.0 --> 95.0] white_mean 104.297 white_sigma 5.42288 gray_mean 72.1342 gray_sigma 9.96578 setting bottom of white matter range wm_low to 82.1 setting top of gray matter range gray_hi to 92.1 wm_low 82.1 wm_hi 125 gray_low 30 gray_hi 92.0658 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=82.1, wm_hi=125, gray_hi=92.0658 white = 491835, nonwhite = 16160683, ambig = 124698, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 82.1 wm_hi 125 gray_low 30 gray_hi 92.0658 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 92.0658, wm_low = 82.1 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=92.0658, wmlow=82.1 113779 voxels processed (0.68%) 52080 voxels white (0.31%) 61699 voxels non-white (0.37%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=77.1, gray_hi=92.0658, wsize=13 208114 voxels tested (1.24%) 43954 voxels changed (0.26%) 49590 multi-scale searches (0.30%) Recovering bright white MRIrecoverBrightWhite() wm_low 82.1 wm_hi 125 slack 5.42288 pct_thresh 0.33 intensity_thresh 130.423 nvox_thresh 8.58 171 voxels tested (0.00%) 89 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=77.1, hithr=92.0658 smoothing input volume with sigma = 0.250 66737 voxels tested (0.40%) 13824 voxels changed (0.08%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 4291 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 2195 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 5893 filled MRIfindBrightNonWM(): 2274 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.1 minutes writing output to wm.seg.mgz... @#@FSTIME 2026:07:08:19:51:53 mri_segment N 6 e 65.47 S 0.25 U 65.19 P 99% M 155936 F 8 R 80616 W 0 c 554 w 76 I 3936 O 856 L 1.09 1.17 3.26 @#@FSLOADPOST 2026:07:08:19:52:59 mri_segment N 6 1.08 1.15 3.11 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.40 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2707 additional wm voxels added 0 additional wm voxels added SEG EDIT: 39713 voxels turned on, 45368 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2026:07:08:19:52:59 mri_edit_wm_with_aseg N 5 e 24.16 S 0.19 U 23.95 P 99% M 463840 F 7 R 40734 W 0 c 85 w 73 I 992 O 768 L 1.08 1.15 3.11 @#@FSLOADPOST 2026:07:08:19:53:23 mri_edit_wm_with_aseg N 5 1.05 1.14 3.05 mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 13 found - 13 modified | TOTAL: 31 pass 2 (xy-): 0 found - 13 modified | TOTAL: 31 pass 1 (yz+): 38 found - 38 modified | TOTAL: 69 pass 2 (yz+): 0 found - 38 modified | TOTAL: 69 pass 1 (yz-): 19 found - 19 modified | TOTAL: 88 pass 2 (yz-): 0 found - 19 modified | TOTAL: 88 pass 1 (xz+): 8 found - 8 modified | TOTAL: 96 pass 2 (xz+): 0 found - 8 modified | TOTAL: 96 pass 1 (xz-): 21 found - 21 modified | TOTAL: 117 pass 2 (xz-): 0 found - 21 modified | TOTAL: 117 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 4 found - 4 modified | TOTAL: 12 pass 2 (+++): 0 found - 4 modified | TOTAL: 12 pass 1 (+++): 18 found - 18 modified | TOTAL: 30 pass 2 (+++): 0 found - 18 modified | TOTAL: 30 pass 1 (+++): 9 found - 9 modified | TOTAL: 39 pass 2 (+++): 0 found - 9 modified | TOTAL: 39 Iteration Number : 1 pass 1 (++): 124 found - 124 modified | TOTAL: 124 pass 2 (++): 0 found - 124 modified | TOTAL: 124 pass 1 (+-): 108 found - 108 modified | TOTAL: 232 pass 2 (+-): 0 found - 108 modified | TOTAL: 232 pass 1 (--): 99 found - 99 modified | TOTAL: 331 pass 2 (--): 0 found - 99 modified | TOTAL: 331 pass 1 (-+): 98 found - 98 modified | TOTAL: 429 pass 2 (-+): 0 found - 98 modified | TOTAL: 429 Iteration Number : 2 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+): 2 found - 2 modified | TOTAL: 11 pass 2 (yz+): 0 found - 2 modified | TOTAL: 11 pass 1 (yz-): 2 found - 2 modified | TOTAL: 13 pass 2 (yz-): 0 found - 2 modified | TOTAL: 13 pass 1 (xz+): 2 found - 2 modified | TOTAL: 15 pass 2 (xz+): 0 found - 2 modified | TOTAL: 15 pass 1 (xz-): 1 found - 1 modified | TOTAL: 16 pass 2 (xz-): 0 found - 1 modified | TOTAL: 16 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 2 found - 2 modified | TOTAL: 4 pass 2 (-+): 0 found - 2 modified | TOTAL: 4 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 607 (out of 534624: 0.113538) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done @#@FSTIME 2026:07:08:19:53:23 mri_pretess N 5 e 2.52 S 0.03 U 2.47 P 99% M 57160 F 22 R 2787 W 0 c 8 w 75 I 4032 O 768 L 1.05 1.14 3.05 @#@FSLOADPOST 2026:07:08:19:53:26 mri_pretess N 5 1.05 1.14 3.04 #-------------------------------------------- #@# Fill Wed Jul 8 07:53:26 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/SubCorticalMassLUT.txt -auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... done. searching for cutting planes...voxel to talairach voxel transform 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24870; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; Using auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt ndiff 0 reading input volume... wm.mgzvoxel to talairach voxel transform 1.07947 -0.03541 -0.00736 -6.68205; 0.03504 1.07545 0.20764 -28.24870; 0.00057 -0.16011 0.94614 21.78835; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1019 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) no need to search using seed (126, 111, 92), TAL = (2.0, -36.0, 17.0) talairach voxel to voxel transform 0.92539 0.03054 0.00050 7.03536; -0.02910 0.89946 -0.19763 29.52017; -0.00549 0.15220 1.02348 -18.03731; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 111, 92) --> (2.0, -36.0, 17.0) done. filling took 0.9 minutes talairach cc position changed to (2.00, -36.00, 17.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -36.00, 17.00) SRC: (110.41, 108.04, 92.42) search lh wm seed point around talairach space (-16.00, -36.00, 17.00), SRC: (143.73, 106.99, 92.23) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... DoAutoMan 1 No edits to apply Writing edits to ../tmp/filled.edits.txt Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2026:07:08:19:53:26 mri_fill N 14 e 56.78 S 0.87 U 55.84 P 99% M 966012 F 8 R 286036 W 0 c 250 w 76 I 1728 O 272 L 1.05 1.14 3.04 @#@FSLOADPOST 2026:07:08:19:54:23 mri_fill N 14 1.02 1.11 2.92 #-------------------------------------------- #@# Tessellate lh Wed Jul 8 07:54:23 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 8 found - 8 modified | TOTAL: 9 pass 2 (yz+): 0 found - 8 modified | TOTAL: 9 pass 1 (yz-): 7 found - 7 modified | TOTAL: 16 pass 2 (yz-): 0 found - 7 modified | TOTAL: 16 pass 1 (xz+): 3 found - 3 modified | TOTAL: 19 pass 2 (xz+): 0 found - 3 modified | TOTAL: 19 pass 1 (xz-): 0 found - 0 modified | TOTAL: 19 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 21 (out of 256807: 0.008177) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2026:07:08:19:54:23 mri_pretess N 4 e 1.04 S 0.02 U 1.01 P 99% M 40420 F 1 R 1653 W 0 c 3 w 50 I 72 O 264 L 1.02 1.11 2.92 @#@FSLOADPOST 2026:07:08:19:54:24 mri_pretess N 4 1.02 1.11 2.92 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.4.1 7.4.1 slice 30: 336 vertices, 387 faces slice 40: 4641 vertices, 4847 faces slice 50: 11794 vertices, 12097 faces slice 60: 21296 vertices, 21633 faces slice 70: 31266 vertices, 31623 faces slice 80: 41019 vertices, 41404 faces slice 90: 51998 vertices, 52352 faces slice 100: 63109 vertices, 63504 faces slice 110: 74321 vertices, 74691 faces slice 120: 85051 vertices, 85460 faces slice 130: 95727 vertices, 96112 faces slice 140: 105882 vertices, 106235 faces slice 150: 115049 vertices, 115360 faces slice 160: 122535 vertices, 122812 faces slice 170: 129548 vertices, 129826 faces slice 180: 135119 vertices, 135303 faces slice 190: 138573 vertices, 138632 faces slice 200: 138692 vertices, 138712 faces slice 210: 138692 vertices, 138712 faces slice 220: 138692 vertices, 138712 faces slice 230: 138692 vertices, 138712 faces slice 240: 138692 vertices, 138712 faces slice 250: 138692 vertices, 138712 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2026:07:08:19:54:24 mri_tessellate N 3 e 1.21 S 0.02 U 1.17 P 98% M 44580 F 5 R 1255 W 0 c 5 w 73 I 832 O 6504 L 1.02 1.11 2.92 @#@FSLOADPOST 2026:07:08:19:54:25 mri_tessellate N 3 1.02 1.11 2.92 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 138692 voxel in cpt #1: X=-20 [v=138692,e=416136,f=277424] located at (-26.737995, -22.447388, 19.790024) For the whole surface: X=-20 [v=138692,e=416136,f=277424] One single component has been found nothing to do done @#@FSTIME 2026:07:08:19:54:25 mris_extract_main_component N 2 e 0.80 S 0.10 U 0.67 P 97% M 277528 F 19 R 26784 W 0 c 3 w 201 I 10048 O 9760 L 1.02 1.11 2.92 @#@FSLOADPOST 2026:07:08:19:54:26 mris_extract_main_component N 2 1.02 1.11 2.91 #-------------------------------------------- #@# Tessellate rh Wed Jul 8 07:54:26 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 8 found - 8 modified | TOTAL: 9 pass 2 (yz+): 0 found - 8 modified | TOTAL: 9 pass 1 (yz-): 3 found - 3 modified | TOTAL: 12 pass 2 (yz-): 0 found - 3 modified | TOTAL: 12 pass 1 (xz+): 1 found - 1 modified | TOTAL: 13 pass 2 (xz+): 0 found - 1 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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 = 19 (out of 254784: 0.007457) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2026:07:08:19:54:26 mri_pretess N 4 e 1.41 S 0.01 U 1.39 P 99% M 40416 F 0 R 1655 W 0 c 3 w 29 I 0 O 264 L 1.02 1.11 2.91 @#@FSLOADPOST 2026:07:08:19:54:27 mri_pretess N 4 1.02 1.11 2.91 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.4.1 7.4.1 slice 30: 318 vertices, 370 faces slice 40: 4613 vertices, 4835 faces slice 50: 12369 vertices, 12673 faces slice 60: 22373 vertices, 22732 faces slice 70: 33511 vertices, 33865 faces slice 80: 44696 vertices, 45077 faces slice 90: 56789 vertices, 57169 faces slice 100: 68164 vertices, 68550 faces slice 110: 79131 vertices, 79514 faces slice 120: 89867 vertices, 90247 faces slice 130: 100067 vertices, 100432 faces slice 140: 110037 vertices, 110368 faces slice 150: 118242 vertices, 118550 faces slice 160: 125433 vertices, 125669 faces slice 170: 131579 vertices, 131797 faces slice 180: 136796 vertices, 136969 faces slice 190: 139490 vertices, 139521 faces slice 200: 139522 vertices, 139540 faces slice 210: 139522 vertices, 139540 faces slice 220: 139522 vertices, 139540 faces slice 230: 139522 vertices, 139540 faces slice 240: 139522 vertices, 139540 faces slice 250: 139522 vertices, 139540 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2026:07:08:19:54:27 mri_tessellate N 3 e 1.19 S 0.01 U 1.16 P 98% M 44544 F 0 R 1252 W 0 c 3 w 88 I 0 O 6544 L 1.02 1.11 2.91 @#@FSLOADPOST 2026:07:08:19:54:29 mri_tessellate N 3 1.02 1.11 2.91 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 139522 voxel in cpt #1: X=-18 [v=139522,e=418620,f=279080] located at (28.535393, -25.270029, 21.667229) For the whole surface: X=-18 [v=139522,e=418620,f=279080] One single component has been found nothing to do done @#@FSTIME 2026:07:08:19:54:29 mris_extract_main_component N 2 e 0.86 S 0.10 U 0.74 P 98% M 279012 F 0 R 27585 W 0 c 4 w 130 I 6544 O 9816 L 1.02 1.11 2.91 @#@FSLOADPOST 2026:07:08:19:54:29 mris_extract_main_component N 2 1.02 1.11 2.91 #-------------------------------------------- #@# Smooth1 lh Wed Jul 8 07:54:29 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:19:54:30 mris_smooth N 5 e 2.55 S 0.13 U 2.40 P 99% M 221088 F 4 R 40291 W 0 c 4 w 156 I 10320 O 9768 L 1.02 1.11 2.91 @#@FSLOADPOST 2026:07:08:19:54:32 mris_smooth N 5 1.01 1.11 2.90 #-------------------------------------------- #@# Smooth1 rh Wed Jul 8 07:54:32 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:19:54:32 mris_smooth N 5 e 2.55 S 0.09 U 2.43 P 99% M 222300 F 0 R 41048 W 0 c 12 w 156 I 9816 O 9816 L 1.01 1.11 2.90 @#@FSLOADPOST 2026:07:08:19:54:35 mris_smooth N 5 1.01 1.11 2.90 #-------------------------------------------- #@# Inflation1 lh Wed Jul 8 07:54:35 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.2 mm, total surface area = 74339 mm^2 step 000: RMS=0.148 (target=0.015) step 005: RMS=0.110 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.028 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 18.142393 mris_inflate stimesec 0.927917 mris_inflate ru_maxrss 221836 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 454347 mris_inflate ru_majflt 21 mris_inflate ru_nswap 0 mris_inflate ru_inblock 13832 mris_inflate ru_oublock 9760 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 195 mris_inflate ru_nivcsw 58 @#@FSTIME 2026:07:08:19:54:35 mris_inflate N 3 e 19.10 S 0.93 U 18.14 P 99% M 221836 F 21 R 454352 W 0 c 58 w 196 I 13832 O 9760 L 1.01 1.11 2.90 @#@FSLOADPOST 2026:07:08:19:54:54 mris_inflate N 3 1.01 1.10 2.86 #-------------------------------------------- #@# Inflation1 rh Wed Jul 8 07:54:54 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.8 mm, total surface area = 75221 mm^2 step 000: RMS=0.147 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.080 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 18.466058 mris_inflate stimesec 1.007894 mris_inflate ru_maxrss 223168 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 472546 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9816 mris_inflate ru_oublock 9816 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 118 mris_inflate ru_nivcsw 157 @#@FSTIME 2026:07:08:19:54:54 mris_inflate N 3 e 19.50 S 1.01 U 18.46 P 99% M 223168 F 0 R 472551 W 0 c 157 w 118 I 9816 O 9824 L 1.01 1.10 2.86 @#@FSLOADPOST 2026:07:08:19:55:13 mris_inflate N 3 1.01 1.09 2.82 #-------------------------------------------- #@# QSphere lh Wed Jul 8 07:55:13 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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: 7.4.1 available threads: 1 scaling brain by 0.305... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.57 (0.00-->6.73) (max @ vno 51570 --> 51571) face area 0.02 +- 0.03 (-0.05-->0.65) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.684, avgs=0 005/300: dt: 0.9000, rms radial error=176.426, avgs=0 010/300: dt: 0.9000, rms radial error=175.869, avgs=0 015/300: dt: 0.9000, rms radial error=175.136, avgs=0 020/300: dt: 0.9000, rms radial error=174.301, avgs=0 025/300: dt: 0.9000, rms radial error=173.409, avgs=0 030/300: dt: 0.9000, rms radial error=172.485, avgs=0 035/300: dt: 0.9000, rms radial error=171.550, avgs=0 040/300: dt: 0.9000, rms radial error=170.608, avgs=0 045/300: dt: 0.9000, rms radial error=169.664, avgs=0 050/300: dt: 0.9000, rms radial error=168.720, avgs=0 055/300: dt: 0.9000, rms radial error=167.778, avgs=0 060/300: dt: 0.9000, rms radial error=166.841, avgs=0 065/300: dt: 0.9000, rms radial error=165.907, avgs=0 070/300: dt: 0.9000, rms radial error=164.978, avgs=0 075/300: dt: 0.9000, rms radial error=164.054, avgs=0 080/300: dt: 0.9000, rms radial error=163.134, avgs=0 085/300: dt: 0.9000, rms radial error=162.219, avgs=0 090/300: dt: 0.9000, rms radial error=161.309, avgs=0 095/300: dt: 0.9000, rms radial error=160.404, avgs=0 100/300: dt: 0.9000, rms radial error=159.504, avgs=0 105/300: dt: 0.9000, rms radial error=158.609, avgs=0 110/300: dt: 0.9000, rms radial error=157.718, avgs=0 115/300: dt: 0.9000, rms radial error=156.832, avgs=0 120/300: dt: 0.9000, rms radial error=155.952, avgs=0 125/300: dt: 0.9000, rms radial error=155.075, avgs=0 130/300: dt: 0.9000, rms radial error=154.204, avgs=0 135/300: dt: 0.9000, rms radial error=153.337, avgs=0 140/300: dt: 0.9000, rms radial error=152.475, avgs=0 145/300: dt: 0.9000, rms radial error=151.618, avgs=0 150/300: dt: 0.9000, rms radial error=150.765, avgs=0 155/300: dt: 0.9000, rms radial error=149.917, avgs=0 160/300: dt: 0.9000, rms radial error=149.074, avgs=0 165/300: dt: 0.9000, rms radial error=148.235, avgs=0 170/300: dt: 0.9000, rms radial error=147.401, avgs=0 175/300: dt: 0.9000, rms radial error=146.571, avgs=0 180/300: dt: 0.9000, rms radial error=145.746, avgs=0 185/300: dt: 0.9000, rms radial error=144.925, avgs=0 190/300: dt: 0.9000, rms radial error=144.109, avgs=0 195/300: dt: 0.9000, rms radial error=143.297, avgs=0 200/300: dt: 0.9000, rms radial error=142.490, avgs=0 205/300: dt: 0.9000, rms radial error=141.687, avgs=0 210/300: dt: 0.9000, rms radial error=140.888, avgs=0 215/300: dt: 0.9000, rms radial error=140.094, avgs=0 220/300: dt: 0.9000, rms radial error=139.305, avgs=0 225/300: dt: 0.9000, rms radial error=138.520, avgs=0 230/300: dt: 0.9000, rms radial error=137.739, avgs=0 235/300: dt: 0.9000, rms radial error=136.962, avgs=0 240/300: dt: 0.9000, rms radial error=136.190, avgs=0 245/300: dt: 0.9000, rms radial error=135.423, avgs=0 250/300: dt: 0.9000, rms radial error=134.659, avgs=0 255/300: dt: 0.9000, rms radial error=133.900, avgs=0 260/300: dt: 0.9000, rms radial error=133.145, avgs=0 265/300: dt: 0.9000, rms radial error=132.394, avgs=0 270/300: dt: 0.9000, rms radial error=131.647, avgs=0 275/300: dt: 0.9000, rms radial error=130.904, avgs=0 280/300: dt: 0.9000, rms radial error=130.166, avgs=0 285/300: dt: 0.9000, rms radial error=129.432, avgs=0 290/300: dt: 0.9000, rms radial error=128.702, avgs=0 295/300: dt: 0.9000, rms radial error=127.976, avgs=0 300/300: dt: 0.9000, rms radial error=127.254, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16274.50 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00037 epoch 2 (K=40.0), pass 1, starting sse = 2656.80 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00015 epoch 3 (K=160.0), pass 1, starting sse = 250.53 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.17/17 = 0.01016 epoch 4 (K=640.0), pass 1, starting sse = 8.96 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.22/18 = 0.01230 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0345 hours FSRUNTIME@ mris_sphere 0.0345 hours 1 threads #VMPC# mris_sphere VmPeak 480688 mris_sphere done @#@FSTIME 2026:07:08:19:55:14 mris_sphere N 9 e 124.30 S 5.02 U 119.21 P 99% M 227348 F 11 R 2025528 W 0 c 1071 w 193 I 11240 O 9768 L 1.01 1.09 2.82 @#@FSLOADPOST 2026:07:08:19:57:18 mris_sphere N 9 1.14 1.11 2.60 #-------------------------------------------- #@# QSphere rh Wed Jul 8 07:57:18 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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: 7.4.1 available threads: 1 scaling brain by 0.304... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.57 (0.00-->9.72) (max @ vno 64473 --> 65597) face area 0.02 +- 0.03 (-0.29-->0.85) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.708, avgs=0 005/300: dt: 0.9000, rms radial error=176.449, avgs=0 010/300: dt: 0.9000, rms radial error=175.891, avgs=0 015/300: dt: 0.9000, rms radial error=175.159, avgs=0 020/300: dt: 0.9000, rms radial error=174.325, avgs=0 025/300: dt: 0.9000, rms radial error=173.431, avgs=0 030/300: dt: 0.9000, rms radial error=172.508, avgs=0 035/300: dt: 0.9000, rms radial error=171.572, avgs=0 040/300: dt: 0.9000, rms radial error=170.627, avgs=0 045/300: dt: 0.9000, rms radial error=169.683, avgs=0 050/300: dt: 0.9000, rms radial error=168.739, avgs=0 055/300: dt: 0.9000, rms radial error=167.798, avgs=0 060/300: dt: 0.9000, rms radial error=166.861, avgs=0 065/300: dt: 0.9000, rms radial error=165.929, avgs=0 070/300: dt: 0.9000, rms radial error=165.001, avgs=0 075/300: dt: 0.9000, rms radial error=164.078, avgs=0 080/300: dt: 0.9000, rms radial error=163.160, avgs=0 085/300: dt: 0.9000, rms radial error=162.247, avgs=0 090/300: dt: 0.9000, rms radial error=161.339, avgs=0 095/300: dt: 0.9000, rms radial error=160.435, avgs=0 100/300: dt: 0.9000, rms radial error=159.537, avgs=0 105/300: dt: 0.9000, rms radial error=158.643, avgs=0 110/300: dt: 0.9000, rms radial error=157.753, avgs=0 115/300: dt: 0.9000, rms radial error=156.869, avgs=0 120/300: dt: 0.9000, rms radial error=155.989, avgs=0 125/300: dt: 0.9000, rms radial error=155.114, avgs=0 130/300: dt: 0.9000, rms radial error=154.244, avgs=0 135/300: dt: 0.9000, rms radial error=153.378, avgs=0 140/300: dt: 0.9000, rms radial error=152.517, avgs=0 145/300: dt: 0.9000, rms radial error=151.661, avgs=0 150/300: dt: 0.9000, rms radial error=150.809, avgs=0 155/300: dt: 0.9000, rms radial error=149.962, avgs=0 160/300: dt: 0.9000, rms radial error=149.119, avgs=0 165/300: dt: 0.9000, rms radial error=148.281, avgs=0 170/300: dt: 0.9000, rms radial error=147.448, avgs=0 175/300: dt: 0.9000, rms radial error=146.619, avgs=0 180/300: dt: 0.9000, rms radial error=145.794, avgs=0 185/300: dt: 0.9000, rms radial error=144.975, avgs=0 190/300: dt: 0.9000, rms radial error=144.159, avgs=0 195/300: dt: 0.9000, rms radial error=143.349, avgs=0 200/300: dt: 0.9000, rms radial error=142.542, avgs=0 205/300: dt: 0.9000, rms radial error=141.740, avgs=0 210/300: dt: 0.9000, rms radial error=140.943, avgs=0 215/300: dt: 0.9000, rms radial error=140.150, avgs=0 220/300: dt: 0.9000, rms radial error=139.361, avgs=0 225/300: dt: 0.9000, rms radial error=138.577, avgs=0 230/300: dt: 0.9000, rms radial error=137.797, avgs=0 235/300: dt: 0.9000, rms radial error=137.022, avgs=0 240/300: dt: 0.9000, rms radial error=136.250, avgs=0 245/300: dt: 0.9000, rms radial error=135.483, avgs=0 250/300: dt: 0.9000, rms radial error=134.721, avgs=0 255/300: dt: 0.9000, rms radial error=133.962, avgs=0 260/300: dt: 0.9000, rms radial error=133.208, avgs=0 265/300: dt: 0.9000, rms radial error=132.458, avgs=0 270/300: dt: 0.9000, rms radial error=131.712, avgs=0 275/300: dt: 0.9000, rms radial error=130.970, avgs=0 280/300: dt: 0.9000, rms radial error=130.232, avgs=0 285/300: dt: 0.9000, rms radial error=129.499, avgs=0 290/300: dt: 0.9000, rms radial error=128.770, avgs=0 295/300: dt: 0.9000, rms radial error=128.044, avgs=0 300/300: dt: 0.9000, rms radial error=127.323, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16380.64 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00029 epoch 2 (K=40.0), pass 1, starting sse = 2701.78 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00029 epoch 3 (K=160.0), pass 1, starting sse = 259.84 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/17 = 0.00834 epoch 4 (K=640.0), pass 1, starting sse = 11.41 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.26/36 = 0.00716 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0421 hours FSRUNTIME@ mris_sphere 0.0421 hours 1 threads #VMPC# mris_sphere VmPeak 481648 mris_sphere done @#@FSTIME 2026:07:08:19:57:18 mris_sphere N 9 e 151.58 S 6.08 U 145.46 P 99% M 228560 F 0 R 2712112 W 0 c 530 w 149 I 0 O 9816 L 1.14 1.11 2.60 @#@FSLOADPOST 2026:07:08:19:59:49 mris_sphere N 9 1.13 1.11 2.37 #@# Fix Topology lh Wed Jul 8 07:59:49 PM CEST 2026 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-20_ses-0 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' 7.4.1 7.4.1 before topology correction, eno=-20 (nv=138692, nf=277424, ne=416136, g=11) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 2077 ambiguous faces found in tessellation segmenting defects... 