Thu Feb 12 13:36:08 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs /usr/local/freesurfer/stable7.4.1/bin/recon-all -subjid PBRHOPE_HOPE089_PETMR -i /autofs/space/hope_002/users/PBR28_HOPE/data/PBRHOPE_HOPE089_PETMR/mprage/mprage.nii.gz subjid PBRHOPE_HOPE089_PETMR setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Actual FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/7.4.1 build-stamp.txt: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 131072 memorylocked unlimited maxproc 1539492 maxlocks unlimited maxsignal 1539492 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 375G 3.5G 254G 395M 117G 369G Swap: 31G 267M 31G SLURM_JOB_ID 7799285 ######################################## program versions used 7.4.1 (freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 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: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.4.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.4.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:08-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 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: 2026/02/12-18:36:09-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 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 /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR mri_convert /autofs/space/hope_002/users/PBR28_HOPE/data/PBRHOPE_HOPE089_PETMR/mprage/mprage.nii.gz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig/001.mgz mri_convert /autofs/space/hope_002/users/PBR28_HOPE/data/PBRHOPE_HOPE089_PETMR/mprage/mprage.nii.gz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig/001.mgz reading from /autofs/space/hope_002/users/PBR28_HOPE/data/PBRHOPE_HOPE089_PETMR/mprage/mprage.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig/001.mgz... Started at Thu Feb 12 13:36:08 EST 2026 Ended at Thu Feb 12 13:36:13 EST 2026 #@#%# recon-all-run-time-hours 0.001 recon-all -s PBRHOPE_HOPE089_PETMR finished without error at Thu Feb 12 13:36:13 EST 2026 #New# invocation of recon-all Thu Feb 12 13:37:14 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs /usr/local/freesurfer/stable7.4.1/bin/recon-all -subjid PBRHOPE_HOPE089_PETMR -autorecon-all subjid PBRHOPE_HOPE089_PETMR setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Actual FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/7.4.1 build-stamp.txt: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 131072 memorylocked unlimited maxproc 1539492 maxlocks unlimited maxsignal 1539492 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 375G 4.0G 253G 399M 118G 369G Swap: 31G 267M 31G SLURM_JOB_ID 7799285 ######################################## program versions used 7.4.1 (freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460) 7.4.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 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: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.4.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.4.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 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: 2026/02/12-18:37:14-GMT BuildTime: Jun 13 2023 22:52:23 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 User: ek657 Machine: r440-05.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 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 /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Thu Feb 12 13:37:15 EST 2026 Found 1 runs /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig/001.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz mri_info /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz type: MGH dimensions: 280 x 280 x 208 voxel sizes: 1.000000, 1.000000, 1.000000 type: SHORT (4) fov: 280.000 dof: 1 xstart: -140.0, xend: 140.0 ystart: -140.0, yend: 140.0 zstart: -104.0, zend: 104.0 TR: 2530.00 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 = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = -2.7991 : x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a = 23.1965 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -7.9313 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: -0.0000 -0.0000 -1.0000 101.2009 -1.0000 -0.0000 -0.0000 163.1965 0.0000 -1.0000 0.0000 132.0687 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -0.0000 -1.0000 -0.0000 163.1965 -0.0000 -0.0000 -1.0000 132.0687 -1.0000 -0.0000 -0.0000 101.2009 -0.0000 -0.0000 -0.0000 1.0000 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR mri_convert /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz --conform mri_convert /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz --conform reading from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 1133 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/transforms/talairach.xfm /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz INFO: extension is mgz mri_info /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz orig.mgz ======================================== Volume information for /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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: 2530.00 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 = -2.7991 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 23.1965 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -7.9313 talairach xfm : /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 125.2009 0.0000 0.0000 1.0000 -104.8035 0.0000 -1.0000 0.0000 120.0687 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 125.2009 -0.0000 -0.0000 -1.0000 120.0687 -0.0000 1.0000 -0.0000 104.8035 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Thu Feb 12 13:37:24 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri /usr/local/freesurfer/stable7.4.1/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 r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux Thu Feb 12 13:37:24 EST 2026 tmpdir is ./tmp.mri_nu_correct.mni.2665312 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2665312/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.2665312/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2665312/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2665312/nu0.mgz... TR=2530.00, 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... Thu Feb 12 13:40:41 EST 2026 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Thu Feb 12 13:40:41 EST 2026 Ended at Thu Feb 12 13:41:08 EST 2026 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/stable7.4.1/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: /usr/local/freesurfer/stable7.4.1/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 1.04137 0.12726 0.18593 6.56313; -0.27641 0.73519 0.61645 3.48359; -0.06689 -0.57171 0.83267 -1.03439; 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 Thu Feb 12 13:41:11 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.1090, pval=0.0051 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable7.4.1/bin/extract_talairach_avi_QA.awk /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/transforms/talairach_avi.log TalAviQA: 0.97373 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Feb 12 13:41:11 EST 2026 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri /usr/local/freesurfer/stable7.4.1/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 r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux Thu Feb 12 13:41:11 EST 2026 tmpdir is ./tmp.mri_nu_correct.mni.2746325 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2746325/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.2746325/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2746325/ones.mgz 7.4.1 cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.2746325/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.2746325/ones.mgz sysname Linux hostname r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 input ./tmp.mri_nu_correct.mni.2746325/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2746325/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.2746325/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2746325/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2746325/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2746325/input.