16 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 16 defects to be corrected 0 vertices coincident reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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: -9.5351 (-4.7676) -vertex loglikelihood: -6.4235 (-3.2118) -normal dot loglikelihood: -3.6571 (-3.6571) -quad curv loglikelihood: -6.1479 (-3.0739) Total Loglikelihood : -25.7636 CORRECTING DEFECT 0 (vertices=40, convex hull=83, v0=616) After retessellation of defect 0 (v0=616), euler #=-13 (137487,412138,274638) : difference with theory (-13) = 0 CORRECTING DEFECT 1 (vertices=242, convex hull=113, v0=8311) After retessellation of defect 1 (v0=8311), euler #=-12 (137533,412323,274778) : difference with theory (-12) = 0 CORRECTING DEFECT 2 (vertices=96, convex hull=80, v0=25854) After retessellation of defect 2 (v0=25854), euler #=-11 (137564,412447,274872) : difference with theory (-11) = 0 CORRECTING DEFECT 3 (vertices=19, convex hull=15, v0=44016) After retessellation of defect 3 (v0=44016), euler #=-10 (137565,412453,274878) : difference with theory (-10) = 0 CORRECTING DEFECT 4 (vertices=9, convex hull=27, v0=56740) After retessellation of defect 4 (v0=56740), euler #=-9 (137568,412470,274893) : difference with theory (-9) = 0 CORRECTING DEFECT 5 (vertices=35, convex hull=59, v0=57312) After retessellation of defect 5 (v0=57312), euler #=-8 (137588,412554,274958) : difference with theory (-8) = 0 CORRECTING DEFECT 6 (vertices=14, convex hull=22, v0=64863) After retessellation of defect 6 (v0=64863), euler #=-7 (137590,412565,274968) : difference with theory (-7) = 0 CORRECTING DEFECT 7 (vertices=7, convex hull=25, v0=66017) After retessellation of defect 7 (v0=66017), euler #=-6 (137593,412580,274981) : difference with theory (-6) = 0 CORRECTING DEFECT 8 (vertices=89, convex hull=53, v0=74000) After retessellation of defect 8 (v0=74000), euler #=-5 (137603,412634,275026) : difference with theory (-5) = 0 CORRECTING DEFECT 9 (vertices=49, convex hull=56, v0=85607) After retessellation of defect 9 (v0=85607), euler #=-4 (137629,412733,275100) : difference with theory (-4) = 0 CORRECTING DEFECT 10 (vertices=53, convex hull=66, v0=90061) After retessellation of defect 10 (v0=90061), euler #=-3 (137657,412844,275184) : difference with theory (-3) = 0 CORRECTING DEFECT 11 (vertices=325, convex hull=61, v0=95334) After retessellation of defect 11 (v0=95334), euler #=-2 (137671,412912,275239) : difference with theory (-2) = 0 CORRECTING DEFECT 12 (vertices=64, convex hull=83, v0=96266) After retessellation of defect 12 (v0=96266), euler #=-1 (137703,413044,275340) : difference with theory (-1) = 0 CORRECTING DEFECT 13 (vertices=8, convex hull=31, v0=97571) After retessellation of defect 13 (v0=97571), euler #=0 (137706,413062,275356) : difference with theory (0) = 0 CORRECTING DEFECT 14 (vertices=22, convex hull=33, v0=100399) After retessellation of defect 14 (v0=100399), euler #=1 (137711,413089,275379) : difference with theory (1) = 0 CORRECTING DEFECT 15 (vertices=142, convex hull=93, v0=103642) After retessellation of defect 15 (v0=103642), euler #=2 (137744,413226,275484) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.05-->6.64) (max @ vno 25583 --> 31565) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.05-->6.64) (max @ vno 25583 --> 31565) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 36 mutations (31.9%), 77 crossovers (68.1%), 31 vertices were eliminated building final representation... 948 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=137744, nf=275484, ne=413226, g=0) writing corrected surface to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 80 intersecting terminating search with 0 intersecting topology fixing took 0.9 minutes FSRUNTIME@ mris_fix_topology lh 0.0152 hours 1 threads #VMPC# mris_fix_topology VmPeak 757348 @#@FSTIME 2026:07:08:19:59:50 mris_fix_topology N 14 e 54.73 S 0.42 U 54.20 P 99% M 740620 F 15 R 174083 W 0 c 118 w 318 I 12000 O 12960 L 1.13 1.11 2.37 @#@FSLOADPOST 2026:07:08:20:00:44 mris_fix_topology N 14 1.13 1.10 2.30 #@# Fix Topology rh Wed Jul 8 08:00:44 PM CEST 2026 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-20_ses-0 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' 7.4.1 7.4.1 before topology correction, eno=-18 (nv=139522, nf=279080, ne=418620, g=10) 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 7 iterations marking ambiguous vertices... 1995 ambiguous faces found in tessellation segmenting defects... 18 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 17 into 16 17 defects to be corrected 0 vertices coincident reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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: -9.6333 (-4.8166) -vertex loglikelihood: -6.4248 (-3.2124) -normal dot loglikelihood: -3.6446 (-3.6446) -quad curv loglikelihood: -6.1416 (-3.0708) Total Loglikelihood : -25.8443 CORRECTING DEFECT 0 (vertices=55, convex hull=89, v0=1921) After retessellation of defect 0 (v0=1921), euler #=-15 (138351,414656,276290) : difference with theory (-14) = 1 CORRECTING DEFECT 1 (vertices=424, convex hull=243, v0=52612) After retessellation of defect 1 (v0=52612), euler #=-14 (138372,414842,276456) : difference with theory (-13) = 1 CORRECTING DEFECT 2 (vertices=14, convex hull=26, v0=55081) After retessellation of defect 2 (v0=55081), euler #=-13 (138376,414862,276473) : difference with theory (-12) = 1 CORRECTING DEFECT 3 (vertices=31, convex hull=33, v0=59567) After retessellation of defect 3 (v0=59567), euler #=-12 (138385,414900,276503) : difference with theory (-11) = 1 CORRECTING DEFECT 4 (vertices=7, convex hull=12, v0=63229) After retessellation of defect 4 (v0=63229), euler #=-11 (138387,414908,276510) : difference with theory (-10) = 1 CORRECTING DEFECT 5 (vertices=30, convex hull=32, v0=64259) After retessellation of defect 5 (v0=64259), euler #=-10 (138392,414937,276535) : difference with theory (-9) = 1 CORRECTING DEFECT 6 (vertices=9, convex hull=23, v0=76287) After retessellation of defect 6 (v0=76287), euler #=-9 (138396,414953,276548) : difference with theory (-8) = 1 CORRECTING DEFECT 7 (vertices=27, convex hull=60, v0=90415) After retessellation of defect 7 (v0=90415), euler #=-8 (138412,415024,276604) : difference with theory (-7) = 1 CORRECTING DEFECT 8 (vertices=20, convex hull=24, v0=96714) After retessellation of defect 8 (v0=96714), euler #=-7 (138421,415059,276631) : difference with theory (-6) = 1 CORRECTING DEFECT 9 (vertices=355, convex hull=145, v0=99728) After retessellation of defect 9 (v0=99728), euler #=-6 (138489,415329,276834) : difference with theory (-5) = 1 CORRECTING DEFECT 10 (vertices=7, convex hull=31, v0=102810) After retessellation of defect 10 (v0=102810), euler #=-5 (138490,415341,276846) : difference with theory (-4) = 1 CORRECTING DEFECT 11 (vertices=7, convex hull=26, v0=102959) After retessellation of defect 11 (v0=102959), euler #=-4 (138491,415348,276853) : difference with theory (-3) = 1 CORRECTING DEFECT 12 (vertices=58, convex hull=36, v0=104702) After retessellation of defect 12 (v0=104702), euler #=-3 (138498,415382,276881) : difference with theory (-2) = 1 CORRECTING DEFECT 13 (vertices=27, convex hull=62, v0=118208) After retessellation of defect 13 (v0=118208), euler #=-2 (138518,415466,276946) : difference with theory (-1) = 1 CORRECTING DEFECT 14 (vertices=22, convex hull=43, v0=131025) After retessellation of defect 14 (v0=131025), euler #=-1 (138528,415512,276983) : difference with theory (0) = 1 CORRECTING DEFECT 15 (vertices=18, convex hull=46, v0=132034) After retessellation of defect 15 (v0=132034), euler #=0 (138537,415555,277018) : difference with theory (1) = 1 CORRECTING DEFECT 16 (vertices=78, convex hull=104, v0=132160) After retessellation of defect 16 (v0=132160), euler #=2 (138562,415680,277120) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.05-->12.88) (max @ vno 53742 --> 61822) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.05-->12.88) (max @ vno 53742 --> 61822) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 60 mutations (35.1%), 111 crossovers (64.9%), 111 vertices were eliminated building final representation... 960 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138562, nf=277120, ne=415680, g=0) writing corrected surface to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 125 intersecting terminating search with 0 intersecting topology fixing took 1.4 minutes FSRUNTIME@ mris_fix_topology rh 0.0230 hours 1 threads #VMPC# mris_fix_topology VmPeak 758352 @#@FSTIME 2026:07:08:20:00:44 mris_fix_topology N 14 e 82.87 S 0.41 U 82.38 P 99% M 741508 F 0 R 175530 W 0 c 188 w 264 I 10104 O 13040 L 1.13 1.10 2.30 @#@FSLOADPOST 2026:07:08:20:02:07 mris_fix_topology N 14 1.03 1.07 2.18 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 137744 - 413226 + 275484 = 2 --> 0 holes F =2V-4: 275484 = 275488-4 (0) 2E=3F: 826452 = 826452 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 138562 - 415680 + 277120 = 2 --> 0 holes F =2V-4: 277120 = 277124-4 (0) 2E=3F: 831360 = 831360 (0) total defect index = 0 Wed Jul 8 08:02:08 PM CEST 2026 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/defect2seg --s sub-20_ses-0 --cortex freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 defect2seg 7.4.1 Linux comps10h04 6.1.0-49-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.174-1 (2026-05-26) x86_64 GNU/Linux pid 68832 mri_label2label --label-cortex /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.nofix /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/aseg.presurf.mgz 0 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 10 non-cortical segments detected only using segment with 7532 vertices erasing segment 1 (vno[0] = 48279) erasing segment 2 (vno[0] = 49423) erasing segment 3 (vno[0] = 58123) erasing segment 4 (vno[0] = 94260) erasing segment 5 (vno[0] = 95352) erasing segment 6 (vno[0] = 95377) erasing segment 7 (vno[0] = 96423) erasing segment 8 (vno[0] = 97437) erasing segment 9 (vno[0] = 98502) mri_label2vol --defects /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.nofix /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.defect_labels /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz 1000 0 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz mris_defects_pointset -s /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.nofix -d /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.defect_labels -o /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.defects.pointset --label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label Reading in surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.nofix Reading in defect segmentation /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.defect_labels Reading in label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 181784 mris_defects_pointset done mri_label2label --label-cortex /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.nofix /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/aseg.presurf.mgz 0 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 20 non-cortical segments detected only using segment with 7333 vertices erasing segment 0 (vno[0] = 50107) erasing segment 2 (vno[0] = 56322) erasing segment 3 (vno[0] = 61999) erasing segment 4 (vno[0] = 62149) erasing segment 5 (vno[0] = 65510) erasing segment 6 (vno[0] = 81983) erasing segment 7 (vno[0] = 93537) erasing segment 8 (vno[0] = 99703) erasing segment 9 (vno[0] = 99729) erasing segment 10 (vno[0] = 99756) erasing segment 11 (vno[0] = 100652) erasing segment 12 (vno[0] = 100707) erasing segment 13 (vno[0] = 100755) erasing segment 14 (vno[0] = 101824) erasing segment 15 (vno[0] = 103772) erasing segment 16 (vno[0] = 103795) erasing segment 17 (vno[0] = 103882) erasing segment 18 (vno[0] = 106471) erasing segment 19 (vno[0] = 109686) mri_label2vol --defects /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.nofix /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.defect_labels /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz 2000 1 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/surface.defects.mgz mris_defects_pointset -s /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.nofix -d /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.defect_labels -o /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.defects.pointset --label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label Reading in surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.nofix Reading in defect segmentation /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.defect_labels Reading in label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 182720 mris_defects_pointset done Started at Wed Jul 8 08:02:08 PM CEST 2026 Ended at Wed Jul 8 08:02:37 PM CEST 2026 Defect2seg-Run-Time-Sec 29 Defect2seg-Run-Time-Min 0.58 Defect2seg-Run-Time-Hours 0.01 tkmeditfv sub-20_ses-0 brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2026:07:08:20:02:08 defect2seg N 3 e 28.41 S 0.79 U 27.52 P 99% M 402540 F 53 R 179816 W 0 c 79 w 961 I 42688 O 23256 L 1.03 1.07 2.18 @#@FSLOADPOST 2026:07:08:20:02:37 defect2seg N 3 1.02 1.07 2.14 mris_remesh --remesh --iters 3 --input /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig.premesh --output /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.708301 remeshing to edge length 0.708301 with 3 iterations avg qual before : 0.889873 after: 0.971209 Removing intersections Remeshed surface quality stats nv0 = 137744 nv = 143635 1.04277 Area 287266 0.30048 0.03331 0.076647 0.4824 Corner 861798 60.00000 8.79531 16.934855 145.8848 Edge 430899 0.84097 0.08198 0.402663 1.2198 Hinge 430899 9.41579 10.12486 0.000004 133.7928 mris_remesh done @#@FSTIME 2026:07:08:20:02:37 mris_remesh N 7 e 28.97 S 0.39 U 28.55 P 99% M 776516 F 20 R 129220 W 0 c 78 w 169 I 3752 O 10112 L 1.02 1.07 2.14 @#@FSLOADPOST 2026:07:08:20:03:06 mris_remesh N 7 1.01 1.06 2.11 mris_remesh --remesh --iters 3 --input /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig.premesh --output /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.709916 remeshing to edge length 0.709916 with 3 iterations avg qual before : 0.891299 after: 0.971316 Removing intersections Remeshed surface quality stats nv0 = 138562 nv = 144774 1.04483 Area 289544 0.30184 0.03352 0.046108 0.4838 Corner 868632 60.00000 8.77697 14.862798 149.9981 Edge 434316 0.84283 0.08212 0.191300 1.2618 Hinge 434316 9.43243 10.16014 0.000060 138.5497 mris_remesh done @#@FSTIME 2026:07:08:20:03:06 mris_remesh N 7 e 31.12 S 0.40 U 30.70 P 99% M 778588 F 0 R 128153 W 0 c 102 w 144 I 0 O 10184 L 1.09 1.07 2.11 @#@FSLOADPOST 2026:07:08:20:03:37 mris_remesh N 7 1.05 1.07 2.07 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/lh.orig @#@FSTIME 2026:07:08:20:03:37 mris_remove_intersection N 2 e 3.57 S 0.21 U 3.33 P 99% M 348552 F 19 R 68031 W 0 c 9 w 129 I 3840 O 10104 L 1.05 1.07 2.07 @#@FSLOADPOST 2026:07:08:20:03:41 mris_remove_intersection N 2 1.05 1.07 2.07 rm -f ../surf/lh.inflated /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/rh.orig @#@FSTIME 2026:07:08:20:03:41 mris_remove_intersection N 2 e 3.58 S 0.14 U 3.42 P 99% M 347280 F 0 R 66611 W 0 c 7 w 166 I 0 O 10192 L 1.05 1.07 2.07 @#@FSLOADPOST 2026:07:08:20:03:44 mris_remove_intersection N 2 1.05 1.06 2.07 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Wed Jul 8 08:03:44 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 252863 voxels (1.51%) border gray 288489 voxels (1.72%) 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=37219, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (104.0): 101.9 +- 8.2 [70.0 --> 110.0] CCS GM (72.0) : 73.0 +- 9.9 [30.0 --> 110.0] white_mean = 101.855 +/- 8.19276, gray_mean = 72.9991 +/- 9.89032 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=231 nbins=232 intensity peaks found at WM=107+-4.3, GM=68+-7.0 white_mode = 107, gray_mode = 68 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 58.1 (was 70.000000) setting MAX_BORDER_WHITE to 115.2 (was 105.000000) setting MIN_BORDER_WHITE to 68.0 (was 85.000000) setting MAX_CSF to 48.2 (was 40.000000) setting MAX_GRAY to 98.8 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 58.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 38.3 (was 40.000000) When placing the white surface white_border_hi = 115.193; white_border_low = 68; white_outside_low = 58.1097; white_inside_hi = 120; white_outside_hi = 115.193; When placing the pial surface pial_border_hi = 58.1097; pial_border_low = 38.329; pial_outside_low = 10; pial_inside_hi = 98.8072; pial_outside_hi = 53.1645; #VMPC# mris_autodet_gwstats VmPeak 260300 mris_autodet_gwstats done @#@FSTIME 2026:07:08:20:03:44 mris_autodet_gwstats N 8 e 3.29 S 0.11 U 3.16 P 99% M 244748 F 18 R 29146 W 0 c 10 w 49 I 6544 O 8 L 1.05 1.06 2.07 @#@FSLOADPOST 2026:07:08:20:03:48 mris_autodet_gwstats N 8 1.04 1.06 2.06 #-------------------------------------------- #@# AutoDetGWStats rh Wed Jul 8 08:03:48 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 252863 voxels (1.51%) border gray 288489 voxels (1.72%) 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=37219, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (104.0): 101.9 +- 8.2 [70.0 --> 110.0] CCS GM (72.0) : 73.0 +- 9.9 [30.0 --> 110.0] white_mean = 101.855 +/- 8.19276, gray_mean = 72.9991 +/- 9.89032 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=231 nbins=232 intensity peaks found at WM=107+-4.3, GM=67+-7.8 white_mode = 107, gray_mode = 67 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 57.1 (was 70.000000) setting MAX_BORDER_WHITE to 115.2 (was 105.000000) setting MIN_BORDER_WHITE to 67.0 (was 85.000000) setting MAX_CSF to 47.2 (was 40.000000) setting MAX_GRAY to 98.8 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 57.1 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40.000000) When placing the white surface white_border_hi = 115.193; white_border_low = 67; white_outside_low = 57.1097; white_inside_hi = 120; white_outside_hi = 115.193; When placing the pial surface pial_border_hi = 57.1097; pial_border_low = 37.329; pial_outside_low = 10; pial_inside_hi = 98.8072; pial_outside_hi = 52.1645; #VMPC# mris_autodet_gwstats VmPeak 261360 mris_autodet_gwstats done @#@FSTIME 2026:07:08:20:03:48 mris_autodet_gwstats N 8 e 3.27 S 0.09 U 3.17 P 99% M 246080 F 0 R 30090 W 0 c 8 w 26 I 0 O 8 L 1.04 1.06 2.06 @#@FSLOADPOST 2026:07:08:20:03:51 mris_autodet_gwstats N 8 1.04 1.06 2.05 #-------------------------------------------- #@# WhitePreAparc lh Wed Jul 8 08:03:51 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 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 before ripping with 5 iterations Area 287266 0.26570 0.06250 0.000867 0.6124 Corner 861798 60.00000 9.64923 4.933826 134.1541 Edge 430899 0.78742 0.11373 0.034158 1.3078 Hinge 430899 6.37270 6.49350 0.000014 148.3080 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37219, wmmin=5, clip=110 MRIfindBrightNonWM(): 2834 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 #FML# MRISripMidline(): nmarked=6335, nmarked2=14, nripped=6335 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 71818: xyz = (-35.2406,-9.24618,49.8161) oxyz = (-35.2406,-9.24618,49.8161) wxzy = (-35.2406,-9.24618,49.8161) pxyz = (0,0,0) CBVO Creating mask 143635 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=6335 #FML# MRISripMidline(): nmarked=6335, nmarked2=14, nripped=6335 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 68.0000000; outside_low = 58.1096800; outside_hi = 115.1927640; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=2 had to be increased for 89 vertices, nripped=6335 mean border=80.0, 74 (74) missing vertices, mean dist 0.4 [0.4 (%32.9)->0.8 (%67.1))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1971 min Finding expansion regions mean absolute distance = 0.68 +- 0.78 5781 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 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=comps, 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=4432849.5, rms=12.480 001: dt: 0.5000, sse=2407110.2, rms=9.063 (27.376%) 002: dt: 0.5000, sse=1477371.5, rms=6.951 (23.310%) 003: dt: 0.5000, sse=985440.4, rms=5.512 (20.702%) 004: dt: 0.5000, sse=734187.2, rms=4.602 (16.503%) 005: dt: 0.5000, sse=611842.8, rms=4.084 (11.263%) 006: dt: 0.5000, sse=554481.1, rms=3.815 (6.590%) 007: dt: 0.5000, sse=530274.4, rms=3.691 (3.247%) 008: dt: 0.5000, sse=516177.6, rms=3.611 (2.166%) rms = 3.5891/3.6109, sse=511990.8/516177.6, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=511990.8, rms=3.589 (0.605%) 010: dt: 0.2500, sse=278623.8, rms=2.063 (42.515%) 011: dt: 0.2500, sse=235504.6, rms=1.636 (20.727%) 012: dt: 0.2500, sse=224272.2, rms=1.503 (8.108%) 013: dt: 0.2500, sse=218301.0, rms=1.421 (5.429%) rms = 1.3775/1.4213, sse=214894.3/218301.0, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=214894.2, rms=1.378 (3.084%) 015: dt: 0.1250, sse=208247.0, rms=1.288 (6.470%) rms = 1.2718/1.2884, sse=207209.9/208247.0, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=207209.9, rms=1.272 (1.287%) maximum number of reductions reached, breaking from loop positioning took 1.4 minutes done positioning surface 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=6335 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6485, nmarked2=14, nripped=6485 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 68.0000000; outside_low = 58.1096800; outside_hi = 115.1927640; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=1 had to be increased for 58 vertices, nripped=6485 mean border=84.7, 99 (46) missing vertices, mean dist -0.3 [0.3 (%83.9)->0.2 (%16.1))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1353 min Finding expansion regions mean absolute distance = 0.32 +- 0.43 3922 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 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=comps, 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=1200126.6, rms=5.996 017: dt: 0.5000, sse=608441.8, rms=3.794 (36.714%) rms = 3.8245/3.7944, sse=613919.4/608441.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=437665.0, rms=2.858 (24.668%) 019: dt: 0.2500, sse=330752.1, rms=2.066 (27.720%) 020: dt: 0.2500, sse=289335.0, rms=1.662 (19.556%) 021: dt: 0.2500, sse=271184.4, rms=1.448 (12.892%) 022: dt: 0.2500, sse=259681.2, rms=1.289 (10.950%) 023: dt: 0.2500, sse=252587.5, rms=1.181 (8.425%) 024: dt: 0.2500, sse=249022.5, rms=1.124 (4.810%) rms = 1.0857/1.1238, sse=246820.0/249022.5, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=246820.0, rms=1.086 (3.394%) 026: dt: 0.1250, sse=243093.3, rms=1.018 (6.261%) rms = 1.0114/1.0177, sse=242495.5/243093.3, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=242495.5, rms=1.011 (0.617%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface 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=6485 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 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 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6537, nmarked2=14, nripped=6537 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 68.0000000; outside_low = 58.1096800; outside_hi = 115.1927640; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 77 vertices, nripped=6537 mean border=87.2, 68 (26) missing vertices, mean dist -0.1 [0.2 (%77.2)->0.2 (%22.8))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0738 min Finding expansion regions mean absolute distance = 0.18 +- 0.25 2970 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 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=comps, 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=509880.4, rms=3.328 028: dt: 0.5000, sse=480892.6, rms=3.135 (5.787%) rms = 3.5065/3.1354, sse=543484.5/480892.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=305384.3, rms=1.870 (40.344%) 030: dt: 0.2500, sse=252936.8, rms=1.276 (31.806%) 031: dt: 0.2500, sse=240476.3, rms=1.085 (14.919%) 032: dt: 0.2500, sse=237338.3, rms=1.033 (4.794%) rms = 1.0259/1.0332, sse=238712.2/237338.3, time step reduction 2 of 3 to 0.125 0 1 1 033: dt: 0.2500, sse=238712.2, rms=1.026 (0.707%) 034: dt: 0.1250, sse=232072.8, rms=0.910 (11.282%) rms = 0.9034/0.9102, sse=231951.0/232072.8, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=231951.0, rms=0.903 (0.744%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface 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=6537 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6662, nmarked2=14, nripped=6662 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 68.0000000; outside_low = 58.1096800; outside_hi = 115.1927640; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 93 vertices, nripped=6662 mean border=87.9, 72 (13) missing vertices, mean dist -0.0 [0.1 (%57.7)->0.1 (%42.3))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0464 min Finding expansion regions mean absolute distance = 0.14 +- 0.21 2358 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 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=comps, 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=250387.6, rms=1.267 rms = 1.7418/1.2667, sse=292811.0/250387.