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2746325/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2746325/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2746325/input.mean.dat sysname Linux hostname r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2746325/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.2746325/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2746325/ones.mgz --i ./tmp.mri_nu_correct.mni.2746325/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2746325/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2746325/output.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2746325/ones.mgz --i ./tmp.mri_nu_correct.mni.2746325/nu0.mgz --sum ./tmp.mri_nu_correct.mni.2746325/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2746325/output.mean.dat sysname Linux hostname r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2746325/ones.mgz Loading ./tmp.mri_nu_correct.mni.2746325/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.2746325/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2746325/nu0.mgz ./tmp.mri_nu_correct.mni.2746325/nu0.mgz mul 1.79530494091521928781 Saving result to './tmp.mri_nu_correct.mni.2746325/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2746325/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.2746325/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.2746325/nu0.mgz... TR=2530.00, 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 5 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 11, i2 = 55 #mri_make_uchar# mapping 28 142 to 3 110 : b -24.3125 m 0.948088 : thresh 25.6437 maxsat 294.606 : nzero 11553710 nsat 1419 Thu Feb 12 13:44:52 EST 2026 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Feb 12 13:44:53 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 1.04137 0.12726 0.18593 6.56313; -0.27641 0.73519 0.61645 3.48359; -0.06689 -0.57171 0.83267 -1.03439; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 103 gm peak at 56 (56), valley at 45 (45) csf peak at 29, setting threshold to 47 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 53 (53), valley at 42 (42) csf peak at 27, setting threshold to 44 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 50 seconds. #-------------------------------------------- #@# Skull Stripping Thu Feb 12 13:46:43 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/stable7.4.1/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 '/usr/local/freesurfer/stable7.4.1/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=11.0 skull bounding box = (40, 45, 0) --> (207, 255, 230) finding center of left hemi white matter using (96, 115, 115) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (75,89,87) --> (116, 140,143) to find MRI wm before smoothing, mri peak at 102 robust fit to distribution - 102 +- 16.5 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.619 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.585915 @ (-10.526, -10.526, 10.526) max log p = -4.560454 @ (5.263, 5.263, -5.263) max log p = -4.497965 @ (2.632, -7.895, 2.632) max log p = -4.478612 @ (1.316, 3.947, 3.947) max log p = -4.464519 @ (4.605, -1.974, -0.658) max log p = -4.450288 @ (0.329, 0.987, -0.329) max log p = -4.450288 @ (0.000, 0.000, 0.000) max log p = -4.450288 @ (0.000, 0.000, 0.000) Found translation: (3.6, -10.2, 10.9): log p = -4.450 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.234, old_max_log_p =-4.450 (thresh=-4.4) 1.04098 0.21155 -0.05638 -29.48533; -0.13827 0.84767 0.62761 -19.48657; 0.18351 -0.65605 0.92651 86.41391; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 30 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.217, old_max_log_p =-4.234 (thresh=-4.2) 1.04098 0.21155 -0.05638 -29.48533; -0.14864 0.91125 0.67468 -31.60633; 0.16975 -0.60685 0.85702 88.27042; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 31 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.210, old_max_log_p =-4.217 (thresh=-4.2) 0.96290 0.19568 -0.05216 -17.89125; -0.15979 0.97959 0.72528 -44.63507; 0.16975 -0.60685 0.85702 88.27042; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 27 seconds. **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.210, old_max_log_p =-4.210 (thresh=-4.2) 0.96290 0.19568 -0.05216 -17.89125; -0.15979 0.97959 0.72528 -44.63507; 0.16975 -0.60685 0.85702 88.27042; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 31 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.165, old_max_log_p =-4.210 (thresh=-4.2) 0.99846 0.18686 -0.10429 -17.85277; -0.13411 0.98408 0.59825 -35.87558; 0.18608 -0.50224 0.92090 67.34605; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 28 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.165, old_max_log_p =-4.165 (thresh=-4.2) 0.99846 0.18686 -0.10429 -17.85277; -0.13411 0.98408 0.59825 -35.87558; 0.18608 -0.50224 0.92090 67.34605; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 29 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.142, old_max_log_p =-4.165 (thresh=-4.2) 0.99890 0.21071 -0.06957 -24.12632; -0.16537 0.97474 0.60906 -30.25908; 0.17048 -0.51269 0.91650 71.69075; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 25 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.134, old_max_log_p =-4.142 (thresh=-4.1) 0.99900 0.21001 -0.04952 -25.51140; -0.17356 0.97305 0.60949 -29.02734; 0.15411 -0.51606 0.91751 74.13767; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 24 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.132, old_max_log_p =-4.134 (thresh=-4.1) 0.99900 0.21001 -0.04952 -25.51140; -0.17376 0.97419 0.61020 -29.22742; 0.15465 -0.51788 0.92074 74.00739; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99900 0.21001 -0.04952 -25.51140; -0.17376 0.97419 0.61020 -29.22742; 0.15465 -0.51788 0.92074 74.00739; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 0.99900 0.21001 -0.04952 -25.51140; -0.17376 0.97419 0.61020 -29.22742; 0.15465 -0.51788 0.92074 74.00739; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.99900 0.21001 -0.04952 -25.51140; -0.17376 0.97419 0.61020 -29.22742; 0.15465 -0.51788 0.92074 74.00739; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.132 (old=-4.619) transform before final EM align: 0.99900 0.21001 -0.04952 -25.51140; -0.17376 0.97419 0.61020 -29.22742; 0.15465 -0.51788 0.92074 74.00739; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99900 0.21001 -0.04952 -25.51140; -0.17376 0.97419 0.61020 -29.22742; 0.15465 -0.51788 0.92074 74.00739; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 0.99900 0.21001 -0.04952 -25.51140; -0.17376 0.97419 0.61020 -29.22742; 0.15465 -0.51788 0.92074 74.00739; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 4.5 tol 0.000000 final transform: 0.99900 0.21001 -0.04952 -25.51140; -0.17376 0.97419 0.61020 -29.22742; 0.15465 -0.51788 0.92074 74.00739; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 805128 FSRUNTIME@ mri_em_register 0.2383 hours 1 threads registration took 14 minutes and 18 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/stable7.4.1/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=130 