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=222791.7, rms=0.784 (38.072%) 037: dt: 0.2500, sse=216992.5, rms=0.652 (16.876%) rms = 0.6758/0.6521, sse=217188.5/216992.5, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.6487/0.6521, sse=216721.1/216992.5, time step reduction 3 of 3 to 0.062 0 0 1 038: dt: 0.1250, sse=216721.1, rms=0.649 (0.512%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Removing intersections #ET# mris_place_surface 3.98 minutes Writing output to ../surf/lh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2259752 mris_place_surface done @#@FSTIME 2026:07:08:20:03:51 mris_place_surface N 18 e 245.47 S 0.75 U 244.66 P 99% M 2007720 F 14 R 271440 W 0 c 985 w 235 I 2072 O 10112 L 1.04 1.06 2.05 @#@FSLOADPOST 2026:07:08:20:07:56 mris_place_surface N 18 1.06 1.06 1.81 #-------------------------------------------- #@# WhitePreAparc rh Wed Jul 8 08:07:57 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 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 before ripping with 5 iterations Area 289544 0.26673 0.06296 0.001217 0.5985 Corner 868632 60.00000 9.65168 3.570521 145.3185 Edge 434316 0.78891 0.11429 0.016269 1.3497 Hinge 434316 6.38008 6.51782 0.000023 132.2345 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37219, wmmin=5, clip=110 MRIfindBrightNonWM(): 2834 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 #FML# MRISripMidline(): nmarked=6239, nmarked2=15, nripped=6239 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 72387: xyz = (14.8079,-13.3767,47.7348) oxyz = (14.8079,-13.3767,47.7348) wxzy = (14.8079,-13.3767,47.7348) pxyz = (0,0,0) CBVO Creating mask 144774 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=6239 #FML# MRISripMidline(): nmarked=6239, nmarked2=15, nripped=6239 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 67.0000000; outside_low = 57.1096800; outside_hi = 115.1927640; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=2 had to be increased for 79 vertices, nripped=6239 mean border=79.7, 52 (52) missing vertices, mean dist 0.4 [0.4 (%32.4)->0.8 (%67.6))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1977 min Finding expansion regions mean absolute distance = 0.68 +- 0.76 5581 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 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=comps, 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=4714007.5, rms=12.822 001: dt: 0.5000, sse=2587523.5, rms=9.369 (26.933%) 002: dt: 0.5000, sse=1596294.9, rms=7.210 (23.041%) 003: dt: 0.5000, sse=1059146.9, rms=5.715 (20.736%) 004: dt: 0.5000, sse=780502.1, rms=4.741 (17.045%) 005: dt: 0.5000, sse=642093.1, rms=4.165 (12.156%) 006: dt: 0.5000, sse=573897.5, rms=3.860 (7.326%) 007: dt: 0.5000, sse=544282.1, rms=3.711 (3.848%) 008: dt: 0.5000, sse=526016.4, rms=3.622 (2.409%) rms = 3.5885/3.6216, sse=523636.5/526016.4, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=523636.5, rms=3.589 (0.912%) 010: dt: 0.2500, sse=285044.0, rms=2.060 (42.582%) 011: dt: 0.2500, sse=242246.5, rms=1.645 (20.179%) 012: dt: 0.2500, sse=236129.8, rms=1.515 (7.907%) 013: dt: 0.2500, sse=228807.7, rms=1.430 (5.580%) rms = 1.3858/1.4301, sse=224710.3/228807.7, time step reduction 2 of 3 to 0.125 0 0 1 014: dt: 0.2500, sse=224710.3, rms=1.386 (3.100%) 015: dt: 0.1250, sse=217672.6, rms=1.292 (6.762%) rms = 1.2751/1.2921, sse=217534.3/217672.6, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=217534.3, rms=1.275 (1.315%) maximum number of reductions reached, breaking from loop positioning took 1.4 minutes done positioning surface 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=6239 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 #FML# MRISripMidline(): nmarked=6456, nmarked2=15, nripped=6456 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 67.0000000; outside_low = 57.1096800; outside_hi = 115.1927640; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=1 had to be increased for 56 vertices, nripped=6456 mean border=84.3, 68 (9) missing vertices, mean dist -0.2 [0.3 (%83.8)->0.2 (%16.2))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1377 min Finding expansion regions mean absolute distance = 0.32 +- 0.41 4841 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 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=comps, 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=1270648.9, rms=6.147 017: dt: 0.5000, sse=640411.0, rms=3.876 (36.949%) 018: dt: 0.5000, sse=633129.7, rms=3.826 (1.290%) 019: dt: 0.5000, sse=603997.4, rms=3.740 (2.240%) rms = 3.8352/3.7401, sse=623944.2/603997.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 020: dt: 0.2500, sse=369756.7, rms=2.339 (37.455%) 021: dt: 0.2500, sse=290671.3, rms=1.619 (30.793%) 022: dt: 0.2500, sse=265913.1, rms=1.312 (18.965%) 023: dt: 0.2500, sse=258877.7, rms=1.203 (8.289%) 024: dt: 0.2500, sse=254342.6, rms=1.141 (5.184%) rms = 1.1127/1.1408, sse=253143.2/254342.6, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=253143.2, rms=1.113 (2.459%) 026: dt: 0.1250, sse=249179.2, rms=1.024 (7.930%) rms = 1.0185/1.0245, sse=249980.3/249179.2, time step reduction 3 of 3 to 0.062 0 1 1 027: dt: 0.1250, sse=249980.3, rms=1.018 (0.588%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface 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=6456 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 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6572, nmarked2=15, nripped=6572 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 67.0000000; outside_low = 57.1096800; outside_hi = 115.1927640; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 74 vertices, nripped=6572 mean border=86.9, 58 (5) missing vertices, mean dist -0.1 [0.2 (%76.9)->0.2 (%23.1))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0739 min Finding expansion regions mean absolute distance = 0.19 +- 0.26 3646 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 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=comps, 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=520946.3, rms=3.340 028: dt: 0.5000, sse=487690.1, rms=3.146 (5.813%) rms = 3.5072/3.1460, sse=549158.4/487690.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=311497.8, rms=1.894 (39.804%) 030: dt: 0.2500, sse=257806.8, rms=1.296 (31.583%) 031: dt: 0.2500, sse=243439.9, rms=1.096 (15.382%) rms = 1.0547/1.0964, sse=240921.6/243439.9, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=240921.6, rms=1.055 (3.802%) 033: dt: 0.1250, sse=233874.9, rms=0.925 (12.255%) rms = 0.9125/0.9254, sse=233248.8/233874.9, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=233248.8, rms=0.913 (1.396%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface 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=6572 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 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=6595, nmarked2=15, nripped=6595 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 67.0000000; outside_low = 57.1096800; outside_hi = 115.1927640; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 108 vertices, nripped=6595 mean border=87.5, 74 (0) missing vertices, mean dist -0.0 [0.1 (%57.4)->0.1 (%42.6))] %94 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0473 min Finding expansion regions mean absolute distance = 0.15 +- 0.21 2787 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 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=comps, 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=254376.6, rms=1.300 rms = 1.7058/1.3000, sse=292692.2/254376.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=227180.4, rms=0.835 (35.788%) 036: dt: 0.2500, sse=221860.2, rms=0.675 (19.186%) rms = 0.6942/0.6746, sse=221862.1/221860.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.6682/0.6746, sse=221421.7/221860.3, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=221421.7, rms=0.668 (0.945%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Removing intersections #ET# mris_place_surface 3.90 minutes Writing output to ../surf/rh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2241864 mris_place_surface done @#@FSTIME 2026:07:08:20:07:57 mris_place_surface N 18 e 240.38 S 0.75 U 239.59 P 99% M 1989884 F 0 R 271970 W 0 c 703 w 277 I 0 O 10192 L 1.06 1.06 1.81 @#@FSLOADPOST 2026:07:08:20:11:57 mris_place_surface N 18 1.01 1.04 1.63 #-------------------------------------------- #@# CortexLabel lh Wed Jul 8 08:11:57 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 5 non-cortical segments detected only using segment with 8209 vertices erasing segment 1 (vno[0] = 41970) erasing segment 2 (vno[0] = 78634) erasing segment 3 (vno[0] = 82215) erasing segment 4 (vno[0] = 83233) @#@FSTIME 2026:07:08:20:11:57 mri_label2label N 5 e 13.74 S 0.15 U 13.56 P 99% M 329652 F 0 R 34346 W 0 c 29 w 193 I 0 O 11792 L 1.01 1.04 1.63 @#@FSLOADPOST 2026:07:08:20:12:11 mri_label2label N 5 1.01 1.04 1.62 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Wed Jul 8 08:12:11 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 15 non-cortical segments detected only using segment with 5896 vertices erasing segment 1 (vno[0] = 41970) erasing segment 2 (vno[0] = 43840) erasing segment 3 (vno[0] = 43912) erasing segment 4 (vno[0] = 47475) erasing segment 5 (vno[0] = 49444) erasing segment 6 (vno[0] = 50462) erasing segment 7 (vno[0] = 52533) erasing segment 8 (vno[0] = 52579) erasing segment 9 (vno[0] = 77786) erasing segment 10 (vno[0] = 78634) erasing segment 11 (vno[0] = 82215) erasing segment 12 (vno[0] = 83233) erasing segment 13 (vno[0] = 118870) erasing segment 14 (vno[0] = 127961) @#@FSTIME 2026:07:08:20:12:11 mri_label2label N 5 e 14.03 S 0.14 U 13.88 P 99% M 380296 F 0 R 39314 W 0 c 29 w 207 I 0 O 11984 L 1.01 1.04 1.62 @#@FSLOADPOST 2026:07:08:20:12:25 mri_label2label N 5 1.01 1.03 1.61 #-------------------------------------------- #@# CortexLabel rh Wed Jul 8 08:12:25 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 8 non-cortical segments detected only using segment with 7975 vertices erasing segment 0 (vno[0] = 43931) erasing segment 2 (vno[0] = 71856) erasing segment 3 (vno[0] = 84619) erasing segment 4 (vno[0] = 86388) erasing segment 5 (vno[0] = 87313) erasing segment 6 (vno[0] = 88907) erasing segment 7 (vno[0] = 126872) @#@FSTIME 2026:07:08:20:12:25 mri_label2label N 5 e 12.10 S 0.14 U 11.93 P 99% M 346544 F 0 R 36476 W 0 c 31 w 151 I 0 O 11648 L 1.01 1.03 1.61 @#@FSLOADPOST 2026:07:08:20:12:37 mri_label2label N 5 1.00 1.03 1.60 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Wed Jul 8 08:12:37 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 10 non-cortical segments detected only using segment with 5674 vertices erasing segment 0 (vno[0] = 43931) erasing segment 2 (vno[0] = 54978) erasing segment 3 (vno[0] = 71856) erasing segment 4 (vno[0] = 82876) erasing segment 5 (vno[0] = 84619) erasing segment 6 (vno[0] = 86388) erasing segment 7 (vno[0] = 87313) erasing segment 8 (vno[0] = 88907) erasing segment 9 (vno[0] = 126872) @#@FSTIME 2026:07:08:20:12:37 mri_label2label N 5 e 12.10 S 0.15 U 11.94 P 99% M 356552 F 0 R 35976 W 0 c 27 w 174 I 0 O 11840 L 1.00 1.03 1.60 @#@FSLOADPOST 2026:07:08:20:12:49 mri_label2label N 5 1.00 1.03 1.59 #-------------------------------------------- #@# Smooth2 lh Wed Jul 8 08:12:49 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:20:12:49 mris_smooth N 7 e 2.78 S 0.11 U 2.64 P 99% M 221896 F 0 R 39872 W 0 c 5 w 100 I 0 O 10104 L 1.00 1.03 1.59 @#@FSLOADPOST 2026:07:08:20:12:52 mris_smooth N 7 1.00 1.03 1.59 #-------------------------------------------- #@# Smooth2 rh Wed Jul 8 08:12:52 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:20:12:52 mris_smooth N 7 e 2.86 S 0.09 U 2.75 P 99% M 223572 F 0 R 38735 W 0 c 8 w 173 I 0 O 10192 L 1.00 1.03 1.59 @#@FSLOADPOST 2026:07:08:20:12:55 mris_smooth N 7 1.00 1.03 1.59 #-------------------------------------------- #@# Inflation2 lh Wed Jul 8 08:12:55 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.1 mm, total surface area = 87436 mm^2 step 000: RMS=0.167 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.018 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 21.711952 mris_inflate stimesec 0.107999 mris_inflate ru_maxrss 223408 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 34114 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 440 mris_inflate ru_oublock 11232 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 180 mris_inflate ru_nivcsw 54 @#@FSTIME 2026:07:08:20:12:55 mris_inflate N 2 e 21.87 S 0.11 U 21.71 P 99% M 223884 F 2 R 34131 W 0 c 54 w 181 I 440 O 11240 L 1.00 1.03 1.59 @#@FSLOADPOST 2026:07:08:20:13:17 mris_inflate N 2 1.15 1.06 1.58 #-------------------------------------------- #@# Inflation2 rh Wed Jul 8 08:13:17 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.8 mm, total surface area = 88707 mm^2 step 000: RMS=0.167 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.019 (target=0.015) step 060: RMS=0.018 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 22.925330 mris_inflate stimesec 0.091989 mris_inflate ru_maxrss 225032 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 33382 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 96 mris_inflate ru_oublock 11320 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 230 mris_inflate ru_nivcsw 54 @#@FSTIME 2026:07:08:20:13:17 mris_inflate N 2 e 23.07 S 0.10 U 22.92 P 99% M 225468 F 0 R 33400 W 0 c 54 w 231 I 96 O 11320 L 1.15 1.06 1.58 @#@FSLOADPOST 2026:07:08:20:13:40 mris_inflate N 2 1.17 1.07 1.58 #-------------------------------------------- #@# Curv .H and .K lh Wed Jul 8 08:13:40 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 8.005*4pi (100.595) --> -7 handles ICI = 127.3, FI = 1493.2, variation=22879.639 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done. @#@FSTIME 2026:07:08:20:13:40 mris_curvature N 4 e 1.55 S 0.08 U 1.40 P 95% M 165948 F 4 R 20293 W 0 c 2 w 102 I 1008 O 2264 L 1.17 1.07 1.58 @#@FSLOADPOST 2026:07:08:20:13:42 mris_curvature N 4 1.16 1.07 1.57 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 248 vertices thresholded to be in k1 ~ [-0.22 0.27], k2 ~ [-0.08 0.05] total integrated curvature = 0.721*4pi (9.056) --> 0 handles ICI = 1.7, FI = 10.8, variation=181.365 132 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 = 0.001 162 vertices thresholded to be in [-0.12 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done. @#@FSTIME 2026:07:08:20:13:42 mris_curvature N 12 e 41.38 S 0.17 U 41.14 P 99% M 390308 F 0 R 75192 W 0 c 115 w 83 I 192 O 2264 L 1.16 1.07 1.57 @#@FSLOADPOST 2026:07:08:20:14:23 mris_curvature N 12 1.08 1.06 1.55 #-------------------------------------------- #@# Curv .H and .K rh Wed Jul 8 08:14:23 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 9.949*4pi (125.023) --> -9 handles ICI = 130.5, FI = 1516.9, variation=23253.985 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done. @#@FSTIME 2026:07:08:20:14:23 mris_curvature N 4 e 1.56 S 0.09 U 1.41 P 96% M 167112 F 0 R 21147 W 0 c 3 w 94 I 192 O 2272 L 1.08 1.06 1.55 @#@FSLOADPOST 2026:07:08:20:14:25 mris_curvature N 4 1.08 1.06 1.55 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 267 vertices thresholded to be in k1 ~ [-0.19 0.34], k2 ~ [-0.07 0.06] total integrated curvature = 0.687*4pi (8.631) --> 0 handles ICI = 1.8, FI = 10.5, variation=181.469 146 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 159 vertices thresholded to be in [-0.12 0.16] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.023 mris_curvature done. @#@FSTIME 2026:07:08:20:14:25 mris_curvature N 12 e 41.68 S 0.20 U 41.43 P 99% M 393272 F 0 R 76325 W 0 c 138 w 91 I 10376 O 2280 L 1.08 1.06 1.55 @#@FSLOADPOST 2026:07:08:20:15:07 mris_curvature N 12 1.04 1.05 1.52 #-------------------------------------------- #@# Sphere lh Wed Jul 8 08:15:07 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.280... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=comps, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.22 pass 1: epoch 2 of 3 starting distance error %20.25 unfolding complete - removing small folds... starting distance error %20.21 removing remaining folds... final distance error %20.21 MRISunfold() return, current seed 1234 -01: dt=0.0000, 96 negative triangles VmPeak 550272 091: dt=0.9900, 96 negative triangles 092: dt=0.9900, 24 negative triangles 093: dt=0.9900, 17 negative triangles 094: dt=0.9900, 18 negative triangles 095: dt=0.9900, 17 negative triangles 096: dt=0.9900, 15 negative triangles 097: dt=0.9900, 10 negative triangles 098: dt=0.9900, 12 negative triangles 099: dt=0.9900, 10 negative triangles 100: dt=0.9900, 15 negative triangles 101: dt=0.9900, 11 negative triangles 102: dt=0.9900, 9 negative triangles 103: dt=0.9900, 11 negative triangles 104: dt=0.9900, 9 negative triangles 105: dt=0.9900, 16 negative triangles 106: dt=0.9900, 10 negative triangles 107: dt=0.9900, 8 negative triangles 108: dt=0.9900, 10 negative triangles 109: dt=0.9900, 9 negative triangles 110: dt=0.9900, 12 negative triangles 111: dt=0.9900, 11 negative triangles 112: dt=0.9900, 8 negative triangles 113: dt=0.9900, 10 negative triangles 114: dt=0.9900, 9 negative triangles 115: dt=0.9900, 12 negative triangles 116: dt=0.9900, 9 negative triangles 117: dt=0.9900, 5 negative triangles 118: dt=0.9900, 8 negative triangles 119: dt=0.9900, 5 negative triangles 120: dt=0.9900, 7 negative triangles 121: dt=0.9900, 5 negative triangles 122: dt=0.9900, 4 negative triangles 123: dt=0.9900, 5 negative triangles 124: dt=0.9900, 2 negative triangles 125: dt=0.9900, 2 negative triangles 126: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1175 hours FSRUNTIME@ mris_sphere 0.1175 hours 1 threads #VMPC# mris_sphere VmPeak 550272 mris_sphere done @#@FSTIME 2026:07:08:20:15:07 mris_sphere N 4 e 423.17 S 12.38 U 410.70 P 99% M 297116 F 0 R 5792817 W 0 c 1821 w 133 I 0 O 10112 L 1.04 1.05 1.52 @#@FSLOADPOST 2026:07:08:20:22:10 mris_sphere N 4 1.14 1.15 1.38 #-------------------------------------------- #@# Sphere rh Wed Jul 8 08:22:10 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: 7.4.1 available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.279... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=comps, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.60 pass 1: epoch 2 of 3 starting distance error %20.59 unfolding complete - removing small folds... starting distance error %20.52 removing remaining folds... final distance error %20.52 MRISunfold() return, current seed 1234 -01: dt=0.0000, 104 negative triangles VmPeak 552520 107: dt=0.9900, 104 negative triangles 108: dt=0.9900, 24 negative triangles 109: dt=0.9900, 18 negative triangles 110: dt=0.9900, 21 negative triangles 111: dt=0.9900, 13 negative triangles 112: dt=0.9900, 7 negative triangles 113: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1300 hours FSRUNTIME@ mris_sphere 0.1300 hours 1 threads #VMPC# mris_sphere VmPeak 552520 mris_sphere done @#@FSTIME 2026:07:08:20:22:10 mris_sphere N 4 e 467.92 S 12.71 U 455.12 P 99% M 299164 F 0 R 6294978 W 0 c 2087 w 181 I 0 O 10184 L 1.14 1.15 1.38 @#@FSLOADPOST 2026:07:08:20:29:58 mris_sphere N 4 1.05 1.06 1.24 #-------------------------------------------- #@# Surf Reg lh Wed Jul 8 08:29:58 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_register -curv ../surf/lh.sphere /software/freesurfer/7.4.1/debian-bookworm-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts cmdline mris_register -curv ../surf/lh.sphere /software/freesurfer/7.4.1/debian-bookworm-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.4.1 7.4.1 reading surface from ../surf/lh.sphere... reading template parameterization from /software/freesurfer/7.4.1/debian-bookworm-amd64/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=comps, 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=comps, 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=comps, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.521 curvature mean = 0.025, std = 0.817 curvature mean = 0.013, std = 0.863 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (1.50, -10.00, -3.50) sse = 271256.1, elapsed since starting=0.3935 min MRISrigidBodyAlignGlobal() done 0.39 min curvature mean = 0.020, std = 0.834 curvature mean = 0.007, std = 0.948 curvature mean = 0.020, std = 0.844 curvature mean = 0.003, std = 0.980 curvature mean = 0.020, std = 0.846 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.017, std = 0.287 curvature mean = 0.047, std = 0.247 curvature mean = 0.059, std = 0.330 curvature mean = 0.044, std = 0.304 curvature mean = 0.031, std = 0.524 curvature mean = 0.043, std = 0.332 curvature mean = 0.018, std = 0.662 curvature mean = 0.043, std = 0.344 curvature mean = 0.006, std = 0.769 MRISregister() return, current seed 0 -01: dt=0.0000, 15 negative triangles VmPeak 529704 106: dt=0.9900, 15 negative triangles expanding nbhd size to 1 107: dt=0.9900, 17 negative triangles 108: dt=0.9900, 15 negative triangles 109: dt=0.9900, 13 negative triangles 110: dt=0.9900, 12 negative triangles 111: dt=0.9900, 12 negative triangles 112: dt=0.9900, 11 negative triangles 113: dt=0.9900, 12 negative triangles 114: dt=0.9900, 12 negative triangles 115: dt=0.9900, 8 negative triangles 116: dt=0.9900, 7 negative triangles 117: dt=0.9900, 7 negative triangles 118: dt=0.9900, 8 negative triangles 119: dt=0.9900, 7 negative triangles 120: dt=0.9900, 7 negative triangles 121: dt=0.9900, 5 negative triangles 122: dt=0.9900, 6 negative triangles 123: dt=0.9900, 5 negative triangles 124: dt=0.9900, 5 negative triangles 125: dt=0.9900, 5 negative triangles 126: dt=0.9900, 5 negative triangles 127: dt=0.9900, 4 negative triangles 128: dt=0.9900, 4 negative triangles 129: dt=0.9900, 3 negative triangles 130: dt=0.9900, 3 negative triangles 131: dt=0.9900, 1 negative triangles 132: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.12 hours #VMPC# mris_register VmPeak 529704 FSRUNTIME@ mris_register 0.1247 hours 1 threads @#@FSTIME 2026:07:08:20:29:58 mris_register N 4 e 449.04 S 12.88 U 436.07 P 99% M 277020 F 18 R 6282931 W 0 c 1628 w 279 I 7976 O 10120 L 1.05 1.06 1.24 @#@FSLOADPOST 2026:07:08:20:37:27 mris_register N 4 1.06 1.05 1.16 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Wed Jul 8 08:37:27 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_register -curv ../surf/rh.sphere /software/freesurfer/7.4.1/debian-bookworm-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts cmdline mris_register -curv ../surf/rh.sphere /software/freesurfer/7.4.1/debian-bookworm-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) 7.4.1 7.4.1 reading surface from ../surf/rh.sphere... reading template parameterization from /software/freesurfer/7.4.1/debian-bookworm-amd64/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=comps, 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=comps, 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=comps, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.604 curvature mean = 0.028, std = 0.814 curvature mean = 0.012, std = 0.860 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (7.50, -6.00, -5.50) sse = 315001.7, elapsed since starting=0.3718 min MRISrigidBodyAlignGlobal() done 0.37 min curvature mean = 0.018, std = 0.821 curvature mean = 0.003, std = 0.937 curvature mean = 0.014, std = 0.826 curvature mean = 0.002, std = 0.972 curvature mean = 0.013, std = 0.827 curvature mean = 0.000, std = 0.987 2 Reading smoothwm curvature mean = -0.017, std = 0.271 curvature mean = 0.038, std = 0.238 curvature mean = 0.058, std = 0.350 curvature mean = 0.038, std = 0.294 curvature mean = 0.031, std = 0.555 curvature mean = 0.037, std = 0.321 curvature mean = 0.016, std = 0.697 curvature mean = 0.037, std = 0.333 curvature mean = 0.004, std = 0.806 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... -01: dt=0.0000, 0 negative triangles VmPeak 530716 registration took 0.16 hours #VMPC# mris_register VmPeak 530716 FSRUNTIME@ mris_register 0.1604 hours 1 threads @#@FSTIME 2026:07:08:20:37:27 mris_register N 4 e 577.53 S 14.62 U 562.75 P 99% M 277948 F 0 R 6806196 W 0 c 2883 w 292 I 5584 O 10200 L 1.06 1.05 1.16 @#@FSLOADPOST 2026:07:08:20:47:05 mris_register N 4 2.07 3.03 2.04 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Wed Jul 8 08:47:05 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:20:47:05 mris_jacobian N 3 e 1.07 S 0.10 U 0.93 P 96% M 221392 F 6 R 34575 W 0 c 2 w 58 I 896 O 1136 L 2.07 3.03 2.04 @#@FSLOADPOST 2026:07:08:20:47:06 mris_jacobian N 3 2.07 3.03 2.04 #-------------------------------------------- #@# Jacobian white rh Wed Jul 8 08:47:06 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:20:47:06 mris_jacobian N 3 e 1.08 S 0.08 U 0.96 P 96% M 223016 F 0 R 40313 W 0 c 3 w 47 I 96 O 1136 L 2.07 3.03 2.04 @#@FSLOADPOST 2026:07:08:20:47:07 mris_jacobian N 3 2.07 3.03 2.04 #-------------------------------------------- #@# AvgCurv lh Wed Jul 8 08:47:07 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mrisp_paint -a 5 /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2026:07:08:20:47:07 mrisp_paint N 5 e 0.80 S 0.08 U 0.68 P 95% M 170492 F 11 R 21035 W 0 c 2 w 63 I 1600 O 1128 L 2.07 3.03 2.04 @#@FSLOADPOST 2026:07:08:20:47:08 mrisp_paint N 5 2.07 3.03 2.04 #-------------------------------------------- #@# AvgCurv rh Wed Jul 8 08:47:08 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mrisp_paint -a 5 /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2026:07:08:20:47:08 mrisp_paint N 5 e 0.82 S 0.06 U 0.72 P 95% M 172148 F 0 R 20719 W 0 c 1 w 48 I 96 O 1136 L 1.98 2.99 2.03 @#@FSLOADPOST 2026:07:08:20:47:09 mrisp_paint N 5 1.98 2.99 2.03 #----------------------------------------- #@# Cortical Parc lh Wed Jul 8 08:47:09 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 lh ../surf/lh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1477 labels changed using aseg relabeling using gibbs priors... 000: 3235 changed, 143635 examined... 001: 732 changed, 13654 examined... 002: 164 changed, 4129 examined... 003: 59 changed, 1031 examined... 004: 20 changed, 389 examined... 005: 15 changed, 134 examined... 006: 5 changed, 81 examined... 007: 2 changed, 30 examined... 008: 2 changed, 11 examined... 009: 0 changed, 11 examined... 264 labels changed using aseg 000: 108 total segments, 66 labels (242 vertices) changed 001: 41 total segments, 1 labels (4 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1941 vertices marked for relabeling... 1941 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 9 seconds. @#@FSTIME 2026:07:08:20:47:09 mris_ca_label N 11 e 9.16 S 0.62 U 8.49 P 99% M 1227920 F 5 R 200960 W 0 c 17 w 75 I 75944 O 2256 L 1.98 2.99 2.03 @#@FSLOADPOST 2026:07:08:20:47:18 mris_ca_label N 11 1.83 2.93 2.02 #----------------------------------------- #@# Cortical Parc rh Wed Jul 8 08:47:18 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 rh ../surf/rh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1168 labels changed using aseg relabeling using gibbs priors... 000: 3031 changed, 144774 examined... 001: 652 changed, 12894 examined... 002: 161 changed, 3724 examined... 003: 71 changed, 1030 examined... 004: 27 changed, 408 examined... 005: 9 changed, 164 examined... 006: 2 changed, 54 examined... 007: 2 changed, 15 examined... 008: 1 changed, 15 examined... 009: 0 changed, 7 examined... 183 labels changed using aseg 000: 85 total segments, 48 labels (157 vertices) changed 001: 39 total segments, 2 labels (2 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1687 vertices marked for relabeling... 1687 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 9 seconds. @#@FSTIME 2026:07:08:20:47:18 mris_ca_label N 11 e 9.03 S 0.57 U 8.41 P 99% M 1115564 F 0 R 180950 W 0 c 25 w 63 I 47992 O 2280 L 1.83 2.93 2.02 @#@FSLOADPOST 2026:07:08:20:47:27 mris_ca_label N 11 1.76 2.89 2.01 #-------------------------------------------- #@# WhiteSurfs lh Wed Jul 8 08:47:27 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 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 287266 0.33158 0.11718 0.001809 1.6498 Corner 861798 60.00000 14.17721 0.368848 179.1906 Edge 430899 0.88536 0.19575 0.013190 3.5581 Hinge 430899 9.86191 10.70563 0.000013 179.9868 Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37219, wmmin=5, clip=110 MRIfindBrightNonWM(): 2834 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label MRISripNotLabel() ripped 8385/143635 vertices (135250 unripped) Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 540 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 71818: xyz = (-35.2183,-8.80051,49.8294) oxyz = (-35.2183,-8.80051,49.8294) wxzy = (-35.2183,-8.80051,49.8294) pxyz = (0,0,0) CBVO Creating mask 143635 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 68.0000000; outside_low = 58.1096800; outside_hi = 115.1927640; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=2 had to be increased for 109 vertices, nripped=8925 mean border=79.4, 63 (63) missing vertices, mean dist 0.4 [1.0 (%7.6)->0.6 (%92.4))] %69 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1828 min Finding expansion regions mean absolute distance = 0.61 +- 0.75 3238 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 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=comps, 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=2784155.2, rms=9.794 001: dt: 0.5000, sse=959328.6, rms=5.321 (45.675%) 002: dt: 0.5000, sse=567774.1, rms=3.713 (30.213%) 003: dt: 0.5000, sse=515498.6, rms=3.441 (7.339%) 004: dt: 0.5000, sse=474083.0, rms=3.206 (6.827%) rms = 3.3603/3.2058, sse=502039.7/474083.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=313509.8, rms=2.061 (35.707%) 006: dt: 0.2500, sse=260260.0, rms=1.497 (27.364%) 007: dt: 0.2500, sse=243923.9, rms=1.274 (14.911%) 008: dt: 0.2500, sse=240812.3, rms=1.222 (4.047%) rms = 1.1855/1.2223, sse=238675.9/240812.3, time step reduction 2 of 3 to 0.125 0 0 1 009: dt: 0.2500, sse=238675.9, rms=1.185 (3.015%) 010: dt: 0.1250, sse=235632.0, rms=1.134 (4.382%) rms = 1.1279/1.1335, sse=235406.2/235632.0, time step reduction 3 of 3 to 0.062 0 0 1 011: dt: 0.1250, sse=235406.2, rms=1.128 (0.491%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 68.0000000; outside_low = 58.1096800; outside_hi = 115.1927640; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=1 had to be increased for 40 vertices, nripped=8925 mean border=84.4, 42 (18) missing vertices, mean dist -0.3 [0.4 (%84.6)->0.2 (%15.4))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1312 min Finding expansion regions mean absolute distance = 0.34 +- 0.42 3658 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 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=comps, 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=1231524.0, rms=6.136 012: dt: 0.5000, sse=614613.0, rms=3.839 (37.433%) 013: dt: 0.5000, sse=589659.1, rms=3.723 (3.027%) 014: dt: 0.5000, sse=573853.4, rms=3.646 (2.066%) rms = 3.7241/3.6460, sse=589009.7/573853.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 015: dt: 0.2500, sse=352406.8, rms=2.242 (38.521%) 016: dt: 0.2500, sse=276683.8, rms=1.486 (33.723%) 017: dt: 0.2500, sse=253554.1, rms=1.157 (22.124%) 018: dt: 0.2500, sse=247495.8, rms=1.056 (8.691%) 019: dt: 0.2500, sse=244631.8, rms=1.006 (4.789%) rms = 0.9906/1.0058, sse=243851.3/244631.8, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=243851.3, rms=0.991 (1.515%) 021: dt: 0.1250, sse=240307.7, rms=0.921 (7.062%) rms = 0.9180/0.9206, sse=240212.1/240307.7, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=240212.1, rms=0.918 (0.278%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 68.0000000; outside_low = 58.1096800; outside_hi = 115.1927640; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 53 vertices, nripped=8925 mean border=87.0, 33 (2) missing vertices, mean dist -0.1 [0.2 (%78.3)->0.2 (%21.7))] %90 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0716 min Finding expansion regions mean absolute distance = 0.18 +- 0.26 2907 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 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=comps, 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=512055.7, rms=3.366 023: dt: 0.5000, sse=480926.7, rms=3.115 (7.471%) rms = 3.4541/3.1149, sse=530234.0/480926.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=305507.8, rms=1.841 (40.883%) 025: dt: 0.2500, sse=251402.7, rms=1.223 (33.583%) 026: dt: 0.2500, sse=238409.1, rms=1.012 (17.290%) rms = 0.9664/1.0116, sse=235541.4/238409.1, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=235541.4, rms=0.966 (4.461%) 028: dt: 0.1250, sse=229841.0, rms=0.851 (11.908%) rms = 0.8399/0.8514, sse=229154.7/229841.0, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=229154.7, rms=0.840 (1.351%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 68.0000000; outside_low = 58.1096800; outside_hi = 115.1927640; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 65 vertices, nripped=8925 mean border=87.8, 57 (0) missing vertices, mean dist -0.0 [0.1 (%58.1)->0.1 (%41.9))] %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0453 min Finding expansion regions mean absolute distance = 0.14 +- 0.20 2306 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 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=comps, 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=250044.0, rms=1.262 rms = 1.7426/1.2617, sse=308005.0/250044.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=224624.1, rms=0.761 (39.716%) 031: dt: 0.2500, sse=223386.5, rms=0.618 (18.774%) rms = 0.6366/0.6178, sse=222637.3/223386.5, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.6133/0.6178, sse=223096.6/223386.5, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=223096.6, rms=0.613 (0.734%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Removing intersections #ET# mris_place_surface 3.45 minutes Writing output to ../surf/lh.white #VMPC# mris_place_surfaces VmPeak 2157104 mris_place_surface done @#@FSTIME 2026:07:08:20:47:27 mris_place_surface N 25 e 213.85 S 0.70 U 213.10 P 99% M 1905064 F 0 R 250301 W 0 c 771 w 243 I 2248 O 10104 L 1.76 2.89 2.01 @#@FSLOADPOST 2026:07:08:20:51:01 mris_place_surface N 25 1.15 1.95 1.81 #-------------------------------------------- #@# WhiteSurfs rh Wed Jul 8 08:51:01 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 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 289544 0.33398 0.11713 0.000891 1.6464 Corner 868632 60.00000 13.95824 0.180423 178.7935 Edge 434316 0.88858 0.19596 0.016269 3.0896 Hinge 434316 9.81897 10.59749 0.000046 179.7252 Reading in aparc ../label/rh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37219, wmmin=5, clip=110 MRIfindBrightNonWM(): 2834 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label MRISripNotLabel() ripped 8252/144774 vertices (136522 unripped) Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Ripping BG MRISripBasalGanglia(): 1 -2 2 0.5 ripped 444 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 72387: xyz = (15.3207,-13.2532,47.3763) oxyz = (15.3207,-13.2532,47.3763) wxzy = (15.3207,-13.2532,47.3763) pxyz = (0,0,0) CBVO Creating mask 144774 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 67.0000000; outside_low = 57.1096800; outside_hi = 115.1927640; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=2 had to be increased for 125 vertices, nripped=8696 mean border=79.1, 52 (52) missing vertices, mean dist 0.4 [0.9 (%8.1)->0.6 (%91.9))] %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1801 min Finding expansion regions mean absolute distance = 0.60 +- 0.72 3311 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 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=comps, 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=2879518.5, rms=9.916 001: dt: 0.5000, sse=1003843.4, rms=5.433 (45.212%) 002: dt: 0.5000, sse=584793.4, rms=3.760 (30.795%) 003: dt: 0.5000, sse=523210.5, rms=3.444 (8.387%) 004: dt: 0.5000, sse=483606.3, rms=3.221 (6.474%) rms = 3.3517/3.2214, sse=507497.2/483606.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=320942.5, rms=2.082 (35.355%) 006: dt: 0.2500, sse=265697.6, rms=1.509 (27.553%) 007: dt: 0.2500, sse=249171.6, rms=1.288 (14.641%) rms = 1.2378/1.2878, sse=246074.7/249171.6, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=246074.7, rms=1.238 (3.879%) 009: dt: 0.1250, sse=241265.9, rms=1.161 (6.196%) rms = 1.1481/1.1611, sse=240550.2/241265.9, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=240550.2, rms=1.148 (1.119%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 67.0000000; outside_low = 57.1096800; outside_hi = 115.1927640; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=1 had to be increased for 73 vertices, nripped=8696 mean border=84.1, 38 (7) missing vertices, mean dist -0.3 [0.4 (%84.7)->0.2 (%15.3))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1326 min Finding expansion regions mean absolute distance = 0.34 +- 0.42 3749 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning 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=comps, 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=1298385.5, rms=6.291 011: dt: 0.5000, sse=638254.3, rms=3.914 (37.795%) 012: dt: 0.5000, sse=603433.5, rms=3.755 (4.053%) 013: dt: 0.5000, sse=583698.8, rms=3.657 (2.596%) rms = 3.7448/3.6575, sse=600551.3/583698.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 014: dt: 0.2500, sse=359888.9, rms=2.263 (38.134%) 015: dt: 0.2500, sse=284361.4, rms=1.529 (32.439%) 016: dt: 0.2500, sse=261194.0, rms=1.217 (20.377%) 017: dt: 0.2500, sse=256351.8, rms=1.139 (6.392%) rms = 1.0897/1.1394, sse=253342.2/256351.8, time step reduction 2 of 3 to 0.125 0 0 1 018: dt: 0.2500, sse=253342.2, rms=1.090 (4.365%) 019: dt: 0.1250, sse=248703.2, rms=1.006 (7.685%) rms = 1.0020/1.0059, sse=248500.7/248703.2, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=248500.7, rms=1.002 (0.397%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes done positioning surface Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 67.0000000; outside_low = 57.1096800; outside_hi = 115.1927640; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 60 vertices, nripped=8696 mean border=86.7, 54 (4) missing vertices, mean dist -0.1 [0.2 (%77.9)->0.2 (%22.1))] %91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0730 min Finding expansion regions mean absolute distance = 0.19 +- 0.26 3622 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 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=comps, 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=524850.4, rms=3.402 021: dt: 0.5000, sse=488692.1, rms=3.143 (7.613%) rms = 3.4667/3.1428, sse=538280.9/488692.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 022: dt: 0.2500, sse=314297.5, rms=1.894 (39.728%) 023: dt: 0.2500, sse=258917.5, rms=1.286 (32.123%) 024: dt: 0.2500, sse=245143.2, rms=1.076 (16.309%) rms = 1.0314/1.0761, sse=242200.8/245143.2, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=242200.8, rms=1.031 (4.153%) 026: dt: 0.1250, sse=236014.8, rms=0.916 (11.183%) rms = 0.9045/0.9160, sse=235151.9/236014.8, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=235151.9, rms=0.905 (1.257%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.1927640; border_low = 67.0000000; outside_low = 57.1096800; outside_hi = 115.1927640; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 86 vertices, nripped=8696 mean border=87.4, 78 (4) missing vertices, mean dist -0.0 [0.2 (%57.9)->0.1 (%42.1))] %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0472 min Finding expansion regions mean absolute distance = 0.15 +- 0.22 2794 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 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=comps, 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=257222.0, rms=1.319 rms = 1.7051/1.3195, sse=303299.4/257222.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=231163.7, rms=0.857 (35.057%) 029: dt: 0.2500, sse=226181.0, rms=0.689 (19.630%) rms = 0.7039/0.6887, sse=226183.0/226181.0, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 0.6838/0.6887, sse=225831.9/226181.0, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=225831.9, rms=0.684 (0.714%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Removing intersections #ET# mris_place_surface 3.31 minutes Writing output to ../surf/rh.white #VMPC# mris_place_surfaces VmPeak 2124472 mris_place_surface done @#@FSTIME 2026:07:08:20:51:01 mris_place_surface N 25 e 205.66 S 0.69 U 204.92 P 99% M 1872464 F 0 R 260915 W 0 c 707 w 145 I 2272 O 10184 L 1.15 1.95 1.81 @#@FSLOADPOST 2026:07:08:20:54:27 mris_place_surface N 25 1.04 1.50 1.65 #-------------------------------------------- #@# T1PialSurf lh Wed Jul 8 08:54:27 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 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 287266 0.33372 0.12922 0.000710 2.5300 Corner 861798 60.00000 15.52187 0.197541 178.8437 Edge 430899 0.88955 0.21269 0.013190 3.6248 Hinge 430899 9.97172 11.07145 0.000011 179.9484 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37219, wmmin=5, clip=110 MRIfindBrightNonWM(): 2834 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 68.5681 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 6175/143635 vertices (137460 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 71818: xyz = (-35.2723,-8.79907,49.8256) oxyz = (-35.2723,-8.79907,49.8256) wxzy = (-35.2723,-8.79907,49.8256) pxyz = (-35.2723,-8.79907,49.8256) CBVO Creating mask 143635 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8072360; border_hi = 58.1096800; border_low = 38.3290410; outside_low = 10.0000000; outside_hi = 53.1645200; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=2 had to be increased for 181 vertices, nripped=6175 mean border=55.9, 108 (108) missing vertices, mean dist 1.8 [0.4 (%0.0)->2.8 (%100.0))] %13 local maxima, %50 large gradients and %32 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1500 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 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=comps, 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=28958396.0, rms=32.353 001: dt: 0.5000, sse=18975170.0, rms=26.140 (19.204%) 002: dt: 0.5000, sse=12536723.0, rms=21.187 (18.949%) 003: dt: 0.5000, sse=8927278.0, rms=17.816 (15.910%) 004: dt: 0.5000, sse=6922913.0, rms=15.631 (12.261%) 005: dt: 0.5000, sse=5654165.0, rms=14.073 (9.972%) 006: dt: 0.5000, sse=4639848.0, rms=12.688 (9.837%) 007: dt: 0.5000, sse=3729775.2, rms=11.302 (10.925%) 008: dt: 0.5000, sse=2911018.2, rms=9.890 (12.496%) 009: dt: 0.5000, sse=2201613.8, rms=8.477 (14.282%) 010: dt: 0.5000, sse=1631341.9, rms=7.141 (15.758%) 011: dt: 0.5000, sse=1226707.5, rms=6.015 (15.769%) 012: dt: 0.5000, sse=978219.5, rms=5.203 (13.500%) 013: dt: 0.5000, sse=852344.1, rms=4.737 (8.959%) 014: dt: 0.5000, sse=784406.4, rms=4.465 (5.754%) 015: dt: 0.5000, sse=756330.3, rms=4.344 (2.689%) 016: dt: 0.5000, sse=737685.1, rms=4.262 (1.904%) rms = 4.2321/4.2618, sse=731611.9/737685.1, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=731611.9, rms=4.232 (0.697%) 018: dt: 0.2500, sse=531562.3, rms=3.231 (23.657%) 019: dt: 0.2500, sse=485945.5, rms=2.959 (8.412%) rms = 2.9110/2.9591, sse=478677.1/485945.5, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=478677.1, rms=2.911 (1.627%) 021: dt: 0.1250, sse=454309.4, rms=2.750 (5.532%) rms = 2.7217/2.7499, sse=450217.7/454309.4, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=450217.7, rms=2.722 (1.025%) maximum number of reductions reached, breaking from loop positioning took 1.7 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8072360; border_hi = 58.1096800; border_low = 38.3290410; outside_low = 10.0000000; outside_hi = 53.1645200; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=1 had to be increased for 8963 vertices, nripped=6175 mean border=54.2, 1387 (27) missing vertices, mean dist 0.1 [0.1 (%47.5)->0.4 (%52.5))] %31 local maxima, %36 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0393 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 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=comps, 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=691395.9, rms=3.770 rms = 3.9431/3.7699, sse=729491.3/691395.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=589816.8, rms=3.237 (14.123%) 024: dt: 0.2500, sse=538531.2, rms=2.930 (9.498%) 025: dt: 0.2500, sse=526150.0, rms=2.854 (2.584%) rms = 2.8350/2.8542, sse=523115.9/526150.0, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=523115.9, rms=2.835 (0.673%) 027: dt: 0.1250, sse=502222.6, rms=2.694 (4.988%) rms = 2.6617/2.6936, sse=497577.2/502222.6, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=497577.2, rms=2.662 (1.185%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8072360; border_hi = 58.1096800; border_low = 38.3290410; outside_low = 10.0000000; outside_hi = 53.1645200; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 9604 vertices, nripped=6175 mean border=52.9, 1502 (17) missing vertices, mean dist 0.1 [0.1 (%40.2)->0.3 (%59.8))] %49 local maxima, %19 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0231 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 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=comps, 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=610016.1, rms=3.325 rms = 4.1062/3.3252, sse=770202.4/610016.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=541571.5, rms=2.922 (12.123%) 030: dt: 0.2500, sse=530289.3, rms=2.850 (2.468%) rms = 2.8551/2.8500, sse=530478.4/530289.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 2.8063/2.8500, sse=523608.7/530289.3, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=523608.7, rms=2.806 (1.534%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8072360; border_hi = 58.1096800; border_low = 38.3290410; outside_low = 10.0000000; outside_hi = 53.1645200; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=143635 Gdiag_no=-1 vno start=0, stop=143635 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 8120 vertices, nripped=6175 mean border=52.1, 3577 (15) missing vertices, mean dist 0.0 [0.1 (%46.1)->0.2 (%53.9))] %52 local maxima, %14 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0151 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 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=comps, 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=550501.6, rms=2.975 rms = 3.6247/2.9751, sse=665745.3/550501.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=526046.0, rms=2.820 (5.231%) rms = 2.7775/2.8195, sse=518695.5/526046.0, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=518695.5, rms=2.778 (1.489%) 034: dt: 0.1250, sse=506081.2, rms=2.692 (3.076%) rms = 2.6601/2.6921, sse=501108.3/506081.2, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=501108.3, rms=2.660 (1.190%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 24 intersecting 001: 15 intersecting 002: 7 intersecting terminating search with 0 intersecting #ET# mris_place_surface 3.34 minutes Writing output to ../surf/lh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1374496 mris_place_surface done @#@FSTIME 2026:07:08:20:54:27 mris_place_surface N 28 e 207.13 S 0.47 U 206.60 P 99% M 1122500 F 0 R 201903 W 0 c 908 w 225 I 0 O 10112 L 1.04 1.50 1.65 @#@FSLOADPOST 2026:07:08:20:57:54 mris_place_surface N 28 1.05 1.30 1.54 #-------------------------------------------- #@# T1PialSurf rh Wed Jul 8 08:57:54 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 7.4.1 7.4.1 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 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 289544 0.33599 0.12840 0.000627 2.0842 Corner 868632 60.00000 15.19791 0.180423 179.4664 Edge 434316 0.89241 0.21131 0.011698 3.9091 Hinge 434316 9.91108 10.90756 0.000016 179.8372 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot [DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36 Reading in input volume brain.finalsurfs.mgz Reading in seg volume aseg.presurf.