y=119 z=88 r=96 first estimation of the main basin volume: 3729171 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=109, y=112, z=47, Imax=255 CSF=14, 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=8342043226 voxels, voxel volume =1.000 = 8342043226 mmm3 = 8342043.136 cm3 done. PostAnalyze...Basin Prior 87 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=127, z=78, r=9854 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 44718 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 3150 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=37 , nb = 3168 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 19368 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 18312 OTHER CSF_MIN=0, CSF_intensity=28, CSF_MAX=52 , nb = 720 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 5, 35, 73 after analyzing : 4, 25, 35, 37 RIGHT_CER before analyzing : 5, 6, 33, 75 after analyzing : 5, 24, 33, 36 LEFT_CER before analyzing : 37, 34, 32, 82 after analyzing : 24, 34, 34, 46 RIGHT_BRAIN before analyzing : 4, 5, 33, 73 after analyzing : 4, 23, 33, 35 LEFT_BRAIN before analyzing : 4, 5, 36, 73 after analyzing : 4, 25, 36, 37 OTHER before analyzing : 52, 68, 76, 87 after analyzing : 52, 73, 76, 76 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...84 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.013 curvature mean = 71.040, std = 9.191 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 8.67, sigma = 20.47 after rotation: sse = 8.67, sigma = 20.47 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 15.20, its var is 29.77 before Erosion-Dilatation 16.78% 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...60 iterations mri_strip_skull: done peeling brain Brain Size = 1811601 voxels, voxel volume = 1.000 mm3 = 1811601 mmm3 = 1811.601 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Feb 12 14:01:21 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable7.4.1/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 '/usr/local/freesurfer/stable7.4.1/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=12.0 skull bounding box = (58, 59, 0) --> (189, 207, 142) finding center of left hemi white matter using (102, 108, 71) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (86,90,54) --> (118, 126,88) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 103 +- 6.2 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 initial log_p = -4.558 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.416187 @ (-10.526, -10.526, 10.526) max log p = -4.267419 @ (5.263, 5.263, 5.263) max log p = -4.235594 @ (2.632, 2.632, 2.632) max log p = -4.234207 @ (1.316, -1.316, -1.316) max log p = -4.186426 @ (-0.658, -3.289, 3.289) max log p = -4.186426 @ (0.000, 0.000, 0.000) max log p = -4.186426 @ (0.000, 0.000, 0.000) max log p = -4.186426 @ (0.000, 0.000, 0.000) Found translation: (-2.0, -7.2, 20.4): log p = -4.186 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.938, old_max_log_p =-4.186 (thresh=-4.2) 0.98325 0.17584 -0.04791 -17.99250; -0.14148 0.93190 0.51689 -24.35067; 0.12608 -0.46647 0.87551 73.76452; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 17 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.938, old_max_log_p =-3.938 (thresh=-3.9) 0.98325 0.17584 -0.04791 -17.99250; -0.14148 0.93190 0.51689 -24.35067; 0.12608 -0.46647 0.87551 73.76452; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 19 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.855, old_max_log_p =-3.938 (thresh=-3.9) 1.03722 0.20325 -0.00426 -32.00436; -0.15848 0.87348 0.56841 -18.89647; 0.10832 -0.53819 0.85735 90.33927; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 17 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.846, old_max_log_p =-3.855 (thresh=-3.9) 1.01375 0.21661 -0.03171 -28.45910; -0.15551 0.85711 0.55776 -16.30546; 0.14487 -0.54121 0.87282 84.77129; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 18 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.846, old_max_log_p =-3.846 (thresh=-3.8) 1.01375 0.21661 -0.03171 -28.45910; -0.15551 0.85711 0.55776 -16.30546; 0.14487 -0.54121 0.87282 84.77129; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 18 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.818, old_max_log_p =-3.846 (thresh=-3.8) 1.01932 0.19094 -0.00872 -26.81169; -0.14145 0.83681 0.59360 -18.42675; 0.11755 -0.58127 0.84785 96.84753; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 15 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.795, old_max_log_p =-3.818 (thresh=-3.8) 1.01366 0.21006 -0.03609 -26.34258; -0.13902 0.82428 0.60526 -19.00078; 0.15313 -0.58831 0.83729 94.07925; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 16 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.793, old_max_log_p =-3.795 (thresh=-3.8) 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 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 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.793 (old=-4.558) transform before final EM align: 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 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 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.2 tol 0.000000 final transform: 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 792572 FSRUNTIME@ mri_em_register 0.1855 hours 1 threads registration took 11 minutes and 8 seconds. #-------------------------------------- #@# CA Normalize Thu Feb 12 14:12:28 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable7.4.1/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 '/usr/local/freesurfer/stable7.4.1/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=12.0 skull bounding box = (58, 59, 0) --> (189, 207, 142) finding center of left hemi white matter using (102, 108, 71) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (86,90,54) --> (118, 126,88) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 103 +- 6.2 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 using 246437 sample points... INFO: compute sample coordinates transform 1.01247 0.20981 -0.03605 -26.16311; -0.13885 0.82332 0.60455 -18.83872; 0.15313 -0.58831 0.83729 94.07925; 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 (113, 63, 13) --> (192, 197, 163) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 15 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (62, 61, 17) --> (135, 182, 163) Right_Cerebral_White_Matter: limiting intensities to 112.0 --> 132.0 18 of 29 (62.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (117, 158, 59) --> (163, 207, 107) Left_Cerebellum_White_Matter: limiting intensities to 122.0 --> 132.0 6 of 7 (85.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (73, 157, 56) --> (120, 198, 109) Right_Cerebellum_White_Matter: limiting intensities to 114.0 --> 132.0 3 of 11 (27.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (104, 138, 79) --> (140, 201, 116) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 11 (0.0%) samples deleted using 73 total control points for intensity normalization... bias field = 0.872 +- 0.107 0 of 46 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (113, 63, 13) --> (192, 197, 163) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 128 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (62, 61, 17) --> (135, 182, 163) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 76 (1.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (117, 158, 59) --> (163, 207, 107) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 16 of 36 (44.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (73, 157, 56) --> (120, 198, 109) Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0 23 of 50 (46.