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=37219, wmmin=5, clip=110 MRIfindBrightNonWM(): 2834 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 68.0681 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 6036/144774 vertices (138738 unripped) INFO: rip surface needed but not specified, so using input surface Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 72387: xyz = (15.3141,-13.2999,47.3723) oxyz = (15.3141,-13.2999,47.3723) wxzy = (15.3141,-13.2999,47.3723) pxyz = (15.3141,-13.2999,47.3723) CBVO Creating mask 144774 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8072360; border_hi = 57.1096800; border_low = 37.3290410; outside_low = 10.0000000; outside_hi = 52.1645200; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=2 had to be increased for 190 vertices, nripped=6036 mean border=55.4, 108 (108) missing vertices, mean dist 1.7 [2.4 (%0.0)->2.8 (%100.0))] %12 local maxima, %47 large gradients and %36 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1487 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 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=comps, 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=29538440.0, rms=32.525 001: dt: 0.5000, sse=19364752.0, rms=26.286 (19.184%) 002: dt: 0.5000, sse=12783612.0, rms=21.296 (18.982%) 003: dt: 0.5000, sse=9073456.0, rms=17.878 (16.050%) 004: dt: 0.5000, sse=6993925.5, rms=15.637 (12.534%) 005: dt: 0.5000, sse=5657253.0, rms=14.007 (10.426%) 006: dt: 0.5000, sse=4563629.5, rms=12.515 (10.653%) 007: dt: 0.5000, sse=3573350.2, rms=10.989 (12.188%) 008: dt: 0.5000, sse=2705075.2, rms=9.451 (13.997%) 009: dt: 0.5000, sse=1987512.1, rms=7.958 (15.799%) 010: dt: 0.5000, sse=1459291.0, rms=6.646 (16.483%) 011: dt: 0.5000, sse=1121949.1, rms=5.650 (14.996%) 012: dt: 0.5000, sse=928943.3, rms=4.989 (11.691%) 013: dt: 0.5000, sse=839118.6, rms=4.648 (6.836%) 014: dt: 0.5000, sse=791765.0, rms=4.456 (4.134%) 015: dt: 0.5000, sse=768925.9, rms=4.359 (2.177%) 016: dt: 0.5000, sse=752169.1, rms=4.285 (1.693%) rms = 4.2553/4.2851, sse=745968.6/752169.1, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=745968.6, rms=4.255 (0.696%) 018: dt: 0.2500, sse=556918.8, rms=3.331 (21.713%) 019: dt: 0.2500, sse=516873.9, rms=3.104 (6.826%) rms = 3.0677/3.1040, sse=511195.8/516873.9, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=511195.8, rms=3.068 (1.169%) 021: dt: 0.1250, sse=487037.3, rms=2.918 (4.890%) rms = 2.8892/2.9177, sse=482618.4/487037.3, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=482618.4, rms=2.889 (0.977%) maximum number of reductions reached, breaking from loop positioning took 1.8 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8072360; border_hi = 57.1096800; border_low = 37.3290410; outside_low = 10.0000000; outside_hi = 52.1645200; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=1 had to be increased for 10805 vertices, nripped=6036 mean border=53.7, 1689 (20) missing vertices, mean dist 0.1 [0.1 (%46.4)->0.4 (%53.6))] %29 local maxima, %35 large gradients and %31 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0399 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 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=comps, 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=721529.5, rms=3.875 rms = 3.9473/3.8749, sse=738563.0/721529.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=620364.4, rms=3.367 (13.121%) 024: dt: 0.2500, sse=567281.1, rms=3.064 (8.995%) 025: dt: 0.2500, sse=553833.0, rms=2.986 (2.547%) rms = 2.9796/2.9857, sse=552874.8/553833.0, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=552874.8, rms=2.980 (0.202%) 027: dt: 0.1250, sse=534715.8, rms=2.864 (3.884%) rms = 2.8417/2.8639, sse=531200.8/534715.7, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=531200.8, rms=2.842 (0.777%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8072360; border_hi = 57.1096800; border_low = 37.3290410; outside_low = 10.0000000; outside_hi = 52.1645200; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 11212 vertices, nripped=6036 mean border=52.5, 1826 (15) missing vertices, mean dist 0.1 [0.1 (%40.7)->0.3 (%59.3))] %45 local maxima, %18 large gradients and %31 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0230 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 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=comps, 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=632947.6, rms=3.408 rms = 4.1064/3.4084, sse=779023.3/632947.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=570187.9, rms=3.054 (10.395%) 030: dt: 0.2500, sse=561727.4, rms=3.003 (1.673%) rms = 3.0064/3.0031, sse=561769.1/561727.4, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 2.9649/3.0031, sse=555537.6/561727.4, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=555537.6, rms=2.965 (1.272%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 98.8072360; border_hi = 57.1096800; border_low = 37.3290410; outside_low = 10.0000000; outside_hi = 52.1645200; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0.5 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=144774 Gdiag_no=-1 vno start=0, stop=144774 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 9316 vertices, nripped=6036 mean border=51.8, 4281 (15) missing vertices, mean dist 0.0 [0.1 (%46.7)->0.2 (%53.3))] %49 local maxima, %14 large gradients and %30 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0153 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 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=comps, 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=581368.4, rms=3.118 rms = 3.6563/3.1175, sse=679925.6/581368.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=556603.8, rms=2.969 (4.769%) 033: dt: 0.2500, sse=544100.2, rms=2.898 (2.388%) rms = 2.8875/2.8980, sse=541845.0/544100.2, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=541845.0, rms=2.887 (0.363%) 035: dt: 0.1250, sse=521568.8, rms=2.756 (4.546%) rms = 2.7239/2.7562, sse=516507.3/521568.8, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=516507.3, rms=2.724 (1.171%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 9 intersecting terminating search with 0 intersecting #ET# mris_place_surface 3.43 minutes Writing output to ../surf/rh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1382500 mris_place_surface done @#@FSTIME 2026:07:08:20:57:54 mris_place_surface N 28 e 213.01 S 0.46 U 212.48 P 99% M 1130436 F 0 R 204101 W 0 c 540 w 227 I 11832 O 10192 L 1.05 1.30 1.54 @#@FSLOADPOST 2026:07:08:21:01:27 mris_place_surface N 28 1.05 1.19 1.44 #@# white curv lh Wed Jul 8 09:01:27 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:21:01:27 mris_place_surface N 5 e 1.74 S 0.08 U 1.65 P 99% M 199336 F 3 R 27191 W 0 c 4 w 63 I 712 O 1128 L 1.05 1.19 1.44 @#@FSLOADPOST 2026:07:08:21:01:29 mris_place_surface N 5 1.04 1.19 1.44 #@# white area lh Wed Jul 8 09:01:29 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2026:07:08:21:01:29 mris_place_surface N 3 e 0.84 S 0.08 U 0.72 P 95% M 199272 F 0 R 27191 W 0 c 3 w 42 I 96 O 1128 L 1.04 1.19 1.44 @#@FSLOADPOST 2026:07:08:21:01:30 mris_place_surface N 3 1.04 1.19 1.44 #@# pial curv lh Wed Jul 8 09:01:30 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:21:01:30 mris_place_surface N 5 e 1.77 S 0.09 U 1.64 P 98% M 199332 F 0 R 27702 W 0 c 4 w 60 I 96 O 1128 L 1.04 1.19 1.44 @#@FSLOADPOST 2026:07:08:21:01:32 mris_place_surface N 5 1.04 1.19 1.44 #@# pial area lh Wed Jul 8 09:01:32 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2026:07:08:21:01:32 mris_place_surface N 3 e 0.86 S 0.09 U 0.74 P 96% M 199264 F 0 R 27190 W 0 c 2 w 43 I 96 O 1136 L 1.04 1.19 1.44 @#@FSLOADPOST 2026:07:08:21:01:33 mris_place_surface N 3 1.04 1.19 1.44 #@# thickness lh Wed Jul 8 09:01:33 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 143635 vertices processed 25000 of 143635 vertices processed 50000 of 143635 vertices processed 75000 of 143635 vertices processed 100000 of 143635 vertices processed 125000 of 143635 vertices processed 0 of 143635 vertices processed 25000 of 143635 vertices processed 50000 of 143635 vertices processed 75000 of 143635 vertices processed 100000 of 143635 vertices processed 125000 of 143635 vertices processed thickness calculation complete, 87:427 truncations. 62963 vertices at 0 distance 124298 vertices at 1 distance 68450 vertices at 2 distance 21950 vertices at 3 distance 6399 vertices at 4 distance 2050 vertices at 5 distance 685 vertices at 6 distance 246 vertices at 7 distance 90 vertices at 8 distance 27 vertices at 9 distance 28 vertices at 10 distance 8 vertices at 11 distance 11 vertices at 12 distance 16 vertices at 13 distance 5 vertices at 14 distance 11 vertices at 15 distance 8 vertices at 16 distance 11 vertices at 17 distance 6 vertices at 18 distance 5 vertices at 19 distance 3 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2026:07:08:21:01:33 mris_place_surface N 6 e 27.50 S 0.16 U 27.29 P 99% M 199408 F 0 R 48023 W 0 c 66 w 44 I 96 O 1136 L 1.04 1.19 1.44 @#@FSLOADPOST 2026:07:08:21:02:00 mris_place_surface N 6 1.02 1.17 1.43 #@# area and vertex vol lh Wed Jul 8 09:02:00 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 lh /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.volume masking with /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Total face volume 272816 Total vertex volume 272592 (mask=0) #@# sub-20_ses-0 lh 272592 vertexvol Done @#@FSTIME 2026:07:08:21:02:00 vertexvol N 4 e 1.71 S 0.15 U 1.48 P 95% M 329764 F 13 R 44993 W 0 c 4 w 235 I 2024 O 3400 L 1.02 1.17 1.43 @#@FSLOADPOST 2026:07:08:21:02:02 vertexvol N 4 1.02 1.17 1.43 #@# white curv rh Wed Jul 8 09:02:02 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:21:02:02 mris_place_surface N 5 e 1.72 S 0.10 U 1.61 P 99% M 200748 F 0 R 28629 W 0 c 4 w 88 I 96 O 1136 L 1.02 1.17 1.43 @#@FSLOADPOST 2026:07:08:21:02:04 mris_place_surface N 5 1.02 1.17 1.42 #@# white area rh Wed Jul 8 09:02:04 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2026:07:08:21:02:04 mris_place_surface N 3 e 0.85 S 0.10 U 0.71 P 96% M 200588 F 0 R 28117 W 0 c 6 w 46 I 96 O 1136 L 1.02 1.17 1.42 @#@FSLOADPOST 2026:07:08:21:02:05 mris_place_surface N 3 1.02 1.17 1.42 #@# pial curv rh Wed Jul 8 09:02:05 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 2026:07:08:21:02:05 mris_place_surface N 5 e 1.75 S 0.09 U 1.62 P 98% M 200772 F 0 R 27610 W 0 c 5 w 57 I 96 O 1136 L 1.02 1.17 1.42 @#@FSLOADPOST 2026:07:08:21:02:07 mris_place_surface N 5 1.02 1.17 1.42 #@# pial area rh Wed Jul 8 09:02:07 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2026:07:08:21:02:07 mris_place_surface N 3 e 0.87 S 0.09 U 0.74 P 96% M 200588 F 0 R 27094 W 0 c 2 w 52 I 96 O 1144 L 1.02 1.17 1.42 @#@FSLOADPOST 2026:07:08:21:02:08 mris_place_surface N 3 1.02 1.17 1.42 #@# thickness rh Wed Jul 8 09:02:08 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 144774 vertices processed 25000 of 144774 vertices processed 50000 of 144774 vertices processed 75000 of 144774 vertices processed 100000 of 144774 vertices processed 125000 of 144774 vertices processed 0 of 144774 vertices processed 25000 of 144774 vertices processed 50000 of 144774 vertices processed 75000 of 144774 vertices processed 100000 of 144774 vertices processed 125000 of 144774 vertices processed thickness calculation complete, 132:507 truncations. 62551 vertices at 0 distance 127819 vertices at 1 distance 67981 vertices at 2 distance 21303 vertices at 3 distance 6396 vertices at 4 distance 2182 vertices at 5 distance 764 vertices at 6 distance 257 vertices at 7 distance 102 vertices at 8 distance 31 vertices at 9 distance 24 vertices at 10 distance 23 vertices at 11 distance 18 vertices at 12 distance 10 vertices at 13 distance 16 vertices at 14 distance 14 vertices at 15 distance 10 vertices at 16 distance 8 vertices at 17 distance 12 vertices at 18 distance 12 vertices at 19 distance 15 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2026:07:08:21:02:08 mris_place_surface N 6 e 27.45 S 0.09 U 27.32 P 99% M 200824 F 0 R 34809 W 0 c 70 w 46 I 96 O 1144 L 1.02 1.17 1.42 @#@FSLOADPOST 2026:07:08:21:02:35 mris_place_surface N 6 1.07 1.17 1.41 #@# area and vertex vol rh Wed Jul 8 09:02:35 PM CEST 2026 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 rh /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.volume masking with /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Total face volume 274761 Total vertex volume 274550 (mask=0) #@# sub-20_ses-0 rh 274550 vertexvol Done @#@FSTIME 2026:07:08:21:02:35 vertexvol N 4 e 1.75 S 0.17 U 1.50 P 95% M 332124 F 0 R 43662 W 0 c 9 w 220 I 192 O 3408 L 1.07 1.17 1.41 @#@FSLOADPOST 2026:07:08:21:02:37 vertexvol N 4 1.07 1.17 1.41 #----------------------------------------- #@# Curvature Stats lh Wed Jul 8 09:02:37 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-20_ses-0 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 [ sub-20_ses-0/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 [ 268 ] Gb_filter = 0 WARN: S lookup min: -0.027689 WARN: S explicit min: 0.000000 vertex = 459 @#@FSTIME 2026:07:08:21:02:37 mris_curvature_stats N 11 e 2.53 S 0.10 U 2.18 P 90% M 198956 F 9 R 26816 W 0 c 5 w 376 I 1912 O 9064 L 1.07 1.17 1.41 @#@FSLOADPOST 2026:07:08:21:02:39 mris_curvature_stats N 11 1.06 1.16 1.41 #----------------------------------------- #@# Curvature Stats rh Wed Jul 8 09:02:40 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-20_ses-0 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 [ sub-20_ses-0/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 [ 252 ] Gb_filter = 0 WARN: S lookup min: -0.204352 WARN: S explicit min: 0.000000 vertex = 331 @#@FSTIME 2026:07:08:21:02:40 mris_curvature_stats N 11 e 2.75 S 0.13 U 2.36 P 90% M 200576 F 0 R 27583 W 0 c 4 w 372 I 768 O 9136 L 1.06 1.16 1.41 @#@FSLOADPOST 2026:07:08:21:02:42 mris_curvature_stats N 11 1.06 1.16 1.41 #-------------------------------------------- #@# Cortical ribbon mask Wed Jul 8 09:02:42 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 SUBJECTS_DIR is /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 loading input data... Running hemis serially Processing left hemi computing distance to left white surface computing distance to left pial surface Processing right hemi computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 241 writing volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/ribbon.mgz mris_volmask took 7.78 minutes writing ribbon files @#@FSTIME 2026:07:08:21:02:42 mris_volmask N 12 e 466.82 S 0.72 U 466.04 P 99% M 1026144 F 9 R 213347 W 0 c 1250 w 76 I 1320 O 904 L 1.06 1.16 1.41 @#@FSLOADPOST 2026:07:08:21:10:29 mris_volmask N 12 1.14 1.11 1.27 #----------------------------------------- #@# Cortical Parc 2 lh Wed Jul 8 09:10:29 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 lh ../surf/lh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 3 labels changed using aseg relabeling using gibbs priors... 000: 9693 changed, 143635 examined... 001: 2263 changed, 37443 examined... 002: 672 changed, 12108 examined... 003: 291 changed, 3907 examined... 004: 131 changed, 1682 examined... 005: 70 changed, 782 examined... 006: 34 changed, 397 examined... 007: 18 changed, 194 examined... 008: 8 changed, 117 examined... 009: 4 changed, 40 examined... 010: 2 changed, 20 examined... 011: 1 changed, 14 examined... 012: 2 changed, 8 examined... 013: 0 changed, 9 examined... 0 labels changed using aseg 000: 258 total segments, 169 labels (2074 vertices) changed 001: 96 total segments, 8 labels (11 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1314 vertices marked for relabeling... 1314 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. @#@FSTIME 2026:07:08:21:10:29 mris_ca_label N 11 e 12.28 S 0.99 U 11.26 P 99% M 2004332 F 0 R 324299 W 0 c 25 w 78 I 42432 O 2264 L 1.14 1.11 1.27 @#@FSLOADPOST 2026:07:08:21:10:42 mris_ca_label N 11 1.12 1.11 1.27 #----------------------------------------- #@# Cortical Parc 2 rh Wed Jul 8 09:10:42 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 rh ../surf/rh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 2 labels changed using aseg relabeling using gibbs priors... 000: 9349 changed, 144774 examined... 001: 2149 changed, 36705 examined... 002: 622 changed, 11389 examined... 003: 266 changed, 3653 examined... 004: 120 changed, 1523 examined... 005: 78 changed, 704 examined... 006: 34 changed, 433 examined... 007: 13 changed, 196 examined... 008: 9 changed, 66 examined... 009: 5 changed, 54 examined... 010: 1 changed, 23 examined... 011: 1 changed, 8 examined... 012: 0 changed, 6 examined... 6 labels changed using aseg 000: 232 total segments, 148 labels (2075 vertices) changed 001: 95 total segments, 12 labels (120 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1251 vertices marked for relabeling... 1251 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. @#@FSTIME 2026:07:08:21:10:42 mris_ca_label N 11 e 12.10 S 0.93 U 11.16 P 99% M 1884636 F 0 R 306767 W 0 c 28 w 55 I 42776 O 2280 L 1.12 1.11 1.27 @#@FSLOADPOST 2026:07:08:21:10:54 mris_ca_label N 11 1.10 1.11 1.27 #----------------------------------------- #@# Cortical Parc 3 lh Wed Jul 8 09:10:54 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 lh ../surf/lh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1524 labels changed using aseg relabeling using gibbs priors... 000: 2063 changed, 143635 examined... 001: 453 changed, 9550 examined... 002: 142 changed, 2669 examined... 003: 54 changed, 826 examined... 004: 20 changed, 291 examined... 005: 10 changed, 110 examined... 006: 9 changed, 60 examined... 007: 9 changed, 48 examined... 008: 11 changed, 47 examined... 009: 8 changed, 45 examined... 010: 8 changed, 45 examined... 011: 15 changed, 42 examined... 012: 12 changed, 62 examined... 013: 6 changed, 59 examined... 014: 4 changed, 30 examined... 015: 3 changed, 18 examined... 016: 4 changed, 18 examined... 017: 4 changed, 22 examined... 018: 4 changed, 18 examined... 019: 4 changed, 16 examined... 020: 3 changed, 16 examined... 021: 3 changed, 15 examined... 022: 3 changed, 20 examined... 023: 1 changed, 18 examined... 024: 0 changed, 7 examined... 273 labels changed using aseg 000: 49 total segments, 16 labels (131 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 929 vertices marked for relabeling... 929 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. @#@FSTIME 2026:07:08:21:10:54 mris_ca_label N 11 e 9.45 S 0.49 U 8.95 P 99% M 942268 F 0 R 166528 W 0 c 19 w 60 I 42976 O 2256 L 1.10 1.11 1.27 @#@FSLOADPOST 2026:07:08:21:11:03 mris_ca_label N 11 1.09 1.10 1.26 #----------------------------------------- #@# Cortical Parc 3 rh Wed Jul 8 09:11:03 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-20_ses-0 rh ../surf/rh.sphere.reg /software/freesurfer/7.4.1/debian-bookworm-amd64/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 7.4.1 7.4.1 reading atlas from /software/freesurfer/7.4.1/debian-bookworm-amd64/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 reading surface from /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1585 labels changed using aseg relabeling using gibbs priors... 000: 2148 changed, 144774 examined... 001: 494 changed, 9832 examined... 002: 150 changed, 2836 examined... 003: 51 changed, 847 examined... 004: 25 changed, 303 examined... 005: 11 changed, 159 examined... 006: 7 changed, 72 examined... 007: 9 changed, 44 examined... 008: 15 changed, 50 examined... 009: 14 changed, 72 examined... 010: 8 changed, 61 examined... 011: 4 changed, 41 examined... 012: 6 changed, 23 examined... 013: 2 changed, 27 examined... 014: 1 changed, 14 examined... 015: 2 changed, 7 examined... 016: 3 changed, 9 examined... 017: 3 changed, 15 examined... 018: 4 changed, 18 examined... 019: 4 changed, 21 examined... 020: 3 changed, 18 examined... 021: 2 changed, 18 examined... 022: 1 changed, 10 examined... 023: 2 changed, 7 examined... 024: 3 changed, 11 examined... 025: 4 changed, 17 examined... 026: 5 changed, 24 examined... 027: 5 changed, 24 examined... 028: 5 changed, 27 examined... 029: 5 changed, 28 examined... 030: 3 changed, 25 examined... 031: 3 changed, 16 examined... 032: 1 changed, 20 examined... 033: 1 changed, 7 examined... 034: 1 changed, 7 examined... 035: 0 changed, 6 examined... 233 labels changed using aseg 000: 50 total segments, 17 labels (240 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 935 vertices marked for relabeling... 935 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. @#@FSTIME 2026:07:08:21:11:03 mris_ca_label N 11 e 9.59 S 0.53 U 9.04 P 99% M 950448 F 0 R 167813 W 0 c 17 w 73 I 42952 O 2280 L 1.09 1.10 1.26 @#@FSLOADPOST 2026:07:08:21:11:13 mris_ca_label N 11 1.07 1.10 1.26 #----------------------------------------- #@# WM/GM Contrast lh Wed Jul 8 09:11:13 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts pctsurfcon --s sub-20_ses-0 --lh-only Log file is /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts/pctsurfcon.log Wed Jul 8 09:11:13 PM CEST 2026 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/pctsurfcon pctsurfcon 7.4.1 Linux comps10h04 6.1.0-49-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.174-1 (2026-05-26) x86_64 GNU/Linux FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 mri_vol2surf --mov /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76427/lh.wm.mgh --regheader sub-20_ses-0 --cortex srcvol = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Reading surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 82894 Masking with /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Writing to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76427/lh.wm.mgh Dim: 143635 1 1 mri_vol2surf done mri_vol2surf --mov /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76427/lh.gm.mgh --projfrac 0.3 --regheader sub-20_ses-0 --cortex srcvol = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Reading surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Done reading source surface Reading thickness /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 99362 Masking with /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Writing to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76427/lh.gm.mgh Dim: 143635 1 1 mri_vol2surf done mri_concat /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76427/lh.wm.mgh /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76427/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh mri_segstats --in /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh --annot sub-20_ses-0 lh aparc --sum /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/stats/lh.w-g.pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh --annot sub-20_ses-0 lh aparc --sum /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/stats/lh.w-g.pct.stats --snr sysname Linux hostname comps10h04 machine x86_64 user asmolova whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot Seg base 1000 MRISannot2seg(): nhits = 135250 Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.w-g.pct.mgh Vertex Area is 0.667425 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 2026:07:08:21:11:13 pctsurfcon N 3 e 3.14 S 0.29 U 2.76 P 97% M 278040 F 20 R 74721 W 0 c 8 w 314 I 18320 O 3616 L 1.07 1.10 1.26 @#@FSLOADPOST 2026:07:08:21:11:16 pctsurfcon N 3 1.07 1.10 1.26 #----------------------------------------- #@# WM/GM Contrast rh Wed Jul 8 09:11:16 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts pctsurfcon --s sub-20_ses-0 --rh-only Log file is /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts/pctsurfcon.log Wed Jul 8 09:11:16 PM CEST 2026 setenv SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 cd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/scripts /software/freesurfer/7.4.1/debian-bookworm-amd64/bin/pctsurfcon pctsurfcon 7.4.1 Linux comps10h04 6.1.0-49-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.174-1 (2026-05-26) x86_64 GNU/Linux FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 mri_vol2surf --mov /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76490/rh.wm.mgh --regheader sub-20_ses-0 --cortex srcvol = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Reading surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface Projecting -1 -1 1 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 83710 Masking with /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Writing to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76490/rh.wm.mgh Dim: 144774 1 1 mri_vol2surf done mri_vol2surf --mov /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76490/rh.gm.mgh --projfrac 0.3 --regheader sub-20_ses-0 --cortex srcvol = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Reading surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Done reading source surface Reading thickness /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.3 0.3 1 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 100121 Masking with /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Writing to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76490/rh.gm.mgh Dim: 144774 1 1 mri_vol2surf done mri_concat /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76490/rh.wm.mgh /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/tmp.pctsurfcon.76490/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh mri_segstats --in /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh --annot sub-20_ses-0 rh aparc --sum /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/stats/rh.w-g.pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh --annot sub-20_ses-0 rh aparc --sum /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/stats/rh.w-g.pct.stats --snr sysname Linux hostname comps10h04 machine x86_64 user asmolova whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.annot Seg base 2000 MRISannot2seg(): nhits = 136522 Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.w-g.pct.mgh Vertex Area is 0.671969 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 2026:07:08:21:11:16 pctsurfcon N 3 e 3.07 S 0.33 U 2.71 P 98% M 279488 F 0 R 83448 W 0 c 13 w 307 I 0 O 3616 L 1.07 1.10 1.26 @#@FSLOADPOST 2026:07:08:21:11:19 pctsurfcon N 3 1.06 1.09 1.26 #----------------------------------------- #@# Relabel Hypointensities Wed Jul 8 09:11:19 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 908 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 728 voxels changed to hypointensity... 1652 hypointense voxels neighboring cortex changed @#@FSTIME 2026:07:08:21:11:19 mri_relabel_hypointensities N 3 e 13.81 S 0.38 U 13.41 P 99% M 510880 F 12 R 62787 W 0 c 45 w 47 I 1648 O 696 L 1.06 1.09 1.26 @#@FSLOADPOST 2026:07:08:21:11:33 mri_relabel_hypointensities N 3 1.05 1.09 1.25 #----------------------------------------- #@# APas-to-ASeg Wed Jul 8 09:11:33 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/ribbon.mgz --threads 1 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 outvol aseg.mgz 96 avail.processors, using 1 Loading aseg.presurf.hypos.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/ribbon.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 nrelabeled = 0 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 955792 mri_surf2volseg done @#@FSTIME 2026:07:08:21:11:33 mri_surf2volseg N 20 e 9.40 S 0.34 U 9.03 P 99% M 935976 F 7 R 97974 W 0 c 29 w 77 I 992 O 736 L 1.05 1.09 1.25 @#@FSLOADPOST 2026:07:08:21:11:43 mri_surf2volseg N 20 1.04 1.09 1.25 mri_brainvol_stats --subject sub-20_ses-0 ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1681893.0 #CBVS2 BrainSegVol 1216724.0 #CBVS2 BrainSegVolNotVent 1201601.0 #CBVS2 SupraTentVol 1075304.0 #CBVS2 SupraTentVolNotVent 1060181.0 #CBVS2 lhCtxGM 273231.3 #CBVS2 rhCtxGM 275154.8 #CBVS2 lhCerebralWM 225125.5 #CBVS2 rhCerebralWM 225960.5 #CBVS2 SubCortGMVol 61910.0 #CBVS2 CerebellumVol 141420.0 #CBVS2 CerebellumGMVol 110196.0 #CBVS2 VentChorVol 12335.0 #CBVS2 3rd4th5thCSF 2788.0 #CBVS2 AllCSF 15123.0 #CBVS2 CCVol 3579.0 @#@FSTIME 2026:07:08:21:11:43 mri_brainvol_stats N 2 e 3.91 S 0.17 U 3.72 P 99% M 232368 F 23 R 38127 W 0 c 7 w 66 I 4160 O 8 L 1.04 1.09 1.25 @#@FSLOADPOST 2026:07:08:21:11:47 mri_brainvol_stats N 2 1.04 1.08 1.25 #----------------------------------------- #@# AParc-to-ASeg aparc Wed Jul 8 09:11:47 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot 1000 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-annot /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.annot 2000 --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 outvol aparc+aseg.mgz 96 avail.processors, using 1 Loading aseg.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8385 vertices from lh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8252 vertices from rh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 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/data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-annot /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 outvol aparc.a2009s+aseg.mgz 96 avail.processors, using 1 Loading aseg.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8385 vertices from lh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.a2009s.annot Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8252 vertices from rh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 nrelabeled = 0 ndotcheck = 26323 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 939020 mri_surf2volseg done @#@FSTIME 2026:07:08:21:13:49 mri_surf2volseg N 25 e 120.55 S 0.34 U 120.18 P 99% M 919328 F 0 R 96064 W 0 c 256 w 104 I 4528 O 920 L 1.09 1.08 1.23 @#@FSLOADPOST 2026:07:08:21:15:49 mri_surf2volseg N 25 1.04 1.07 1.20 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Wed Jul 8 09:15:49 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-annot /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 outvol aparc.DKTatlas+aseg.mgz 96 avail.processors, using 1 Loading aseg.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8385 vertices from lh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.DKTatlas.annot Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8252 vertices from rh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 nrelabeled = 0 ndotcheck = 26323 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 938960 mri_surf2volseg done @#@FSTIME 2026:07:08:21:15:50 mri_surf2volseg N 25 e 124.74 S 0.44 U 124.27 P 99% M 919300 F 0 R 99341 W 0 c 303 w 95 I 4520 O 840 L 1.04 1.07 1.20 @#@FSLOADPOST 2026:07:08:21:17:54 mri_surf2volseg N 25 1.04 1.06 1.18 #----------------------------------------- #@# WMParc Wed Jul 8 09:17:54 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 1 --lh-annot /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot 3000 --lh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label --lh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white --lh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial --rh-annot /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.aparc.annot 4000 --rh-cortex-mask /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label --rh-white /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white --rh-pial /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 outvol wmparc.mgz 96 avail.processors, using 1 Loading aparc+aseg.mgz Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8385 vertices from lh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.aparc.annot Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8252 vertices from rh hemi Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 nrelabeled = 0 ndotcheck = 4075 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 938960 mri_surf2volseg done @#@FSTIME 2026:07:08:21:17:54 mri_surf2volseg N 25 e 36.01 S 0.35 U 35.63 P 99% M 919196 F 0 R 100144 W 0 c 80 w 96 I 0 O 952 L 1.04 1.06 1.18 @#@FSLOADPOST 2026:07:08:21:18:30 mri_surf2volseg N 25 1.14 1.08 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 sub-20_ses-0 --surf-wm-vol --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 7.4.1 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 sub-20_ses-0 --surf-wm-vol --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/WMParcStatsLUT.txt --etiv sysname Linux hostname comps10h04 machine x86_64 user asmolova whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1572797 mm^3 (det: 1.238625 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2026:07:08:21:18:30 mri_segstats N 24 e 300.82 S 0.34 U 300.42 P 99% M 239828 F 1 R 43507 W 0 c 1320 w 55 I 312 O 24 L 1.14 1.08 1.18 @#@FSLOADPOST 2026:07:08:21:23:31 mri_segstats N 24 1.12 1.08 1.15 #----------------------------------------- #@# Parcellation Stats lh Wed Jul 8 09:23:31 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 272816 Total vertex volume 272592 (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) = 1572797 mm^3 (det: 1.238625 ) 1767 1136 3073 2.680 0.477 0.084 0.015 10 1.1 bankssts 1077 694 2005 2.469 0.785 0.115 0.017 13 0.8 caudalanteriorcingulate 3453 2190 6895 2.787 0.468 0.097 0.016 25 2.3 caudalmiddlefrontal 2608 1823 4212 2.148 0.473 0.148 0.031 37 3.6 cuneus 710 501 2029 3.331 0.780 0.116 0.025 5 0.7 entorhinal 5283 3584 11695 2.731 0.588 0.115 0.021 60 4.5 fusiform 6355 4327 12826 2.612 0.515 0.106 0.017 65 4.5 inferiorparietal 5436 3678 11909 2.772 0.604 0.103 0.019 54 4.1 inferiortemporal 1526 1038 2710 2.303 0.801 0.125 0.031 21 1.7 isthmuscingulate 8523 5762 14465 2.205 0.513 0.126 0.025 104 8.7 lateraloccipital 4158 2866 8632 2.781 0.654 0.117 0.025 44 4.1 lateralorbitofrontal 5628 3952 9525 2.227 0.586 0.129 0.030 75 6.6 lingual 2658 1887 5177 2.523 0.544 0.109 0.023 28 2.1 medialorbitofrontal 4884 3318 12748 3.115 0.603 0.107 0.019 47 3.7 middletemporal 1145 760 2460 2.817 0.580 0.101 0.020 9 0.9 parahippocampal 2287 1446 4363 2.720 0.572 0.101 0.017 18 1.6 paracentral 2387 1616 5131 2.754 0.463 0.111 0.019 25 1.9 parsopercularis 1092 744 2776 2.843 0.568 0.128 0.024 14 1.1 parsorbitalis 2001 1307 4233 2.773 0.496 0.115 0.018 20 1.6 parstriangularis 2485 1689 2978 1.963 0.430 0.110 0.022 20 2.2 pericalcarine 6369 4069 11271 2.378 0.607 0.105 0.019 55 5.2 postcentral 2093 1447 4051 2.453 0.722 0.117 0.023 26 2.1 posteriorcingulate 6708 4196 13602 2.859 0.610 0.096 0.016 45 4.3 precentral 6232 4181 10968 2.440 0.497 0.111 0.020 61 4.8 precuneus 1593 1101 3724 2.856 0.613 0.107 0.023 20 1.4 rostralanteriorcingulate 8688 5946 17825 2.601 0.486 0.120 0.023 107 7.8 rostralmiddlefrontal 11974 8066 26401 2.828 0.548 0.113 0.021 109 10.2 superiorfrontal 8180 5384 14333 2.400 0.454 0.114 0.019 87 6.4 superiorparietal 6452 4202 15112 3.074 0.629 0.092 0.015 44 4.2 superiortemporal 5746 3868 12362 2.760 0.529 0.114 0.021 58 5.0 supramarginal 400 292 1172 2.933 0.374 0.146 0.034 9 0.4 frontalpole 777 593 2762 3.583 0.703 0.132 0.031 12 1.0 temporalpole 683 434 1296 2.696 0.336 0.117 0.018 7 0.5 transversetemporal 3892 2653 7872 2.993 0.717 0.114 0.029 38 4.0 insula @#@FSTIME 2026:07:08:21:23:31 mris_anatomical_stats N 14 e 15.98 S 0.19 U 15.74 P 99% M 508952 F 10 R 70602 W 0 c 35 w 191 I 1704 O 304 L 1.12 1.08 1.15 @#@FSLOADPOST 2026:07:08:21:23:47 mris_anatomical_stats N 14 1.09 1.08 1.15 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 sub-20_ses-0 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 272816 Total vertex volume 272592 (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) = 1572797 mm^3 (det: 1.238625 ) 1767 1124 3073 2.680 0.477 0.114 0.027 19 2.0 bankssts 1077 884 2005 2.469 0.785 0.171 0.053 59 2.0 caudalanteriorcingulate 3453 2623 6895 2.787 0.468 0.116 0.023 39 3.3 caudalmiddlefrontal 2608 2224 4212 2.148 0.473 0.154 0.039 55 4.1 cuneus 710 778 2029 3.331 0.780 0.288 0.089 26 3.6 entorhinal 5283 4835 11695 2.731 0.588 0.157 0.041 108 8.9 fusiform 6355 5312 12826 2.612 0.515 0.136 0.028 86 7.6 inferiorparietal 5436 4669 11909 2.772 0.604 0.142 0.034 104 7.4 inferiortemporal 1526 1362 2710 2.303 0.801 0.191 0.057 53 3.8 isthmuscingulate 8523 7307 14465 2.205 0.513 0.145 0.032 129 11.5 lateraloccipital 4158 3304 8632 2.781 0.654 0.146 0.040 114 6.5 lateralorbitofrontal 5628 4871 9525 2.227 0.586 0.158 0.042 125 9.8 lingual 2658 2252 5177 2.523 0.544 0.154 0.037 47 4.2 medialorbitofrontal 4884 4653 12748 3.115 0.603 0.151 0.033 93 6.8 middletemporal 1145 1057 2460 2.817 0.580 0.204 0.058 45 3.2 parahippocampal 2287 1734 4363 2.720 0.572 0.121 0.030 37 2.8 paracentral 2387 2093 5131 2.754 0.463 0.152 0.032 46 3.5 parsopercularis 1092 1155 2776 2.843 0.568 0.168 0.039 18 1.8 parsorbitalis 2001 1708 4233 2.773 0.496 0.145 0.032 28 2.7 parstriangularis 2485 1389 2978 1.963 0.430 0.106 0.028 52 2.3 pericalcarine 6369 5291 11271 2.378 0.607 0.134 0.027 72 7.5 postcentral 2093 1835 4051 2.453 0.722 0.180 0.052 136 4.7 posteriorcingulate 6708 5092 13602 2.859 0.610 0.108 0.022 63 6.1 precentral 6232 4712 10968 2.440 0.497 0.135 0.032 140 7.9 precuneus 1593 1550 3724 2.856 0.613 0.182 0.056 44 3.2 rostralanteriorcingulate 8688 7494 17825 2.601 0.486 0.154 0.035 1103 12.2 rostralmiddlefrontal 11974 10138 26401 2.828 0.548 0.141 0.034 388 15.4 superiorfrontal 8180 6443 14333 2.400 0.454 0.127 0.027 110 8.3 superiorparietal 6452 5415 15112 3.074 0.629 0.139 0.032 96 8.8 superiortemporal 5746 4882 12362 2.760 0.529 0.148 0.036 112 8.4 supramarginal 400 526 1172 2.933 0.374 0.189 0.038 4 0.6 frontalpole 777 989 2762 3.583 0.703 0.204 0.043 17 1.6 temporalpole 683 541 1296 2.696 0.336 0.129 0.037 10 1.0 transversetemporal 3892 2556 7872 2.993 0.717 0.150 0.047 136 6.8 insula @#@FSTIME 2026:07:08:21:23:47 mris_anatomical_stats N 14 e 15.87 S 0.21 U 15.62 P 99% M 508992 F 0 R 69532 W 0 c 31 w 165 I 0 O 304 L 1.09 1.08 1.15 @#@FSLOADPOST 2026:07:08:21:24:03 mris_anatomical_stats N 14 1.07 1.08 1.14 #----------------------------------------- #@# Parcellation Stats rh Wed Jul 8 09:24:03 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 274761 Total vertex volume 274550 (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) = 1572797 mm^3 (det: 1.238625 ) 1629 1036 2818 2.842 0.352 0.082 0.014 7 0.9 bankssts 1030 646 1738 2.227 0.819 0.106 0.015 11 0.7 caudalanteriorcingulate 4442 2907 9267 2.768 0.538 0.100 0.016 31 3.1 caudalmiddlefrontal 2836 1902 4779 2.225 0.426 0.138 0.031 35 3.4 cuneus 561 373 1818 3.607 0.600 0.101 0.024 3 0.5 entorhinal 5186 3457 11753 2.878 0.594 0.109 0.022 54 4.5 fusiform 7887 5239 16085 2.640 0.483 0.105 0.017 77 6.0 inferiorparietal 4584 3150 10213 2.875 0.576 0.114 0.020 49 3.8 inferiortemporal 1685 1159 3068 2.305 0.778 0.124 0.028 27 1.8 isthmuscingulate 8613 5770 15744 2.417 0.476 0.123 0.022 98 7.7 lateraloccipital 4436 3069 8973 2.678 0.597 0.126 0.028 68 5.0 lateralorbitofrontal 6522 4674 11153 2.238 0.570 0.135 0.032 94 8.4 lingual 3272 2370 7112 2.591 0.650 0.126 0.028 51 3.7 medialorbitofrontal 5124 3507 13143 3.035 0.558 0.109 0.019 51 4.1 middletemporal 1175 751 2349 2.753 0.528 0.088 0.016 8 0.6 parahippocampal 2002 1300 3526 2.548 0.474 0.112 0.018 18 1.5 paracentral 2786 1962 6111 2.692 0.486 0.117 0.019 32 2.3 parsopercularis 1494 1043 3297 2.629 0.557 0.129 0.020 19 1.2 parsorbitalis 2497 1735 5078 2.540 0.482 0.110 0.019 26 2.0 parstriangularis 2925 2032 3503 1.944 0.593 0.121 0.025 25 3.1 pericalcarine 4762 3280 9866 2.596 0.463 0.119 0.021 49 4.3 postcentral 1989 1394 3931 2.482 0.777 0.126 0.025 26 2.0 posteriorcingulate 6659 4286 10719 2.307 0.550 0.106 0.018 58 5.0 precentral 5985 4023 10732 2.508 0.539 0.114 0.021 64 5.1 precuneus 1086 744 2401 2.913 0.557 0.120 0.025 14 1.2 rostralanteriorcingulate 10764 7499 21497 2.517 0.492 0.121 0.022 131 9.6 rostralmiddlefrontal 14174 9281 30520 2.848 0.529 0.105 0.019 118 10.7 superiorfrontal 6088 3980 10654 2.410 0.458 0.108 0.019 53 4.5 superiorparietal 5617 3680 12451 2.944 0.528 0.090 0.014 42 3.3 superiortemporal 3634 2430 7373 2.738 0.500 0.114 0.021 36 3.2 supramarginal 503 417 1516 2.831 0.399 0.181 0.052 11 1.3 frontalpole 602 457 2942 4.297 0.531 0.139 0.033 7 0.8 temporalpole 493 313 1085 2.856 0.333 0.119 0.021 4 0.4 transversetemporal 3480 2364 7336 3.086 0.749 0.110 0.029 30 3.7 insula @#@FSTIME 2026:07:08:21:24:03 mris_anatomical_stats N 14 e 16.14 S 0.20 U 15.90 P 99% M 512536 F 0 R 66835 W 0 c 24 w 171 I 0 O 304 L 1.07 1.08 1.14 @#@FSLOADPOST 2026:07:08:21:24:19 mris_anatomical_stats N 14 1.22 1.10 1.15 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 sub-20_ses-0 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 274761 Total vertex volume 274550 (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) = 1572797 mm^3 (det: 1.238625 ) 1629 926 2818 2.842 0.352 0.108 0.036 29 2.0 bankssts 1030 861 1738 2.227 0.819 0.159 0.050 43 1.6 caudalanteriorcingulate 4442 3602 9267 2.768 0.538 0.119 0.024 53 4.3 caudalmiddlefrontal 2836 2512 4779 2.225 0.426 0.152 0.041 50 4.3 cuneus 561 639 1818 3.607 0.600 0.235 0.071 15 1.8 entorhinal 5186 4709 11753 2.878 0.594 0.157 0.038 143 8.3 fusiform 7887 6690 16085 2.640 0.483 0.134 0.027 82 9.6 inferiorparietal 4584 3784 10213 2.875 0.576 0.155 0.049 2919 6.5 inferiortemporal 1685 1534 3068 2.305 0.778 0.187 0.057 83 3.5 isthmuscingulate 8613 7315 15744 2.417 0.476 0.144 0.035 213 13.2 lateraloccipital 4436 3674 8973 2.678 0.597 0.156 0.042 86 7.8 lateralorbitofrontal 6522 5617 11153 2.238 0.570 0.153 0.043 151 11.3 lingual 3272 3134 7112 2.591 0.650 0.172 0.045 79 5.9 medialorbitofrontal 5124 4940 13143 3.035 0.558 0.155 0.032 78 6.9 middletemporal 1175 1024 2349 2.753 0.528 0.180 0.046 23 2.8 parahippocampal 2002 1451 3526 2.548 0.474 0.128 0.034 37 2.6 paracentral 2786 2596 6111 2.692 0.486 0.147 0.029 50 3.5 parsopercularis 1494 1408 3297 2.629 0.557 0.157 0.035 26 2.2 parsorbitalis 2497 2191 5078 2.540 0.482 0.146 0.031 41 3.2 parstriangularis 2925 1728 3503 1.944 0.593 0.110 0.029 47 3.1 pericalcarine 4762 4239 9866 2.596 0.463 0.145 0.030 63 6.2 postcentral 1989 1754 3931 2.482 0.777 0.180 0.045 44 4.1 posteriorcingulate 6659 4976 10719 2.307 0.550 0.124 0.027 78 7.2 precentral 5985 4472 10732 2.508 0.539 0.136 0.034 133 8.0 precuneus 1086 909 2401 2.913 0.557 0.153 0.040 37 1.5 rostralanteriorcingulate 10764 9268 21497 2.517 0.492 0.151 0.033 206 14.4 rostralmiddlefrontal 14174 11700 30520 2.848 0.529 0.134 0.032 248 17.9 superiorfrontal 6088 4773 10654 2.410 0.458 0.127 0.026 82 6.6 superiorparietal 5617 4665 12451 2.944 0.528 0.134 0.030 83 6.8 superiortemporal 3634 2838 7373 2.738 0.500 0.136 0.035 62 4.8 supramarginal 503 656 1516 2.831 0.399 0.229 0.051 10 1.1 frontalpole 602 930 2942 4.297 0.531 0.223 0.058 15 1.6 temporalpole 493 455 1085 2.856 0.333 0.142 0.036 6 0.8 transversetemporal 3480 2378 7336 3.086 0.749 0.169 0.055 123 7.6 insula @#@FSTIME 2026:07:08:21:24:20 mris_anatomical_stats N 14 e 16.29 S 0.22 U 16.03 P 99% M 512764 F 0 R 66368 W 0 c 31 w 175 I 0 O 304 L 1.22 1.10 1.15 @#@FSLOADPOST 2026:07:08:21:24:36 mris_anatomical_stats N 14 1.15 1.10 1.15 #----------------------------------------- #@# Parcellation Stats 2 lh Wed Jul 8 09:24:36 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 272816 Total vertex volume 272592 (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) = 1572797 mm^3 (det: 1.238625 ) 1500 1079 3037 2.491 0.481 0.131 0.026 20 1.6 G_and_S_frontomargin 1583 1090 3143 2.354 0.511 0.122 0.024 18 1.5 G_and_S_occipital_inf 1686 1061 3453 2.685 0.614 0.106 0.020 17 1.3 G_and_S_paracentral 1456 970 3493 2.910 0.534 0.124 0.025 17 1.4 G_and_S_subcentral 899 687 2301 2.658 0.444 0.143 0.023 19 0.9 G_and_S_transv_frontopol 2619 1839 5662 2.806 0.448 0.111 0.022 28 2.3 G_and_S_cingul-Ant 1376 911 2647 2.748 0.474 0.103 0.016 10 1.0 G_and_S_cingul-Mid-Ant 1589 1084 3036 2.665 0.434 0.109 0.022 13 1.5 G_and_S_cingul-Mid-Post 743 510 1945 2.886 0.419 0.140 0.029 12 0.9 G_cingul-Post-dorsal 356 238 852 2.692 0.505 0.149 0.046 8 0.5 G_cingul-Post-ventral 2319 1625 3941 2.121 0.544 0.158 0.039 42 3.6 G_cuneus 1413 956 3821 2.982 0.440 0.120 0.024 21 1.3 G_front_inf-Opercular 367 240 949 2.819 0.480 0.134 0.031 6 0.4 G_front_inf-Orbital 1135 736 2982 2.918 0.446 0.120 0.021 14 1.0 G_front_inf-Triangul 4572 3003 11792 2.887 0.500 0.118 0.021 63 3.9 G_front_middle 8094 5433 20685 2.972 0.565 0.120 0.023 92 7.3 G_front_sup 672 495 1589 3.123 0.695 0.130 0.035 9 0.9 G_Ins_lg_and_S_cent_ins 792 553 2647 3.524 0.654 0.122 0.031 11 0.8 G_insular_short 2353 1625 5186 2.488 0.534 0.124 0.025 41 2.1 G_occipital_middle 1595 1070 2660 2.199 0.484 0.135 0.025 20 1.7 G_occipital_sup 2356 1561 5616 2.810 0.504 0.121 0.024 37 2.1 G_oc-temp_lat-fusifor 3828 2705 6822 2.173 0.618 0.140 0.035 60 5.1 G_oc-temp_med-Lingual 1342 913 3630 3.183 0.761 0.115 0.027 13 1.4 G_oc-temp_med-Parahip 2432 1735 6760 2.922 0.713 0.130 0.027 37 2.6 G_orbital 2362 1648 6638 2.982 0.475 0.129 0.024 42 2.2 G_pariet_inf-Angular 2769 1908 7182 2.915 0.524 0.122 0.023 36 2.5 G_pariet_inf-Supramar 2676 1808 6061 2.575 0.481 0.122 0.020 38 2.1 G_parietal_sup 2423 1482 4980 2.543 0.540 0.111 0.021 28 2.1 G_postcentral 2380 1391 6248 3.263 0.554 0.097 0.017 20 1.7 G_precentral 2744 1855 6311 2.614 0.503 0.115 0.024 38 2.3 G_precuneus 1095 828 2831 2.628 0.539 0.126 0.031 19 1.2 G_rectus 812 559 1281 2.458 0.883 0.133 0.048 11 1.3 G_subcallosal 480 285 1107 2.905 0.335 0.104 0.016 5 0.3 G_temp_sup-G_T_transv 2406 1578 7428 3.282 0.587 0.112 0.020 29 2.0 G_temp_sup-Lateral 711 486 2213 3.996 0.445 0.084 0.013 3 0.4 G_temp_sup-Plan_polar 859 566 1849 2.718 0.612 0.091 0.014 6 0.5 G_temp_sup-Plan_tempo 2673 1850 7133 2.887 0.602 0.111 0.022 37 2.3 G_temporal_inf 2462 1713 8230 3.327 0.603 0.114 0.021 33 1.9 G_temporal_middle 264 189 507 2.758 0.740 0.120 0.015 2 0.2 Lat_Fis-ant-Horizont 397 268 614 2.591 0.433 0.090 0.013 2 0.2 Lat_Fis-ant-Vertical 974 631 1247 2.484 0.351 0.099 0.016 5 0.7 Lat_Fis-post 2348 1597 4105 2.190 0.539 0.145 0.032 37 3.1 Pole_occipital 1974 1477 6952 3.297 0.640 0.139 0.031 29 2.3 Pole_temporal 3391 2301 4388 2.157 0.500 0.100 0.017 19 2.5 S_calcarine 2645 1753 3260 2.103 0.532 0.091 0.014 11 1.7 S_central 1261 804 1726 2.404 0.439 0.090 0.011 6 0.7 S_cingul-Marginalis 660 444 975 2.729 0.526 0.094 0.016 3 0.5 S_circular_insula_ant 1734 1087 2663 2.975 0.547 0.070 0.012 5 0.8 S_circular_insula_inf 1827 1179 2502 2.637 0.425 0.099 0.016 8 1.4 S_circular_insula_sup 1082 707 1885 2.645 0.558 0.097 0.012 7 0.6 S_collat_transv_ant 600 410 739 2.036 0.405 0.131 0.023 5 0.6 S_collat_transv_post 2089 1355 3238 2.538 0.402 0.097 0.016 12 1.4 S_front_inf 1761 1177 2496 2.386 0.385 0.111 0.019 12 1.5 S_front_middle 3234 2168 5449 2.577 0.410 0.103 0.019 21 2.5 S_front_sup 325 220 464 2.519 0.355 0.107 0.018 1 0.3 S_interm_prim-Jensen 2970 1932 3974 2.321 0.353 0.095 0.015 15 1.9 S_intrapariet_and_P_trans 1504 983 1798 1.957 0.381 0.104 0.015 10 1.1 S_oc_middle_and_Lunatus 1221 801 1618 2.170 0.386 0.099 0.014 8 0.7 S_oc_sup_and_transversal 800 520 1199 2.311 0.468 0.090 0.011 4 0.4 S_occipital_ant 1245 809 1650 2.322 0.384 0.086 0.011 6 0.6 S_oc-temp_lat 2632 1826 4289 2.552 0.448 0.115 0.022 24 2.5 S_oc-temp_med_and_Lingual 460 307 619 2.355 0.310 0.103 0.017 2 0.3 S_orbital_lateral 746 516 1031 2.332 0.425 0.109 0.018 6 0.5 S_orbital_med-olfact 1589 1092 3071 2.803 0.549 0.114 0.023 13 1.5 S_orbital-H_Shaped 2871 1911 4092 2.291 0.446 0.114 0.018 24 2.2 S_parieto_occipital 1574 994 1495 1.695 0.775 0.102 0.018 20 1.1 S_pericallosal 3666 2400 5095 2.309 0.385 0.100 0.017 21 2.7 S_postcentral 1639 1035 2345 2.577 0.423 0.084 0.010 6 0.7 S_precentral-inf-part 1203 775 1743 2.576 0.401 0.087 0.014 5 0.7 S_precentral-sup-part 716 471 881 2.276 0.386 0.089 0.012 3 0.3 S_suborbital 853 601 1158 2.240 0.360 0.117 0.024 5 0.9 S_subparietal 1905 1245 2932 2.672 0.559 0.093 0.014 9 1.2 S_temporal_inf 6660 4357 11433 2.726 0.494 0.090 0.015 33 4.2 S_temporal_sup 501 331 815 2.764 0.388 0.106 0.013 3 0.3 S_temporal_transverse @#@FSTIME 2026:07:08:21:24:36 mris_anatomical_stats N 14 e 16.38 S 0.21 U 16.09 P 99% M 508948 F 0 R 69536 W 0 c 53 w 287 I 0 O 640 L 1.15 1.10 1.15 @#@FSLOADPOST 2026:07:08:21:24:52 mris_anatomical_stats N 14 1.12 1.09 1.15 #----------------------------------------- #@# Parcellation Stats 2 rh Wed Jul 8 09:24:52 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 274761 Total vertex volume 274550 (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) = 1572797 mm^3 (det: 1.238625 ) 990 741 2076 2.501 0.524 0.128 0.024 13 1.1 G_and_S_frontomargin 1658 1122 3335 2.481 0.504 0.116 0.020 22 1.3 G_and_S_occipital_inf 1094 746 2405 2.560 0.501 0.132 0.026 15 1.1 G_and_S_paracentral 1268 878 2646 2.775 0.393 0.138 0.026 17 1.4 G_and_S_subcentral 1680 1261 4058 2.599 0.498 0.138 0.026 26 1.8 G_and_S_transv_frontopol 3841 2674 8006 2.831 0.560 0.119 0.024 42 4.0 G_and_S_cingul-Ant 1706 1111 3249 2.728 0.476 0.105 0.017 13 1.2 