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (104, 138, 79) --> (140, 201, 116) Brain_Stem: limiting intensities to 89.0 --> 132.0 35 of 61 (57.4%) samples deleted using 351 total control points for intensity normalization... bias field = 1.006 +- 0.091 0 of 276 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (113, 63, 13) --> (192, 197, 163) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 178 (1.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (62, 61, 17) --> (135, 182, 163) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 240 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (117, 158, 59) --> (163, 207, 107) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 21 of 44 (47.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (73, 157, 56) --> (120, 198, 109) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 26 of 37 (70.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (104, 138, 79) --> (140, 201, 116) Brain_Stem: limiting intensities to 88.0 --> 132.0 103 of 134 (76.9%) samples deleted using 633 total control points for intensity normalization... bias field = 0.998 +- 0.080 0 of 474 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 16 seconds. #-------------------------------------- #@# CA Reg Thu Feb 12 14:13:45 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable7.4.1/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 '/usr/local/freesurfer/stable7.4.1/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 1.03785 #GCAMreg# pass 0 level1 5 level2 1 tsec 473.526 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 0.763438 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 0.782832 #GCAMreg# pass 0 level1 4 level2 1 tsec 66.275 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 0.779647 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 0.818625 #GCAMreg# pass 0 level1 3 level2 1 tsec 58.393 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 0.81762 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 0.913914 #GCAMreg# pass 0 level1 2 level2 1 tsec 55.451 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 0.902317 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 1.02126 #GCAMreg# pass 0 level1 1 level2 1 tsec 171.128 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 0.971686 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 0.928511 #GCAMreg# pass 0 level1 0 level2 1 tsec 47.32 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 0.921345 GCAMregister done in 20.3638 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.08369 (17) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (1417 voxels, overlap=0.535) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (1417 voxels, peak = 12), gca=12.1 gca peak = 0.17690 (16) mri peak = 0.15653 (17) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (1589 voxels, overlap=0.734) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (1589 voxels, peak = 16), gca=16.2 gca peak = 0.28275 (96) mri peak = 0.07638 (91) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (580 voxels, overlap=0.991) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (580 voxels, peak = 92), gca=91.7 gca peak = 0.18948 (93) mri peak = 0.05361 (98) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (456 voxels, overlap=0.918) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (456 voxels, peak = 94), gca=94.4 gca peak = 0.20755 (55) mri peak = 0.06490 (66) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (463 voxels, overlap=0.241) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (463 voxels, peak = 65), gca=65.2 gca peak = 0.31831 (58) mri peak = 0.06036 (68) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (455 voxels, overlap=0.192) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (455 voxels, peak = 68), gca=67.6 gca peak = 0.11957 (102) mri peak = 0.05499 (104) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (49735 voxels, overlap=0.827) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (49735 voxels, peak = 107), gca=106.6 gca peak = 0.11429 (102) mri peak = 0.06321 (104) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (49889 voxels, overlap=0.838) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (49889 voxels, peak = 106), gca=105.6 gca peak = 0.14521 (59) mri peak = 0.03266 (70) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (10163 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (10163 voxels, peak = 75), gca=75.2 gca peak = 0.14336 (58) mri peak = 0.03397 (82) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (9694 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (9694 voxels, peak = 81), gca=81.5 gca peak = 0.13305 (70) mri peak = 0.07781 (88) Right_Caudate (50): linear fit = 1.27 x + 0.0 (456 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.27 x + 0.0 (456 voxels, peak = 89), gca=89.2 gca peak = 0.15761 (71) mri peak = 0.06478 (77) Left_Caudate (11): linear fit = 1.11 x + 0.0 (318 voxels, overlap=0.645) Left_Caudate (11): linear fit = 1.11 x + 0.0 (318 voxels, peak = 78), gca=78.5 gca peak = 0.13537 (57) mri peak = 0.02424 (72) Left_Cerebellum_Cortex (8): linear fit = 1.35 x + 0.0 (11798 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.35 x + 0.0 (11798 voxels, peak = 77), gca=76.7 gca peak = 0.13487 (56) mri peak = 0.03046 (72) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (13391 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (13391 voxels, peak = 73), gca=72.5 gca peak = 0.19040 (84) mri peak = 0.03917 (83) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5515 voxels, overlap=0.980) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5515 voxels, peak = 88), gca=87.8 gca peak = 0.18871 (83) mri peak = 0.05011 (82) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5588 voxels, overlap=0.979) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5588 voxels, peak = 83), gca=82.6 gca peak = 0.24248 (57) mri peak = 0.08935 (72) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (218 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (218 voxels, peak = 73), gca=72.7 gca peak = 0.35833 (56) mri peak = 0.09193 (73) Right_Amygdala (54): linear fit = 1.22 x + 0.0 (205 voxels, overlap=0.080) Right_Amygdala (54): linear fit = 1.22 x + 0.0 (205 voxels, peak = 68), gca=68.0 gca peak = 0.12897 (85) mri peak = 0.07449 (89) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4108 voxels, overlap=0.960) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (4108 voxels, peak = 85), gca=84.6 gca peak = 0.13127 (83) mri peak = 0.07623 (83) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (3571 voxels, overlap=0.906) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (3571 voxels, peak = 84), gca=84.2 gca peak = 0.12974 (78) mri peak = 0.07595 (83) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1238 voxels, overlap=0.770) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1238 voxels, peak = 85), gca=84.6 gca peak = 0.17796 (79) mri peak = 0.08793 (81) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1614 voxels, overlap=0.841) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1614 voxels, peak = 83), gca=82.6 gca peak = 0.10999 (80) mri peak = 0.11312 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9010 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9010 voxels, peak = 84), gca=84.4 gca peak = 0.13215 (88) mri peak = 0.07988 (85) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (859 voxels, overlap=0.728) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (859 voxels, peak = 91), gca=91.1 gca peak = 0.11941 (89) mri peak = 0.09848 (84) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (858 voxels, overlap=0.847) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (858 voxels, peak = 88), gca=87.7 gca peak = 0.20775 (25) mri peak = 0.14894 (18) gca peak = 0.13297 (21) mri peak = 0.11181 (21) Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (302 voxels, overlap=0.855) Fourth_Ventricle (15): linear fit = 1.26 x + 0.0 (302 voxels, peak = 27), gca=26.6 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 1.25 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 3.59253 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 0.968154 #GCAMreg# pass 0 level1 5 level2 1 tsec 1253.39 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 0.708126 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 0.710433 #GCAMreg# pass 0 level1 4 level2 1 tsec 901.094 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 0.634943 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 0.614671 #GCAMreg# pass 0 level1 3 level2 1 tsec 977.133 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.569286 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 0.574496 #GCAMreg# pass 0 level1 2 level2 1 tsec 50.052 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 0.574496 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 0.632863 #GCAMreg# pass 0 level1 1 level2 1 tsec 48.691 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 0.632207 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 0.542455 #GCAMreg# pass 0 level1 0 level2 1 tsec 257.429 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 0.512255 GCAMregister done in 84.0913 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 0.503176 #GCAMreg# pass 0 level1 5 level2 1 tsec 58.61 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 0.503176 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 0.501909 #GCAMreg# pass 0 level1 4 level2 1 tsec 57.895 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 0.501886 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 0.497014 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 6 after 11 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 18 after 15 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 19 after 5 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 16 after 12 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 152.305 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 0.491139 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 4 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 1 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 3 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.476629 #GCAMreg# pass 0 level1 2 level2 1 tsec 52.962 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 0.476629 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 0.484993 #GCAMreg# pass 0 level1 1 level2 1 tsec 53.839 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 0.484204 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 0.477124 iter 0, gcam->neg = 1038 after 14 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 64.12 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 0.436192 label assignment complete, 0 changed (0.00%) GCAMregister done in 17.0877 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 0.41832 #GCAMreg# pass 0 level1 5 level2 1 tsec 28.304 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 0.41832 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 0.418528 #GCAMreg# pass 0 level1 4 level2 1 tsec 28.192 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 0.418528 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 0.419244 #GCAMreg# pass 0 level1 3 level2 1 tsec 52.958 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 0.419068 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 4 after 12 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 0.400 #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 0.41536 #GCAMreg# pass 0 level1 2 level2 1 tsec 49.365 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 0.415351 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 11 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_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 0.421351 #GCAMreg# pass 0 level1 1 level2 1 tsec 50.302 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 0.421351 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 0.410107 iter 0, gcam->neg = 621 after 14 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 61.387 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 0.398733 GCAMregister done in 12.29 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4864 tmin = 15.9629 Calls to gcamLabelEnergy 4307 tmin = 1.6685 Calls to gcamJacobianEnergy 4864 tmin = 18.6312 Calls to gcamSmoothnessEnergy 4864 tmin = 15.4436 Calls to gcamLogLikelihoodTerm 648 tmin = 4.54398 Calls to gcamLabelTerm 602 tmin = 8.3012 Calls to gcamJacobianTerm 648 tmin = 12.4312 Calls to gcamSmoothnessTerm 648 tmin = 3.65052 Calls to gcamComputeGradient 648 tmin = 54.1154 Calls to gcamComputeMetricProperties 6693 tmin = 18.7292 mri_ca_register took 2 hours, 17 minutes and 39 seconds. #VMPC# mri_ca_register VmPeak 2066964 FSRUNTIME@ mri_ca_register 2.2941 hours 1 threads #-------------------------------------- #@# SubCort Seg Thu Feb 12 16:31:24 EST 2026 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable7.4.1/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname r440-05.nmr.mgh.harvard.edu machine x86_64 setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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 7.25 Atlas used for the 3D morph was /usr/local/freesurfer/stable7.4.1/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 = 0.11298 (15) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (11170 voxels, overlap=0.573) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (11170 voxels, peak = 13), gca=13.1 gca peak = 0.20380 (13) mri peak = 0.13746 (17) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (9617 voxels, overlap=0.575) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (9617 voxels, peak = 14), gca=14.5 gca peak = 0.26283 (96) mri peak = 0.08260 (90) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (340 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (340 voxels, peak = 92), gca=91.7 gca peak = 0.15814 (97) mri peak = 0.09818 (91) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (352 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (352 voxels, peak = 97), gca=96.5 gca peak = 0.27624 (56) mri peak = 0.09078 (71) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (682 voxels, overlap=0.297) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (682 voxels, peak = 67), gca=67.5 gca peak = 0.28723 (59) mri peak = 0.07265 (64) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (667 voxels, overlap=0.554) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (667 voxels, peak = 67), gca=67.0 gca peak = 0.07623 (103) mri peak = 0.05759 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (30252 voxels, overlap=0.713) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (30252 voxels, peak = 107), gca=106.6 gca peak = 0.07837 (105) mri peak = 0.06900 (104) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (39614 voxels, overlap=0.759) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (39614 voxels, peak = 108), gca=107.6 gca peak = 0.10165 (58) mri peak = 0.04363 (76) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (10427 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (10427 voxels, peak = 78), gca=78.0 gca peak = 0.11113 (58) mri peak = 0.03817 (76) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (11858 