G_and_S_cingul-Mid-Ant 1677 1139 3126 2.694 0.493 0.114 0.022 14 1.5 G_and_S_cingul-Mid-Post 659 445 1856 3.022 0.392 0.147 0.030 17 0.8 G_cingul-Post-dorsal 426 301 974 2.619 0.370 0.137 0.036 8 0.4 G_cingul-Post-ventral 2745 1867 4406 2.122 0.497 0.143 0.034 36 3.7 G_cuneus 1806 1309 4662 2.801 0.513 0.137 0.025 30 1.9 G_front_inf-Opercular 613 412 1537 2.824 0.339 0.121 0.020 10 0.5 G_front_inf-Orbital 878 644 2257 2.772 0.401 0.125 0.027 11 0.9 G_front_inf-Triangul 5484 3784 14478 2.838 0.526 0.128 0.024 83 5.2 G_front_middle 7938 5246 20244 2.950 0.530 0.112 0.021 83 6.5 G_front_sup 739 526 1877 3.393 0.862 0.123 0.036 10 1.0 G_Ins_lg_and_S_cent_ins 654 467 2162 3.594 0.709 0.128 0.035 9 1.0 G_insular_short 2499 1680 6163 2.795 0.453 0.129 0.027 40 2.6 G_occipital_middle 1534 1001 3115 2.433 0.453 0.132 0.026 19 1.7 G_occipital_sup 2535 1691 6719 2.988 0.604 0.118 0.025 36 2.4 G_oc-temp_lat-fusifor 3805 2749 7149 2.247 0.661 0.140 0.035 64 5.4 G_oc-temp_med-Lingual 1062 677 3099 3.159 0.744 0.098 0.024 8 0.8 G_oc-temp_med-Parahip 3077 2214 8058 2.799 0.598 0.136 0.031 58 3.5 G_orbital 2481 1709 6994 2.930 0.492 0.129 0.022 39 2.3 G_pariet_inf-Angular 1728 1173 4470 2.949 0.516 0.115 0.021 20 1.4 G_pariet_inf-Supramar 1678 1111 3424 2.479 0.548 0.107 0.018 17 1.2 G_parietal_sup 1615 1114 4282 2.842 0.457 0.133 0.026 23 1.7 G_postcentral 2571 1616 4933 2.384 0.482 0.103 0.017 27 1.8 G_precentral 2497 1728 5844 2.655 0.498 0.121 0.023 39 2.4 G_precuneus 943 673 2605 2.781 0.647 0.138 0.033 26 1.3 G_rectus 548 371 998 2.573 0.839 0.124 0.043 9 0.8 G_subcallosal 381 234 957 2.966 0.287 0.120 0.020 4 0.3 G_temp_sup-G_T_transv 1831 1239 5645 3.267 0.441 0.119 0.022 25 1.6 G_temp_sup-Lateral 919 589 2255 3.432 0.675 0.073 0.014 3 0.5 G_temp_sup-Plan_polar 668 432 1400 2.703 0.572 0.091 0.013 5 0.4 G_temp_sup-Plan_tempo 2174 1540 6442 3.081 0.596 0.123 0.023 34 2.0 G_temporal_inf 2952 2060 9562 3.263 0.489 0.125 0.022 42 2.7 G_temporal_middle 501 329 613 2.106 0.346 0.080 0.009 1 0.2 Lat_Fis-ant-Horizont 175 131 328 2.674 0.543 0.119 0.015 1 0.2 Lat_Fis-ant-Vertical 1152 754 1583 2.531 0.352 0.093 0.015 5 0.8 Lat_Fis-post 3887 2650 6785 2.223 0.510 0.139 0.030 54 4.5 Pole_occipital 1575 1163 5969 3.537 0.761 0.129 0.029 19 1.9 Pole_temporal 3883 2700 5284 2.178 0.607 0.123 0.025 39 4.1 S_calcarine 2722 1772 3460 2.213 0.323 0.100 0.016 17 2.0 S_central 1224 830 1800 2.412 0.445 0.100 0.016 7 0.9 S_cingul-Marginalis 924 603 1284 2.586 0.574 0.091 0.014 4 0.6 S_circular_insula_ant 1234 781 1772 2.807 0.469 0.073 0.012 4 0.7 S_circular_insula_inf 1598 1035 2460 2.755 0.536 0.101 0.017 8 1.2 S_circular_insula_sup 1077 700 2041 2.853 0.499 0.080 0.011 4 0.4 S_collat_transv_ant 532 371 761 2.488 0.336 0.115 0.021 4 0.4 S_collat_transv_post 2962 1951 4226 2.403 0.354 0.100 0.016 18 2.0 S_front_inf 2667 1805 4316 2.374 0.450 0.113 0.019 25 2.2 S_front_middle 4326 2773 6884 2.653 0.469 0.091 0.015 21 2.9 S_front_sup 341 238 431 2.339 0.256 0.120 0.027 2 0.4 S_interm_prim-Jensen 2365 1528 3255 2.357 0.375 0.103 0.016 15 1.6 S_intrapariet_and_P_trans 978 655 1218 2.246 0.285 0.092 0.014 4 0.6 S_oc_middle_and_Lunatus 1592 1038 2197 2.359 0.352 0.103 0.016 9 1.1 S_oc_sup_and_transversal 765 512 1050 2.443 0.339 0.102 0.016 5 0.5 S_occipital_ant 1325 894 1981 2.619 0.438 0.106 0.019 8 1.1 S_oc-temp_lat 2889 1932 4267 2.519 0.404 0.098 0.016 17 1.9 S_oc-temp_med_and_Lingual 474 352 739 2.320 0.449 0.138 0.021 5 0.5 S_orbital_lateral 946 653 1318 2.223 0.540 0.120 0.026 9 1.0 S_orbital_med-olfact 1685 1145 2941 2.645 0.473 0.111 0.019 16 1.4 S_orbital-H_Shaped 2839 1868 4128 2.371 0.473 0.112 0.018 22 2.1 S_parieto_occipital 1492 950 1244 1.469 0.610 0.110 0.022 21 1.3 S_pericallosal 1485 982 2386 2.369 0.435 0.097 0.015 9 1.0 S_postcentral 1861 1229 3014 2.419 0.588 0.093 0.014 10 1.3 S_precentral-inf-part 1278 847 1439 2.035 0.465 0.096 0.016 6 0.9 S_precentral-sup-part 448 309 649 2.096 0.550 0.096 0.015 2 0.3 S_suborbital 891 611 1425 2.520 0.404 0.110 0.020 5 0.8 S_subparietal 1391 923 1979 2.644 0.412 0.098 0.015 6 0.9 S_temporal_inf 7338 4704 11251 2.598 0.417 0.079 0.012 28 3.8 S_temporal_sup 346 237 600 2.671 0.453 0.117 0.015 3 0.2 S_temporal_transverse @#@FSTIME 2026:07:08:21:24:52 mris_anatomical_stats N 14 e 16.68 S 0.17 U 16.43 P 99% M 512700 F 0 R 63259 W 0 c 84 w 273 I 0 O 632 L 1.12 1.09 1.15 @#@FSLOADPOST 2026:07:08:21:25:09 mris_anatomical_stats N 14 1.09 1.09 1.14 #----------------------------------------- #@# Parcellation Stats 3 lh Wed Jul 8 09:25:09 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 272816 Total vertex volume 272592 (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) = 1572797 mm^3 (det: 1.238625 ) 1881 1215 3573 2.603 0.708 0.111 0.018 20 1.4 caudalanteriorcingulate 3669 2325 7311 2.785 0.470 0.096 0.015 26 2.3 caudalmiddlefrontal 3633 2493 5848 2.188 0.479 0.141 0.029 49 4.5 cuneus 645 441 1794 3.414 0.726 0.117 0.027 5 0.7 entorhinal 4976 3323 10033 2.650 0.538 0.113 0.020 53 4.1 fusiform 6316 4305 12995 2.638 0.524 0.107 0.018 67 4.5 inferiorparietal 5486 3781 13192 2.826 0.651 0.110 0.020 62 4.5 inferiortemporal 1549 1048 2756 2.344 0.784 0.126 0.031 22 1.7 isthmuscingulate 8534 5764 14517 2.211 0.502 0.127 0.025 106 8.7 lateraloccipital 4632 3264 10029 2.756 0.657 0.125 0.029 60 5.0 lateralorbitofrontal 5675 3994 9475 2.203 0.588 0.130 0.030 76 6.8 lingual 2394 1717 4844 2.477 0.595 0.111 0.027 29 2.2 medialorbitofrontal 6686 4489 16028 3.006 0.615 0.101 0.018 54 4.7 middletemporal 1196 793 2578 2.812 0.587 0.100 0.020 10 0.9 parahippocampal 2708 1723 5222 2.739 0.566 0.101 0.017 21 1.9 paracentral 2222 1506 4791 2.774 0.456 0.116 0.021 25 1.9 parsopercularis 1076 712 2190 2.652 0.592 0.116 0.021 11 1.0 parsorbitalis 2358 1536 4730 2.718 0.470 0.109 0.018 20 1.8 parstriangularis 2446 1656 2918 1.966 0.431 0.108 0.021 20 2.1 pericalcarine 7230 4654 12550 2.367 0.594 0.106 0.019 62 5.9 postcentral 2241 1539 4199 2.454 0.710 0.117 0.023 27 2.2 posteriorcingulate 6639 4154 13421 2.863 0.605 0.096 0.016 45 4.4 precentral 5883 3976 10674 2.455 0.494 0.112 0.021 59 4.8 precuneus 2155 1462 4567 2.827 0.560 0.111 0.022 25 1.9 rostralanteriorcingulate 6218 4202 13125 2.656 0.501 0.118 0.023 72 5.5 rostralmiddlefrontal 12915 8827 28757 2.781 0.559 0.117 0.021 132 11.5 superiorfrontal 6413 4214 11368 2.430 0.443 0.112 0.018 63 4.8 superiorparietal 8398 5543 19889 3.068 0.648 0.095 0.017 63 5.9 superiortemporal 5311 3570 11251 2.740 0.524 0.114 0.021 53 4.6 supramarginal 664 424 1263 2.687 0.344 0.118 0.018 7 0.5 transversetemporal 3101 2100 6704 3.134 0.642 0.106 0.023 27 2.7 insula @#@FSTIME 2026:07:08:21:25:09 mris_anatomical_stats N 14 e 15.92 S 0.22 U 15.66 P 99% M 509016 F 0 R 68800 W 0 c 27 w 157 I 0 O 272 L 1.09 1.09 1.14 @#@FSLOADPOST 2026:07:08:21:25:25 mris_anatomical_stats N 14 1.13 1.10 1.15 #----------------------------------------- #@# Parcellation Stats 3 rh Wed Jul 8 09:25:25 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 sub-20_ses-0 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 274761 Total vertex volume 274550 (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) = 1572797 mm^3 (det: 1.238625 ) 1121 706 1883 2.253 0.814 0.107 0.015 12 0.7 caudalanteriorcingulate 4556 2984 9396 2.751 0.550 0.100 0.017 31 3.3 caudalmiddlefrontal 3479 2315 5710 2.220 0.434 0.135 0.028 42 3.9 cuneus 492 327 1630 3.561 0.610 0.099 0.024 2 0.5 entorhinal 4817 3220 10399 2.828 0.560 0.106 0.021 47 3.9 fusiform 7806 5185 15873 2.639 0.484 0.106 0.018 78 6.1 inferiorparietal 4977 3425 11918 2.947 0.621 0.116 0.021 56 4.3 inferiortemporal 1653 1141 3016 2.328 0.767 0.125 0.028 26 1.8 isthmuscingulate 8686 5812 15950 2.409 0.480 0.123 0.022 100 7.8 lateraloccipital 4784 3373 10227 2.710 0.570 0.129 0.030 73 5.8 lateralorbitofrontal 6483 4641 11052 2.240 0.567 0.135 0.032 94 8.5 lingual 2528 1785 5281 2.496 0.696 0.129 0.032 47 3.4 medialorbitofrontal 6463 4356 15323 2.971 0.546 0.103 0.018 56 4.8 middletemporal 1255 806 2486 2.742 0.543 0.090 0.017 9 0.7 parahippocampal 2098 1373 3726 2.548 0.473 0.112 0.018 18 1.6 paracentral 3089 2186 6689 2.685 0.469 0.118 0.019 36 2.7 parsopercularis 1473 965 2895 2.530 0.539 0.109 0.016 15 1.0 parsorbitalis 2364 1644 4488 2.477 0.484 0.112 0.019 24 1.9 parstriangularis 2819 1954 3413 1.965 0.586 0.121 0.026 24 2.9 pericalcarine 5265 3619 10941 2.584 0.482 0.118 0.021 54 4.8 postcentral 2075 1449 4026 2.477 0.774 0.125 0.025 26 2.1 posteriorcingulate 6562 4218 10715 2.331 0.556 0.105 0.017 57 4.9 precentral 6035 4063 11043 2.521 0.540 0.111 0.021 64 5.0 precuneus 1417 1003 3320 2.947 0.600 0.128 0.028 19 1.8 rostralanteriorcingulate 7538 5206 14593 2.512 0.469 0.122 0.022 92 6.8 rostralmiddlefrontal 17820 11962 38837 2.786 0.546 0.111 0.020 170 14.4 superiorfrontal 4712 3076 8259 2.420 0.463 0.109 0.019 43 3.5 superiorparietal 7130 4712 16840 3.045 0.634 0.095 0.017 53 4.9 superiortemporal 3433 2301 6738 2.713 0.506 0.113 0.021 31 3.0 supramarginal 501 319 1093 2.847 0.339 0.118 0.020 4 0.4 transversetemporal 3091 2102 6791 3.181 0.695 0.104 0.021 24 2.6 insula @#@FSTIME 2026:07:08:21:25:25 mris_anatomical_stats N 14 e 16.23 S 0.18 U 16.01 P 99% M 512696 F 0 R 62703 W 0 c 24 w 169 I 0 O 272 L 1.13 1.10 1.15 @#@FSLOADPOST 2026:07:08:21:25:41 mris_anatomical_stats N 14 1.10 1.09 1.14 #-------------------------------------------- #@# ASeg Stats Wed Jul 8 09:25:41 PM CEST 2026 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0 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 /software/freesurfer/7.4.1/debian-bookworm-amd64/ASegStatsLUT.txt --subject sub-20_ses-0 setting seed for random number genererator to 1234 7.4.1 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 /software/freesurfer/7.4.1/debian-bookworm-amd64/ASegStatsLUT.txt --subject sub-20_ses-0 sysname Linux hostname comps10h04 machine x86_64 user asmolova whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1572797 mm^3 (det: 1.238625 ) Computing euler number orig.nofix lheno = -20, rheno = -18 orig.nofix lhholes = 11, rhholes = 10 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2026:07:08:21:25:41 mri_segstats N 32 e 164.55 S 0.23 U 164.29 P 99% M 291636 F 0 R 47101 W 0 c 481 w 71 I 0 O 24 L 1.10 1.09 1.14 @#@FSLOADPOST 2026:07:08:21:28:26 mri_segstats N 32 1.00 1.05 1.11 /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed Jul 8 09:28:26 PM CEST 2026 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4344 mri_label2label: Done @#@FSTIME 2026:07:08:21:28:26 mri_label2label N 12 e 4.16 S 0.24 U 3.89 P 99% M 573992 F 0 R 74513 W 0 c 17 w 75 I 16184 O 288 L 1.00 1.05 1.11 @#@FSLOADPOST 2026:07:08:21:28:30 mri_label2label N 12 1.00 1.05 1.11 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 483 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8392 mri_label2label: Done @#@FSTIME 2026:07:08:21:28:30 mri_label2label N 12 e 4.90 S 0.23 U 4.66 P 99% M 574216 F 0 R 74596 W 0 c 10 w 29 I 632 O 560 L 1.00 1.05 1.11 @#@FSLOADPOST 2026:07:08:21:28:35 mri_label2label N 12 1.00 1.04 1.11 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4093 mri_label2label: Done @#@FSTIME 2026:07:08:21:28:35 mri_label2label N 12 e 4.25 S 0.24 U 4.00 P 99% M 573948 F 0 R 75553 W 0 c 11 w 29 I 320 O 216 L 1.00 1.04 1.11 @#@FSLOADPOST 2026:07:08:21:28:39 mri_label2label N 12 1.00 1.04 1.11 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 154 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6137 mri_label2label: Done @#@FSTIME 2026:07:08:21:28:39 mri_label2label N 12 e 4.40 S 0.23 U 4.16 P 99% M 574128 F 0 R 74548 W 0 c 12 w 31 I 472 O 352 L 1.00 1.04 1.11 @#@FSLOADPOST 2026:07:08:21:28:44 mri_label2label N 12 1.00 1.04 1.11 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5837 mri_label2label: Done @#@FSTIME 2026:07:08:21:28:44 mri_label2label N 12 e 4.34 S 0.23 U 4.10 P 99% M 574068 F 0 R 74539 W 0 c 11 w 31 I 456 O 328 L 1.00 1.04 1.11 @#@FSLOADPOST 2026:07:08:21:28:48 mri_label2label N 12 1.00 1.04 1.11 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4111 mri_label2label: Done @#@FSTIME 2026:07:08:21:28:48 mri_label2label N 12 e 4.18 S 0.23 U 3.93 P 99% M 573948 F 0 R 75026 W 0 c 13 w 29 I 320 O 216 L 1.00 1.04 1.11 @#@FSLOADPOST 2026:07:08:21:28:53 mri_label2label N 12 1.00 1.04 1.11 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 595 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14184 mri_label2label: Done @#@FSTIME 2026:07:08:21:28:53 mri_label2label N 12 e 7.34 S 0.24 U 7.09 P 99% M 574684 F 0 R 75259 W 0 c 16 w 41 I 1056 O 888 L 1.00 1.04 1.11 @#@FSLOADPOST 2026:07:08:21:29:00 mri_label2label N 12 1.00 1.04 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4321 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:00 mri_label2label N 12 e 4.11 S 0.24 U 3.85 P 99% M 574008 F 0 R 74519 W 0 c 7 w 33 I 328 O 280 L 1.00 1.04 1.10 @#@FSLOADPOST 2026:07:08:21:29:04 mri_label2label N 12 1.00 1.04 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 374 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3796 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:04 mri_label2label N 12 e 3.99 S 0.26 U 3.73 P 99% M 573896 F 0 R 75788 W 0 c 6 w 30 I 272 O 288 L 1.00 1.04 1.10 @#@FSLOADPOST 2026:07:08:21:29:08 mri_label2label N 12 1.00 1.04 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 1731 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6372 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:08 mri_label2label N 12 e 4.31 S 0.24 U 4.06 P 99% M 574032 F 0 R 75043 W 0 c 9 w 37 I 376 O 544 L 1.00 1.04 1.10 @#@FSLOADPOST 2026:07:08:21:29:12 mri_label2label N 12 1.00 1.04 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 3564 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11678 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:12 mri_label2label N 12 e 5.53 S 0.24 U 5.28 P 99% M 574320 F 0 R 74141 W 0 c 17 w 43 I 664 O 992 L 1.00 1.04 1.10 @#@FSLOADPOST 2026:07:08:21:29:18 mri_label2label N 12 1.08 1.05 1.11 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 411 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2429 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:18 mri_label2label N 12 e 3.89 S 0.28 U 3.61 P 99% M 573860 F 0 R 74963 W 0 c 11 w 28 I 168 O 208 L 1.08 1.05 1.11 @#@FSLOADPOST 2026:07:08:21:29:22 mri_label2label N 12 1.07 1.05 1.11 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 91 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1381 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:22 mri_label2label N 12 e 3.83 S 0.25 U 3.58 P 99% M 573688 F 0 R 75412 W 0 c 8 w 27 I 120 O 96 L 1.07 1.05 1.11 @#@FSLOADPOST 2026:07:08:21:29:26 mri_label2label N 12 1.07 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1300 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:26 mri_label2label N 12 e 3.84 S 0.24 U 3.58 P 99% M 573764 F 0 R 73370 W 0 c 9 w 45 I 112 O 104 L 1.07 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:29:30 mri_label2label N 12 1.07 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 646 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:30 mri_label2label N 12 e 3.75 S 0.25 U 3.49 P 99% M 573748 F 0 R 74132 W 0 c 12 w 31 I 40 O 64 L 1.07 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:29:34 mri_label2label N 12 1.06 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 308 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 1011 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:34 mri_label2label N 12 e 3.80 S 0.23 U 3.56 P 99% M 573712 F 0 R 73867 W 0 c 8 w 27 I 72 O 88 L 1.06 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:29:37 mri_label2label N 12 1.06 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 2096 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:37 mri_label2label N 12 e 3.86 S 0.26 U 3.60 P 99% M 573836 F 0 R 75447 W 0 c 10 w 29 I 176 O 160 L 1.06 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:29:41 mri_label2label N 12 1.05 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 723 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2824 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:41 mri_label2label N 12 e 3.90 S 0.23 U 3.66 P 99% M 573848 F 0 R 75242 W 0 c 9 w 31 I 200 O 248 L 1.05 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:29:45 mri_label2label N 12 1.05 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 1363 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 5240 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:45 mri_label2label N 12 e 4.18 S 0.27 U 3.90 P 99% M 574004 F 0 R 73502 W 0 c 8 w 34 I 360 O 440 L 1.05 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:29:49 mri_label2label N 12 1.05 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 1396 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 4315 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:50 mri_label2label N 12 e 4.00 S 0.22 U 3.76 P 99% M 573960 F 0 R 74512 W 0 c 9 w 33 I 272 O 368 L 1.05 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:29:54 mri_label2label N 12 1.04 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 765 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 2051 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:54 mri_label2label N 12 e 3.81 S 0.28 U 3.53 P 99% M 573816 F 0 R 74397 W 0 c 11 w 28 I 128 O 184 L 1.04 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:29:57 mri_label2label N 12 1.04 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 568 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1574 mri_label2label: Done @#@FSTIME 2026:07:08:21:29:57 mri_label2label N 12 e 3.83 S 0.23 U 3.59 P 99% M 573748 F 0 R 75673 W 0 c 12 w 28 I 96 O 152 L 1.04 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:30:01 mri_label2label N 12 1.04 1.05 1.10 mris_label2annot --s sub-20_ses-0 --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 comps10h04 machine x86_64 user asmolova subject sub-20_ses-0 hemi lh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig Index Offset 0 0 reading lh.FG1.mpm.vpnl.label 1 1376057 FG1 1 reading lh.FG2.mpm.vpnl.label 2 16711935 FG2 2 reading lh.FG3.mpm.vpnl.label 3 16711680 FG3 3 reading lh.FG4.mpm.vpnl.label 4 1705837 FG4 4 reading lh.hOc1.mpm.vpnl.label 5 25600 hOc1 5 reading lh.hOc2.mpm.vpnl.label 6 255 hOc2 6 reading lh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v 7 reading lh.hOc4v.mpm.vpnl.label 8 65535 hOc4v Mapping unhit to unknown Found 124720 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.mpm.vpnl.annot @#@FSTIME 2026:07:08:21:30:01 mris_label2annot N 26 e 0.70 S 0.09 U 0.59 P 97% M 166076 F 5 R 21075 W 0 c 3 w 102 I 680 O 2248 L 1.04 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:30:02 mris_label2annot N 26 1.04 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1062 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:02 mri_label2label N 12 e 3.73 S 0.21 U 3.51 P 99% M 573756 F 0 R 74384 W 0 c 12 w 34 I 96 O 72 L 1.04 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:30:06 mri_label2label N 12 1.03 1.04 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2284 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:06 mri_label2label N 12 e 3.86 S 0.20 U 3.65 P 99% M 573828 F 0 R 73137 W 0 c 11 w 28 I 192 O 176 L 1.03 1.04 1.10 @#@FSLOADPOST 2026:07:08:21:30:10 mri_label2label N 12 1.03 1.04 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 5 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1509 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:10 mri_label2label N 12 e 3.80 S 0.26 U 3.53 P 99% M 573784 F 0 R 73374 W 0 c 9 w 27 I 136 O 88 L 1.03 1.04 1.10 @#@FSLOADPOST 2026:07:08:21:30:14 mri_label2label N 12 1.11 1.06 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2008 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:14 mri_label2label N 12 e 4.02 S 0.24 U 3.77 P 99% M 573820 F 0 R 74743 W 0 c 13 w 27 I 184 O 112 L 1.11 1.06 1.10 @#@FSLOADPOST 2026:07:08:21:30:18 mri_label2label N 12 1.10 1.06 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2336 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:18 mri_label2label N 12 e 3.89 S 0.23 U 3.65 P 99% M 573816 F 0 R 73429 W 0 c 20 w 27 I 208 O 144 L 1.10 1.06 1.10 @#@FSLOADPOST 2026:07:08:21:30:22 mri_label2label N 12 1.09 1.06 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1574 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:22 mri_label2label N 12 e 3.88 S 0.21 U 3.65 P 99% M 573816 F 0 R 75448 W 0 c 7 w 28 I 144 O 88 L 1.09 1.06 1.10 @#@FSLOADPOST 2026:07:08:21:30:26 mri_label2label N 12 1.08 1.06 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7173 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:26 mri_label2label N 12 e 4.58 S 0.29 U 4.28 P 99% M 574112 F 0 R 74554 W 0 c 13 w 41 I 616 O 416 L 1.08 1.06 1.10 @#@FSLOADPOST 2026:07:08:21:30:30 mri_label2label N 12 1.08 1.06 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1976 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:30 mri_label2label N 12 e 3.89 S 0.27 U 3.62 P 99% M 573820 F 0 R 74441 W 0 c 5 w 32 I 168 O 136 L 1.08 1.06 1.10 @#@FSLOADPOST 2026:07:08:21:30:34 mri_label2label N 12 1.08 1.06 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1290 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:34 mri_label2label N 12 e 3.76 S 0.24 U 3.51 P 99% M 573768 F 0 R 74389 W 0 c 8 w 27 I 104 O 104 L 1.08 1.06 1.10 @#@FSLOADPOST 2026:07:08:21:30:38 mri_label2label N 12 1.07 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 1251 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4656 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:38 mri_label2label N 12 e 4.04 S 0.24 U 3.79 P 99% M 573952 F 0 R 73499 W 0 c 12 w 31 I 304 O 400 L 1.07 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:30:42 mri_label2label N 12 1.07 1.05 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 1473 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4807 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:42 mri_label2label N 12 e 4.17 S 0.24 U 3.92 P 99% M 573988 F 0 R 74519 W 0 c 8 w 34 I 296 O 416 L 1.07 1.05 1.10 @#@FSLOADPOST 2026:07:08:21:30:46 mri_label2label N 12 1.06 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 603 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:46 mri_label2label N 12 e 3.71 S 0.25 U 3.45 P 99% M 573728 F 0 R 73355 W 0 c 10 w 26 I 48 O 56 L 1.06 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:30:50 mri_label2label N 12 1.06 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 497 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:50 mri_label2label N 12 e 3.70 S 0.21 U 3.48 P 99% M 573672 F 0 R 73351 W 0 c 9 w 26 I 48 O 48 L 1.06 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:30:54 mri_label2label N 12 1.14 1.07 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/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 143635 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 502 mri_label2label: Done @#@FSTIME 2026:07:08:21:30:54 mri_label2label N 12 e 3.66 S 0.27 U 3.38 P 99% M 573676 F 0 R 74887 W 0 c 11 w 26 I 48 O 40 L 1.14 1.07 1.10 @#@FSLOADPOST 2026:07:08:21:30:57 mri_label2label N 12 1.12 1.07 1.10 mris_label2annot --s sub-20_ses-0 --hemi lh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --hemi lh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 comps10h04 machine x86_64 user asmolova subject sub-20_ses-0 hemi lh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig Index Offset 0 0 reading lh.BA1_exvivo.label 1 1530880 BA1_exvivo 1 reading lh.BA2_exvivo.label 2 16749699 BA2_exvivo 2 reading lh.BA3a_exvivo.label 3 16711680 BA3a_exvivo 3 reading lh.BA3b_exvivo.label 4 3368703 BA3b_exvivo 4 reading lh.BA4a_exvivo.label 5 1376196 BA4a_exvivo 5 reading lh.BA4p_exvivo.label 6 13382655 BA4p_exvivo 6 reading lh.BA6_exvivo.label 7 10036737 BA6_exvivo 7 reading lh.BA44_exvivo.label 8 2490521 BA44_exvivo 8 reading lh.BA45_exvivo.label 9 39283 BA45_exvivo 9 reading lh.V1_exvivo.label 10 3993 V1_exvivo 10 reading lh.V2_exvivo.label 11 8508928 V2_exvivo 11 reading lh.MT_exvivo.label 12 10027163 MT_exvivo 12 reading lh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo 13 reading lh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 100337 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.BA_exvivo.annot @#@FSTIME 2026:07:08:21:30:57 mris_label2annot N 38 e 0.73 S 0.08 U 0.63 P 97% M 166712 F 0 R 21283 W 0 c 2 w 147 I 8 O 2248 L 1.12 1.07 1.10 @#@FSLOADPOST 2026:07:08:21:30:58 mris_label2annot N 38 1.12 1.07 1.10 mris_label2annot --s sub-20_ses-0 --hemi lh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --hemi lh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 comps10h04 machine x86_64 user asmolova subject sub-20_ses-0 hemi lh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.orig Index Offset 0 0 reading lh.BA1_exvivo.thresh.label 1 1530880 BA1_exvivo 1 reading lh.BA2_exvivo.thresh.label 2 16749699 BA2_exvivo 2 reading lh.BA3a_exvivo.thresh.label 3 16711680 BA3a_exvivo 3 reading lh.BA3b_exvivo.thresh.label 4 3368703 BA3b_exvivo 4 reading lh.BA4a_exvivo.thresh.label 5 1376196 BA4a_exvivo 5 reading lh.BA4p_exvivo.thresh.label 6 13382655 BA4p_exvivo 6 reading lh.BA6_exvivo.thresh.label 7 10036737 BA6_exvivo 7 reading lh.BA44_exvivo.thresh.label 8 2490521 BA44_exvivo 8 reading lh.BA45_exvivo.thresh.label 9 39283 BA45_exvivo 9 reading lh.V1_exvivo.thresh.label 10 3993 V1_exvivo 10 reading lh.V2_exvivo.thresh.label 11 8508928 V2_exvivo 11 reading lh.MT_exvivo.thresh.label 12 10027163 MT_exvivo 12 reading lh.perirhinal_exvivo.thresh.label 13 16422433 perirhinal_exvivo 13 reading lh.entorhinal_exvivo.thresh.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 118884 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2026:07:08:21:30:58 mris_label2annot N 38 e 0.70 S 0.08 U 0.60 P 97% M 166404 F 0 R 21193 W 0 c 4 w 145 I 0 O 2256 L 1.12 1.07 1.10 @#@FSLOADPOST 2026:07:08:21:30:59 mris_label2annot N 38 1.12 1.07 1.10 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-20_ses-0 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 272816 Total vertex volume 272592 (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) = 1572797 mm^3 (det: 1.238625 ) 1115 660 2428 2.650 0.565 0.109 0.025 14 1.0 BA1_exvivo 4583 2989 7474 2.417 0.459 0.107 0.018 35 3.7 BA2_exvivo 923 609 933 1.913 0.372 0.120 0.020 7 0.7 BA3a_exvivo 2210 1422 3736 2.233 0.662 0.105 0.019 18 1.9 BA3b_exvivo 1503 931 3539 3.158 0.494 0.093 0.015 9 1.0 BA4a_exvivo 1112 693 1905 2.826 0.537 0.076 0.013 4 0.6 BA4p_exvivo 9182 5922 20769 2.902 0.573 0.103 0.017 72 6.8 BA6_exvivo 2284 1521 4925 2.800 0.494 0.108 0.019 23 1.6 BA44_exvivo 2869 1879 6281 2.742 0.470 0.109 0.019 28 2.2 BA45_exvivo 4238 2933 5670 1.912 0.470 0.117 0.027 46 4.5 V1_exvivo 9685 6684 16017 2.213 0.525 0.141 0.031 128 12.3 V2_exvivo 2221 1514 3774 2.313 0.469 0.110 0.018 23 1.6 MT_exvivo 758 550 1677 2.920 0.594 0.125 0.024 8 0.8 perirhinal_exvivo 615 418 1976 3.308 1.053 0.095 0.023 4 0.4 entorhinal_exvivo @#@FSTIME 2026:07:08:21:30:59 mris_anatomical_stats N 12 e 4.12 S 0.25 U 3.85 P 99% M 504240 F 0 R 70336 W 0 c 7 w 114 I 2248 O 136 L 1.12 1.07 1.10 @#@FSLOADPOST 2026:07:08:21:31:03 mris_anatomical_stats N 12 1.11 1.07 1.10 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-20_ses-0 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 272816 Total vertex volume 272592 (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) = 1572797 mm^3 (det: 1.238625 ) 744 428 1693 2.687 0.534 0.123 0.027 11 0.8 BA1_exvivo 1840 1192 3213 2.443 0.454 0.103 0.016 15 1.3 BA2_exvivo 749 492 690 1.887 0.341 0.124 0.022 5 0.6 BA3a_exvivo 1254 817 1608 1.845 0.416 0.080 0.013 6 0.7 BA3b_exvivo 1390 871 3196 3.173 0.479 0.084 0.012 7 0.8 BA4a_exvivo 930 579 1466 2.694 0.526 0.080 0.014 4 0.5 BA4p_exvivo 4743 3015 11137 2.976 0.593 0.105 0.018 38 3.6 BA6_exvivo 1446 980 3042 2.693 0.474 0.113 0.020 17 1.1 BA44_exvivo 1160 762 3012 2.882 0.494 0.115 0.020 13 1.0 BA45_exvivo 4513 3131 6211 1.931 0.469 0.116 0.026 48 4.9 V1_exvivo 4688 3336 7349 2.094 0.528 0.151 0.035 71 6.5 V2_exvivo 553 370 1061 2.493 0.546 0.117 0.018 7 0.4 MT_exvivo 343 238 599 2.845 0.601 0.124 0.024 3 0.4 perirhinal_exvivo 398 266 1327 3.666 0.681 0.086 0.018 2 0.3 entorhinal_exvivo @#@FSTIME 2026:07:08:21:31:03 mris_anatomical_stats N 12 e 4.06 S 0.23 U 3.81 P 99% M 504056 F 0 R 69216 W 0 c 13 w 106 I 2248 O 144 L 1.11 1.07 1.10 @#@FSLOADPOST 2026:07:08:21:31:07 mris_anatomical_stats N 12 1.11 1.06 1.10 #-------------------------------------------- #@# BA_exvivo Labels rh Wed Jul 8 09:31:07 PM CEST 2026 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 3982 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:07 mri_label2label N 12 e 4.18 S 0.24 U 3.93 P 99% M 576436 F 0 R 72025 W 0 c 9 w 41 I 16160 O 184 L 1.11 1.06 1.10 @#@FSLOADPOST 2026:07:08:21:31:11 mri_label2label N 12 1.10 1.06 1.10 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6704 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:12 mri_label2label N 12 e 4.76 S 0.22 U 4.53 P 99% M 576624 F 0 R 70045 W 0 c 12 w 31 I 520 O 288 L 1.10 1.06 1.10 @#@FSLOADPOST 2026:07:08:21:31:16 mri_label2label N 12 1.09 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4006 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:16 mri_label2label N 12 e 4.19 S 0.21 U 3.96 P 99% M 576412 F 0 R 69471 W 0 c 8 w 29 I 312 O 208 L 1.09 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:31:21 mri_label2label N 12 1.08 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4553 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:21 mri_label2label N 12 e 4.18 S 0.26 U 3.91 P 99% M 576460 F 0 R 71010 W 0 c 12 w 29 I 352 O 232 L 1.08 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:31:25 mri_label2label N 12 1.08 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5795 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:25 mri_label2label N 12 e 4.41 S 0.20 U 4.20 P 99% M 576560 F 0 R 71030 W 0 c 15 w 36 I 440 O 296 L 1.08 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:31:29 mri_label2label N 12 1.07 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4488 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:29 mri_label2label N 12 e 4.16 S 0.17 U 3.98 P 99% M 576500 F 0 R 69995 W 0 c 10 w 33 I 344 O 232 L 1.07 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:31:33 mri_label2label N 12 1.07 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 1006 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13262 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:33 mri_label2label N 12 e 6.73 S 0.22 U 6.49 P 99% M 577056 F 0 R 71225 W 0 c 17 w 45 I 936 O 840 L 1.07 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:31:40 mri_label2label N 12 1.06 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 994 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7906 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:40 mri_label2label N 12 e 5.02 S 0.21 U 4.80 P 99% M 576712 F 0 R 71080 W 0 c 12 w 36 I 528 O 552 L 1.06 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:31:45 mri_label2label N 12 1.05 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 1291 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6646 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:45 mri_label2label N 12 e 4.36 S 0.22 U 4.13 P 99% M 576568 F 0 R 71039 W 0 c 11 w 27 I 416 O 520 L 1.05 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:31:50 mri_label2label N 12 1.05 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 2339 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 7066 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:50 mri_label2label N 12 e 4.41 S 0.21 U 4.19 P 99% M 576572 F 0 R 70015 W 0 c 10 w 36 I 376 O 592 L 1.05 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:31:54 mri_label2label N 12 1.05 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 4125 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 12141 mri_label2label: Done @#@FSTIME 2026:07:08:21:31:54 mri_label2label N 12 e 5.47 S 0.25 U 5.21 P 99% M 576856 F 0 R 71150 W 0 c 12 w 48 I 640 O 1016 L 1.05 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:32:00 mri_label2label N 12 1.04 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 581 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2513 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:00 mri_label2label N 12 e 3.99 S 0.25 U 3.74 P 99% M 576340 F 0 R 71741 W 0 c 8 w 29 I 160 O 216 L 1.04 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:32:04 mri_label2label N 12 1.04 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1070 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:04 mri_label2label N 12 e 3.81 S 0.23 U 3.57 P 99% M 576152 F 0 R 75354 W 0 c 4 w 28 I 96 O 72 L 1.04 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:32:08 mri_label2label N 12 1.04 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-20_ses-0 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 778 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:08 mri_label2label N 12 e 3.74 S 0.24 U 3.49 P 99% M 576120 F 0 R 70865 W 0 c 10 w 29 I 72 O 64 L 1.04 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:32:11 mri_label2label N 12 1.11 1.07 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 394 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 935 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:11 mri_label2label N 12 e 3.80 S 0.24 U 3.55 P 99% M 576232 F 0 R 71380 W 0 c 6 w 27 I 56 O 88 L 1.11 1.07 1.09 @#@FSLOADPOST 2026:07:08:21:32:15 mri_label2label N 12 1.10 1.07 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 490 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 1211 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:15 mri_label2label N 12 e 3.84 S 0.28 U 3.55 P 99% M 576208 F 0 R 71385 W 0 c 7 w 27 I 72 O 120 L 1.10 1.07 1.09 @#@FSLOADPOST 2026:07:08:21:32:19 mri_label2label N 12 1.10 1.07 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 442 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1965 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:19 mri_label2label N 12 e 3.83 S 0.23 U 3.59 P 99% M 576224 F 0 R 75878 W 0 c 12 w 29 I 144 O 168 L 1.10 1.07 1.09 @#@FSLOADPOST 2026:07:08:21:32:23 mri_label2label N 12 1.10 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 519 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 2105 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:23 mri_label2label N 12 e 3.94 S 0.22 U 3.72 P 99% M 576264 F 0 R 71479 W 0 c 5 w 30 I 152 O 192 L 1.10 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:27 mri_label2label N 12 1.09 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 1822 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 5489 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:27 mri_label2label N 12 e 4.21 S 0.27 U 3.93 P 99% M 576468 F 0 R 71524 W 0 c 11 w 34 I 328 O 456 L 1.09 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:31 mri_label2label N 12 1.08 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 1471 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 4190 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:31 mri_label2label N 12 e 4.14 S 0.24 U 3.89 P 99% M 576380 F 0 R 75213 W 0 c 8 w 36 I 248 O 352 L 1.08 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:35 mri_label2label N 12 1.07 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 823 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 2051 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:35 mri_label2label N 12 e 3.93 S 0.22 U 3.70 P 99% M 576292 F 0 R 71725 W 0 c 13 w 32 I 112 O 176 L 1.07 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:39 mri_label2label N 12 1.07 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject sub-20_ses-0 --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 698 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1723 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:39 mri_label2label N 12 e 3.91 S 0.21 U 3.68 P 99% M 576240 F 0 R 74659 W 0 c 15 w 28 I 96 O 160 L 1.07 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:43 mri_label2label N 12 1.07 1.06 1.09 mris_label2annot --s sub-20_ses-0 --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 comps10h04 machine x86_64 user asmolova subject sub-20_ses-0 hemi rh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig Index Offset 0 0 reading rh.FG1.mpm.vpnl.label 1 1376057 FG1 1 reading rh.FG2.mpm.vpnl.label 2 16711935 FG2 2 reading rh.FG3.mpm.vpnl.label 3 16711680 FG3 3 reading rh.FG4.mpm.vpnl.label 4 1705837 FG4 4 reading rh.hOc1.mpm.vpnl.label 5 25600 hOc1 5 reading rh.hOc2.mpm.vpnl.label 6 255 hOc2 6 reading rh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v 7 reading rh.hOc4v.mpm.vpnl.label 8 65535 hOc4v Mapping unhit to unknown Found 125584 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.mpm.vpnl.annot @#@FSTIME 2026:07:08:21:32:43 mris_label2annot N 26 e 0.71 S 0.06 U 0.63 P 97% M 167356 F 0 R 21275 W 0 c 2 w 114 I 0 O 2264 L 1.07 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:44 mris_label2annot N 26 1.07 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 2 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 878 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:44 mri_label2label N 12 e 3.80 S 0.24 U 3.55 P 99% M 576240 F 0 R 75869 W 0 c 10 w 25 I 80 O 56 L 1.07 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:48 mri_label2label N 12 1.06 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2692 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:48 mri_label2label N 12 e 3.96 S 0.24 U 3.71 P 99% M 576328 F 0 R 69956 W 0 c 13 w 28 I 240 O 112 L 1.06 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:52 mri_label2label N 12 1.06 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1702 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:52 mri_label2label N 12 e 3.87 S 0.18 U 3.68 P 99% M 576228 F 0 R 71930 W 0 c 13 w 28 I 152 O 96 L 1.06 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:32:56 mri_label2label N 12 1.05 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2208 mri_label2label: Done @#@FSTIME 2026:07:08:21:32:56 mri_label2label N 12 e 3.95 S 0.26 U 3.68 P 99% M 576336 F 0 R 74685 W 0 c 10 w 27 I 192 O 120 L 1.05 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:33:00 mri_label2label N 12 1.05 1.06 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 6 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1394 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:00 mri_label2label N 12 e 3.86 S 0.25 U 3.60 P 99% M 576216 F 0 R 75375 W 0 c 11 w 28 I 120 O 80 L 1.05 1.06 1.09 @#@FSLOADPOST 2026:07:08:21:33:04 mri_label2label N 12 1.05 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1492 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:04 mri_label2label N 12 e 3.82 S 0.20 U 3.61 P 99% M 576296 F 0 R 71388 W 0 c 7 w 27 I 136 O 80 L 1.05 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:33:08 mri_label2label N 12 1.04 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 366 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7325 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:08 mri_label2label N 12 e 4.69 S 0.21 U 4.47 P 99% M 576708 F 0 R 72095 W 0 c 11 w 41 I 592 O 448 L 1.04 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:33:12 mri_label2label N 12 1.04 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 331 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1343 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:12 mri_label2label N 12 e 3.81 S 0.23 U 3.57 P 99% M 576152 F 0 R 71897 W 0 c 10 w 28 I 88 O 120 L 1.04 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:33:16 mri_label2label N 12 1.04 1.05 1.09 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1293 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:16 mri_label2label N 12 e 3.83 S 0.25 U 3.57 P 99% M 576232 F 0 R 70874 W 0 c 9 w 27 I 104 O 96 L 1.04 1.05 1.09 @#@FSLOADPOST 2026:07:08:21:33:20 mri_label2label N 12 1.03 1.05 1.08 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 1594 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4826 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:20 mri_label2label N 12 e 4.22 S 0.23 U 3.98 P 99% M 576460 F 0 R 74721 W 0 c 10 w 39 I 280 O 400 L 1.03 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:24 mri_label2label N 12 1.03 1.05 1.08 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 1947 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5384 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:24 mri_label2label N 12 e 4.26 S 0.22 U 4.03 P 99% M 576472 F 0 R 72031 W 0 c 9 w 27 I 296 O 448 L 1.03 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:29 mri_label2label N 12 1.03 1.05 1.08 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 339 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:29 mri_label2label N 12 e 3.75 S 0.25 U 3.49 P 99% M 576152 F 0 R 71115 W 0 c 7 w 26 I 24 O 32 L 1.03 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:33 mri_label2label N 12 1.03 1.05 1.08 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 709 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:33 mri_label2label N 12 e 3.79 S 0.24 U 3.54 P 99% M 576192 F 0 R 70861 W 0 c 9 w 30 I 64 O 48 L 1.03 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:36 mri_label2label N 12 1.02 1.05 1.08 mri_label2label --srcsubject fsaverage --srclabel /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-20_ses-0 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-20_ses-0 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 FREESURFER_HOME /software/freesurfer/7.4.1/debian-bookworm-amd64 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white Reading target registration /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 144774 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 302 mri_label2label: Done @#@FSTIME 2026:07:08:21:33:36 mri_label2label N 12 e 3.68 S 0.22 U 3.45 P 99% M 576096 F 0 R 71370 W 0 c 9 w 30 I 32 O 24 L 1.02 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:40 mri_label2label N 12 1.02 1.05 1.08 mris_label2annot --s sub-20_ses-0 --hemi rh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --hemi rh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 comps10h04 machine x86_64 user asmolova subject sub-20_ses-0 hemi rh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig Index Offset 0 0 reading rh.BA1_exvivo.label 1 1530880 BA1_exvivo 1 reading rh.BA2_exvivo.label 2 16749699 BA2_exvivo 2 reading rh.BA3a_exvivo.label 3 16711680 BA3a_exvivo 3 reading rh.BA3b_exvivo.label 4 3368703 BA3b_exvivo 4 reading rh.BA4a_exvivo.label 5 1376196 BA4a_exvivo 5 reading rh.BA4p_exvivo.label 6 13382655 BA4p_exvivo 6 reading rh.BA6_exvivo.label 7 10036737 BA6_exvivo 7 reading rh.BA44_exvivo.label 8 2490521 BA44_exvivo 8 reading rh.BA45_exvivo.label 9 39283 BA45_exvivo 9 reading rh.V1_exvivo.label 10 3993 V1_exvivo 10 reading rh.V2_exvivo.label 11 8508928 V2_exvivo 11 reading rh.MT_exvivo.label 12 10027163 MT_exvivo 12 reading rh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo 13 reading rh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 100785 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.BA_exvivo.annot @#@FSTIME 2026:07:08:21:33:40 mris_label2annot N 38 e 0.75 S 0.05 U 0.67 P 97% M 167948 F 0 R 22155 W 0 c 2 w 160 I 0 O 2272 L 1.02 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:41 mris_label2annot N 38 1.02 1.05 1.08 mris_label2annot --s sub-20_ses-0 --hemi rh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label cmdline mris_label2annot --s sub-20_ses-0 --hemi rh --ctab /software/freesurfer/7.4.1/debian-bookworm-amd64/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 comps10h04 machine x86_64 user asmolova subject sub-20_ses-0 hemi rh SUBJECTS_DIR /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0 ColorTable /software/freesurfer/7.4.1/debian-bookworm-amd64/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.orig Index Offset 0 0 reading rh.BA1_exvivo.thresh.label 1 1530880 BA1_exvivo 1 reading rh.BA2_exvivo.thresh.label 2 16749699 BA2_exvivo 2 reading rh.BA3a_exvivo.thresh.label 3 16711680 BA3a_exvivo 3 reading rh.BA3b_exvivo.thresh.label 4 3368703 BA3b_exvivo 4 reading rh.BA4a_exvivo.thresh.label 5 1376196 BA4a_exvivo 5 reading rh.BA4p_exvivo.thresh.label 6 13382655 BA4p_exvivo 6 reading rh.BA6_exvivo.thresh.label 7 10036737 BA6_exvivo 7 reading rh.BA44_exvivo.thresh.label 8 2490521 BA44_exvivo 8 reading rh.BA45_exvivo.thresh.label 9 39283 BA45_exvivo 9 reading rh.V1_exvivo.thresh.label 10 3993 V1_exvivo 10 reading rh.V2_exvivo.thresh.label 11 8508928 V2_exvivo 11 reading rh.MT_exvivo.thresh.label 12 10027163 MT_exvivo 12 reading rh.perirhinal_exvivo.thresh.label 13 16422433 perirhinal_exvivo 13 reading rh.entorhinal_exvivo.thresh.label 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 120724 unhit vertices Writing annot to /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2026:07:08:21:33:41 mris_label2annot N 38 e 0.71 S 0.06 U 0.62 P 97% M 167680 F 0 R 21971 W 0 c 4 w 154 I 0 O 2264 L 1.02 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:42 mris_label2annot N 38 1.02 1.05 1.08 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-20_ses-0 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 274761 Total vertex volume 274550 (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) = 1572797 mm^3 (det: 1.238625 ) 654 447 1742 2.838 0.423 0.155 0.033 12 0.8 BA1_exvivo 2128 1446 4576 2.584 0.582 0.107 0.018 18 1.6 BA2_exvivo 1009 655 1130 2.183 0.301 0.129 0.027 9 1.1 BA3a_exvivo 1633 1108 2952 2.496 0.372 0.111 0.018 15 1.3 BA3b_exvivo 1282 842 2484 2.503 0.443 0.095 0.013 9 0.8 BA4a_exvivo 1079 703 1503 2.161 0.392 0.098 0.015 8 0.8 BA4p_exvivo 8781 5608 17626 2.665 0.644 0.104 0.018 74 6.6 BA6_exvivo 4285 2873 8285 2.637 0.509 0.106 0.018 36 3.2 BA44_exvivo 4845 3373 9864 2.545 0.486 0.118 0.020 57 4.1 BA45_exvivo 4925 3502 7137 2.015 0.559 0.136 0.031 57 6.5 V1_exvivo 10066 6943 16783 2.220 0.524 0.135 0.029 133 11.7 V2_exvivo 2397 1593 4440 2.544 0.361 0.108 0.018 25 1.8 MT_exvivo 379 256 868 3.248 0.488 0.088 0.017 1 0.3 perirhinal_exvivo 526 352 1889 3.555 0.732 0.094 0.023 3 0.5 entorhinal_exvivo @#@FSTIME 2026:07:08:21:33:42 mris_anatomical_stats N 12 e 4.10 S 0.18 U 3.89 P 99% M 507904 F 0 R 62471 W 0 c 11 w 115 I 2264 O 136 L 1.02 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:46 mris_anatomical_stats N 12 1.02 1.05 1.08 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-20_ses-0 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/mri/wm.mgz... reading input surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white... reading input pial surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.pial... reading input white surface /data/pt_02904/Diffusion/surface_segmentation/Nastya/sub-20/ses-0/sub-20_ses-0/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 274761 Total vertex volume 274550 (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) = 1572797 mm^3 (det: 1.238625 ) 416 286 1120 2.864 0.417 0.143 0.028 7 0.4 BA1_exvivo 1251 864 2858 2.642 0.509 0.108 0.019 11 1.0 BA2_exvivo 916 582 886 2.121 0.264 0.126 0.026 6 1.0 BA3a_exvivo 1327 889 2210 2.438 0.340 0.100 0.015 10 0.9 BA3b_exvivo 779 506 1594 2.522 0.430 0.116 0.018 9 0.6 BA4a_exvivo 912 608 1213 2.112 0.317 0.086 0.013 4 0.6 BA4p_exvivo 5174 3262 10423 2.586 0.670 0.100 0.018 43 3.7 BA6_exvivo 1292 907 3069 2.736 0.541 0.128 0.022 17 1.2 BA44_exvivo 1053 815 2685 2.704 0.453 0.132 0.027 16 1.1 BA45_exvivo 4736 3343 6750 2.013 0.564 0.132 0.030 52 5.8 V1_exvivo 5295 3707 8199 2.083 0.558 0.143 0.033 71 7.1 V2_exvivo 326 207 735 2.751 0.329 0.120 0.019 3 0.2 MT_exvivo 35 22 57 3.296 0.274 0.077 0.020 0 0.0 perirhinal_exvivo 538 357 1693 3.535 0.580 0.094 0.020 2 0.5 entorhinal_exvivo @#@FSTIME 2026:07:08:21:33:46 mris_anatomical_stats N 12 e 4.22 S 0.20 U 3.99 P 99% M 507864 F 0 R 69816 W 0 c 8 w 107 I 2264 O 136 L 1.02 1.05 1.08 @#@FSLOADPOST 2026:07:08:21:33:50 mris_anatomical_stats N 12 1.02 1.04 1.08 Started at Wed Jul 8 04:56:56 PM CEST 2026 Ended at Wed Jul 8 09:33:50 PM CEST 2026 #@#%# recon-all-run-time-hours 4.615 recon-all -s sub-20_ses-0 finished without error at Wed Jul 8 09:33:50 PM CEST 2026