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (11858 voxels, peak = 78), gca=78.0 gca peak = 0.27796 (67) mri peak = 0.07796 (84) Right_Caudate (50): linear fit = 1.22 x + 0.0 (692 voxels, overlap=0.028) Right_Caudate (50): linear fit = 1.22 x + 0.0 (692 voxels, peak = 81), gca=81.4 gca peak = 0.14473 (69) mri peak = 0.08108 (80) Left_Caudate (11): linear fit = 1.12 x + 0.0 (883 voxels, overlap=0.693) Left_Caudate (11): linear fit = 1.12 x + 0.0 (883 voxels, peak = 78), gca=77.6 gca peak = 0.14301 (56) mri peak = 0.06082 (72) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (11918 voxels, overlap=0.017) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (11918 voxels, peak = 71), gca=70.8 gca peak = 0.14610 (55) mri peak = 0.05146 (72) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (13306 voxels, overlap=0.054) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (13306 voxels, peak = 70), gca=69.6 gca peak = 0.16309 (85) mri peak = 0.08441 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4170 voxels, overlap=0.820) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4170 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.08376 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4501 voxels, overlap=0.952) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4501 voxels, peak = 86), gca=86.1 gca peak = 0.30461 (58) mri peak = 0.10250 (70) Left_Amygdala (18): linear fit = 1.24 x + 0.0 (355 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.24 x + 0.0 (355 voxels, peak = 72), gca=71.6 gca peak = 0.32293 (57) mri peak = 0.10610 (69) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (370 voxels, overlap=0.058) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (370 voxels, peak = 73), gca=72.7 gca peak = 0.11083 (90) mri peak = 0.07306 (86) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (3755 voxels, overlap=0.992) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (3755 voxels, peak = 88), gca=87.8 gca peak = 0.11393 (83) mri peak = 0.08051 (84) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3824 voxels, overlap=0.975) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3824 voxels, peak = 83), gca=82.6 gca peak = 0.08575 (81) mri peak = 0.08542 (82) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1152 voxels, overlap=0.718) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1152 voxels, peak = 86), gca=86.3 gca peak = 0.08618 (78) mri peak = 0.09162 (81) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1020 voxels, overlap=0.822) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1020 voxels, peak = 82), gca=81.5 gca peak = 0.08005 (78) mri peak = 0.11422 (80) Brain_Stem (16): linear fit = 1.03 x + 0.0 (11583 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.03 x + 0.0 (11583 voxels, peak = 81), gca=80.7 gca peak = 0.12854 (88) mri peak = 0.11620 (85) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1027 voxels, overlap=0.824) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1027 voxels, peak = 87), gca=86.7 gca peak = 0.15703 (87) mri peak = 0.10850 (86) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (980 voxels, overlap=0.926) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (980 voxels, peak = 87), gca=86.6 gca peak = 0.17522 (25) mri peak = 0.14634 (21) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (240 voxels, overlap=0.635) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (240 voxels, peak = 19), gca=19.4 gca peak = 0.17113 (14) mri peak = 0.12149 (18) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (638 voxels, overlap=0.859) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (638 voxels, peak = 16), gca=16.3 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.26 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.93 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.21452 (12) mri peak = 0.11298 (15) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (11170 voxels, overlap=0.879) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (11170 voxels, peak = 12), gca=12.4 gca peak = 0.16935 (14) mri peak = 0.13746 (17) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (9617 voxels, overlap=0.668) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (9617 voxels, peak = 14), gca=14.5 gca peak = 0.23619 (90) mri peak = 0.08260 (90) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (340 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (340 voxels, peak = 90), gca=89.6 gca peak = 0.16220 (96) mri peak = 0.09818 (91) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (352 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (352 voxels, peak = 96), gca=95.5 gca peak = 0.26697 (67) mri peak = 0.09078 (71) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (682 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (682 voxels, peak = 67), gca=67.0 gca peak = 0.32151 (64) mri peak = 0.07265 (64) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (667 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (667 voxels, peak = 63), gca=63.0 gca peak = 0.07636 (107) mri peak = 0.05759 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (30252 voxels, overlap=0.845) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (30252 voxels, peak = 107), gca=107.0 gca peak = 0.07733 (107) mri peak = 0.06900 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39614 voxels, overlap=0.856) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39614 voxels, peak = 107), gca=107.0 gca peak = 0.07345 (78) mri peak = 0.04363 (76) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (10427 voxels, overlap=0.923) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (10427 voxels, peak = 76), gca=76.1 gca peak = 0.08422 (78) mri peak = 0.03817 (76) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (11858 voxels, overlap=0.939) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (11858 voxels, peak = 77), gca=76.8 gca peak = 0.20111 (81) mri peak = 0.07796 (84) Right_Caudate (50): linear fit = 0.99 x + 0.0 (692 voxels, overlap=1.005) Right_Caudate (50): linear fit = 0.99 x + 0.0 (692 voxels, peak = 80), gca=79.8 gca peak = 0.14099 (77) mri peak = 0.08108 (80) Left_Caudate (11): linear fit = 0.99 x + 0.0 (883 voxels, overlap=1.001) Left_Caudate (11): linear fit = 0.99 x + 0.0 (883 voxels, peak = 76), gca=75.8 gca peak = 0.10869 (70) mri peak = 0.06082 (72) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (11918 voxels, overlap=0.978) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (11918 voxels, peak = 72), gca=72.4 gca peak = 0.12813 (70) mri peak = 0.05146 (72) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (13306 voxels, overlap=0.983) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (13306 voxels, peak = 69), gca=69.0 gca peak = 0.15236 (90) mri peak = 0.08441 (89) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4170 voxels, overlap=0.981) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4170 voxels, peak = 89), gca=88.7 gca peak = 0.15434 (86) mri peak = 0.08376 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4501 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4501 voxels, peak = 86), gca=85.6 gca peak = 0.27515 (72) mri peak = 0.10250 (70) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (355 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (355 voxels, peak = 72), gca=72.0 gca peak = 0.22024 (72) mri peak = 0.10610 (69) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (370 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (370 voxels, peak = 72), gca=72.0 gca peak = 0.11534 (86) mri peak = 0.07306 (86) Left_Thalamus (10): linear fit = 1.02 x + 0.0 (3755 voxels, overlap=0.955) Left_Thalamus (10): linear fit = 1.02 x + 0.0 (3755 voxels, peak = 88), gca=88.2 gca peak = 0.10513 (82) mri peak = 0.08051 (84) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (3824 voxels, overlap=0.972) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (3824 voxels, peak = 83), gca=83.2 gca peak = 0.07448 (88) mri peak = 0.08542 (82) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1152 voxels, overlap=0.906) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1152 voxels, peak = 88), gca=87.6 gca peak = 0.11265 (79) mri peak = 0.09162 (81) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1020 voxels, overlap=0.954) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1020 voxels, peak = 80), gca=80.2 gca peak = 0.09023 (81) mri peak = 0.11422 (80) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11583 voxels, overlap=0.640) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11583 voxels, peak = 82), gca=82.2 gca peak = 0.14426 (88) mri peak = 0.11620 (85) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1027 voxels, overlap=0.802) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1027 voxels, peak = 89), gca=89.3 gca peak = 0.16415 (86) mri peak = 0.10850 (86) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (980 voxels, overlap=0.927) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (980 voxels, peak = 86), gca=85.6 gca peak = 0.23325 (20) mri peak = 0.14634 (21) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (240 voxels, overlap=1.017) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (240 voxels, peak = 20), gca=20.0 gca peak = 0.17390 (17) mri peak = 0.12149 (18) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (638 voxels, overlap=0.731) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (638 voxels, peak = 17), gca=17.4 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.20602 (32) gca peak CSF = 0.19291 (34) gca peak Left_Accumbens_area = 0.53995 (70) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89837 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.26261 (28) gca peak Right_Accumbens_area = 0.36234 (79) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.91795 (30) gca peak WM_hypointensities = 0.10366 (79) gca peak non_WM_hypointensities = 0.14635 (42) gca peak Optic_Chiasm = 0.52492 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 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 85858 voxels changed in iteration 0 of unlikely voxel relabeling 302 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 86197 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 570 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 93443 changed. image ll: -2.155, PF=0.500 pass 2: 20347 changed. image ll: -2.154, PF=0.500 pass 3: 5129 changed. pass 4: 1674 changed. 58390 voxels changed in iteration 0 of unlikely voxel relabeling 377 voxels changed in iteration 1 of unlikely voxel relabeling 52 voxels changed in iteration 2 of unlikely voxel relabeling 4 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 7584 voxels changed in iteration 0 of unlikely voxel relabeling 192 voxels changed in iteration 1 of unlikely voxel relabeling 20 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7199 voxels changed in iteration 0 of unlikely voxel relabeling 69 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 5983 voxels changed in iteration 0 of unlikely voxel relabeling 21 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 5 with volume 28350 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 186 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 377 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 3 with volume 25686 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 504 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 3 with volume 387 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2958.495598 mri_ca_label stimesec 1.535924 mri_ca_label ru_maxrss 2231344 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 435248 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 768 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 183 mri_ca_label ru_nivcsw 982 mri_ca_label took 49 minutes and 27 seconds. mri_ca_label done #-------------------------------------- #@# CC Seg Thu Feb 12 17:20:51 EST 2026 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/transforms/cc_up.lta PBRHOPE_HOPE089_PETMR will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/transforms/cc_up.lta reading aseg from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/norm.mgz 139933 voxels in left wm, 238105 in right wm, xrange [102, 142] searching rotation angles z=[-20 -6], y=[-15 -1] searching scale 1 Z rot -19.7 searching scale 1 Z rot -19.5 searching scale 1 Z rot -19.2 searching scale 1 Z rot -19.0 searching scale 1 Z rot -18.7 searching scale 1 Z rot -18.5 searching scale 1 Z rot -18.2 searching scale 1 Z rot -18.0 searching scale 1 Z rot -17.7 searching scale 1 Z rot -17.5 searching scale 1 Z rot -17.2 searching scale 1 Z rot -17.0 searching scale 1 Z rot -16.7 searching scale 1 Z rot -16.5 searching scale 1 Z rot -16.2 searching scale 1 Z rot -16.0 searching scale 1 Z rot -15.7 searching scale 1 Z rot -15.5 searching scale 1 Z rot -15.2 searching scale 1 Z rot -15.0 searching scale 1 Z rot -14.7 searching scale 1 Z rot -14.5 searching scale 1 Z rot -14.2 searching scale 1 Z rot -14.0 searching scale 1 Z rot -13.7 searching scale 1 Z rot -13.5 searching scale 1 Z rot -13.2 searching scale 1 Z rot -13.0 searching scale 1 Z rot -12.7 searching scale 1 Z rot -12.5 searching scale 1 Z rot -12.2 searching scale 1 Z rot -12.0 searching scale 1 Z rot -11.7 searching scale 1 Z rot -11.5 searching scale 1 Z rot -11.2 searching scale 1 Z rot -11.0 searching scale 1 Z rot -10.7 searching scale 1 Z rot -10.5 searching scale 1 Z rot -10.2 searching scale 1 Z rot -10.0 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 global minimum found at slice 124.0, rotations (-8.23, -12.70) final transformation (x=124.0, yr=-8.226, zr=-12.703): 0.96549 0.21989 -0.13957 -9.79273; -0.21763 0.97552 0.03146 37.07431; 0.14307 0.00000 0.98971 52.85559; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 133] in xformed coordinates best xformed slice 128 min_x_fornix = 134 min_x_fornix = 136 min_x_fornix = 135 min_x_fornix = 134 min_x_fornix = 134 cc center is found at 128 119 58 eigenvectors: -0.00025 0.01478 0.99989; -0.37849 -0.92551 0.01358; 0.92561 -0.37844 0.00582; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/aseg.auto.mgz... corpus callosum segmentation took 6.5 minutes #VMPC# mri_cc VmPeak 465304 mri_cc done #-------------------------------------- #@# Merge ASeg Thu Feb 12 17:27:21 EST 2026 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Feb 12 17:27:21 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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... 2846 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 102 gm peak at 77 (77), valley at 42 (42) csf peak at 16, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 103 gm peak at 81 (81), valley at 40 (40) csf peak at 16, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 24 seconds. #-------------------------------------------- #@# Mask BFS Thu Feb 12 17:29:50 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1691489 voxels in mask (pct= 10.08) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Thu Feb 12 17:29:51 EST 2026 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 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 = 332482, nonwhite = 16018556, ambig = 426178, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (100.0): 99.5 +- 6.8 [79.0 --> 125.0] CCS GM (74.0) : 72.1 +- 10.5 [30.0 --> 95.0] white_mean 99.4613 white_sigma 6.81179 gray_mean 72.0595 gray_sigma 10.4722 setting bottom of white matter range wm_low to 82.5 setting top of gray matter range gray_hi to 93.0 wm_low 82.5317 wm_hi 125 gray_low 30 gray_hi 93.004 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=82.5317, wm_hi=125, gray_hi=93.004 white = 459187, nonwhite = 16101908, ambig = 216121, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 82.5317 wm_hi 125 gray_low 30 gray_hi 93.004 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 93.004, wm_low = 82.5317 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=93.004, wmlow=82.5317 188023 voxels processed (1.12%) 93248 voxels white (0.56%) 94775 voxels non-white (0.56%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=77.5317, gray_hi=93.004, wsize=13 321539 voxels tested (1.92%) 68421 voxels changed (0.41%) 57978 multi-scale searches (0.35%) Recovering bright white MRIrecoverBrightWhite() wm_low 82.5317 wm_hi 125 slack 6.81179 pct_thresh 0.33 intensity_thresh 131.812 nvox_thresh 8.58 54 voxels tested (0.00%) 35 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=77.5317, hithr=93.004 smoothing input volume with sigma = 0.250 150914 voxels tested (0.90%) 26052 voxels changed (0.16%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 3840 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 3969 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 2801 filled MRIfindBrightNonWM(): 258 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.5 minutes writing output to wm.seg.mgz... 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 0.47 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 5373 additional wm voxels added 0 additional wm voxels added SEG EDIT: 112177 voxels turned on, 24350 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 31 found - 31 modified | TOTAL: 31 pass 2 (xy+): 0 found - 31 modified | TOTAL: 31 pass 1 (xy-): 33 found - 33 modified | TOTAL: 64 pass 2 (xy-): 0 found - 33 modified | TOTAL: 64 pass 1 (yz+): 28 found - 28 modified | TOTAL: 92 pass 2 (yz+): 0 found - 28 modified | TOTAL: 92 pass 1 (yz-): 26 found - 26 modified | TOTAL: 118 pass 2 (yz-): 0 found - 26 modified | TOTAL: 118 pass 1 (xz+): 23 found - 23 modified | TOTAL: 141 pass 2 (xz+): 0 found - 23 modified | TOTAL: 141 pass 1 (xz-): 34 found - 34 modified | TOTAL: 175 pass 2 (xz-): 0 found - 34 modified | TOTAL: 175 Iteration Number : 1 pass 1 (+++): 30 found - 30 modified | TOTAL: 30 pass 2 (+++): 0 found - 30 modified | TOTAL: 30 pass 1 (+++): 33 found - 33 modified | TOTAL: 63 pass 2 (+++): 0 found - 33 modified | TOTAL: 63 pass 1 (+++): 18 found - 18 modified | TOTAL: 81 pass 2 (+++): 0 found - 18 modified | TOTAL: 81 pass 1 (+++): 41 found - 41 modified | TOTAL: 122 pass 2 (+++): 0 found - 41 modified | TOTAL: 122 Iteration Number : 1 pass 1 (++): 104 found - 104 modified | TOTAL: 104 pass 2 (++): 0 found - 104 modified | TOTAL: 104 pass 1 (+-): 83 found - 83 modified | TOTAL: 187 pass 2 (+-): 0 found - 83 modified | TOTAL: 187 pass 1 (--): 105 found - 105 modified | TOTAL: 292 pass 2 (--): 0 found - 105 modified | TOTAL: 292 pass 1 (-+): 94 found - 94 modified | TOTAL: 386 pass 2 (-+): 0 found - 94 modified | TOTAL: 386 Iteration Number : 2 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 11 found - 11 modified | TOTAL: 24 pass 2 (xy-): 0 found - 11 modified | TOTAL: 24 pass 1 (yz+): 11 found - 11 modified | TOTAL: 35 pass 2 (yz+): 0 found - 11 modified | TOTAL: 35 pass 1 (yz-): 4 found - 4 modified | TOTAL: 39 pass 2 (yz-): 0 found - 4 modified | TOTAL: 39 pass 1 (xz+): 13 found - 13 modified | TOTAL: 52 pass 2 (xz+): 0 found - 13 modified | TOTAL: 52 pass 1 (xz-): 7 found - 7 modified | TOTAL: 59 pass 2 (xz-): 0 found - 7 modified | TOTAL: 59 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 3 found - 3 modified | TOTAL: 7 pass 2 (+++): 0 found - 3 modified | TOTAL: 7 pass 1 (+++): 4 found - 4 modified | TOTAL: 11 pass 2 (+++): 0 found - 4 modified | TOTAL: 11 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 5 found - 5 modified | TOTAL: 9 pass 2 (+-): 0 found - 5 modified | TOTAL: 9 pass 1 (--): 10 found - 10 modified | TOTAL: 19 pass 2 (--): 0 found - 10 modified | TOTAL: 19 pass 1 (-+): 2 found - 2 modified | TOTAL: 21 pass 2 (-+): 0 found - 2 modified | TOTAL: 21 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 776 (out of 652030: 0.119013) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Feb 12 17:32:42 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/stable7.4.1/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 1.01247 0.20981 -0.03605 -26.16312; -0.13885 0.82332 0.60455 -18.83871; 0.15313 -0.58831 0.83729 94.07925; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.01247 0.20981 -0.03605 -26.16312; -0.13885 0.82332 0.60455 -18.83871; 0.15313 -0.58831 0.83729 94.07925; 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] = 1937 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) need search nearby using seed (129, 117, 155), TAL = (-1.0, 27.0, 11.0) talairach voxel to voxel transform 0.94703 -0.13998 0.14184 8.79565; 0.18926 0.77325 -0.55016 71.27689; -0.04023 0.56892 0.78183 -63.88850; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (129, 117, 155) --> (-1.0, 27.0, 11.0) done. filling took 1.2 minutes badRH = 68/313433, badLH=16881/324597 talairach cc position changed to (-1.00, 27.00, 11.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(17.00, 27.00, 11.00) SRC: (119.52, 97.48, 119.39) search lh wm seed point around talairach space (-19.00, 27.00, 11.00), SRC: (153.62, 104.29, 117.94) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... Embedding colortable mri_fill done, writing output to filled.mgz... error: Please check filled volume. Cerebellum may be included. cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Thu Feb 12 17:33:54 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 6 found - 6 modified | TOTAL: 8 pass 2 (xy-): 0 found - 6 modified | TOTAL: 8 pass 1 (yz+): 5 found - 5 modified | TOTAL: 13 pass 2 (yz+): 0 found - 5 modified | TOTAL: 13 pass 1 (yz-): 4 found - 4 modified | TOTAL: 17 pass 2 (yz-): 0 found - 4 modified | TOTAL: 17 pass 1 (xz+): 3 found - 3 modified | TOTAL: 20 pass 2 (xz+): 0 found - 3 modified | TOTAL: 20 pass 1 (xz-): 4 found - 4 modified | TOTAL: 24 pass 2 (xz-): 0 found - 4 modified | TOTAL: 24 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 0 found - 0 modified | TOTAL: 6 pass 1 (--): 1 found - 1 modified | TOTAL: 7 pass 2 (--): 0 found - 1 modified | TOTAL: 7 pass 1 (-+): 1 found - 1 modified | TOTAL: 8 pass 2 (-+): 0 found - 1 modified | TOTAL: 8 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 = 34 (out of 324631: 0.010473) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.4.1 7.4.1 slice 10: 3774 vertices, 4088 faces slice 20: 15921 vertices, 16430 faces slice 30: 31069 vertices, 31590 faces slice 40: 46763 vertices, 47281 faces slice 50: 60010 vertices, 60447 faces slice 60: 71073 vertices, 71483 faces slice 70: 82079 vertices, 82511 faces slice 80: 92778 vertices, 93218 faces slice 90: 102209 vertices, 102617 faces slice 100: 111173 vertices, 111597 faces slice 110: 119888 vertices, 120288 faces slice 120: 127841 vertices, 128212 faces slice 130: 135231 vertices, 135523 faces slice 140: 139893 vertices, 140120 faces slice 150: 143437 vertices, 143615 faces slice 160: 144684 vertices, 144776 faces slice 170: 144684 vertices, 144776 faces slice 180: 144684 vertices, 144776 faces slice 190: 144684 vertices, 144776 faces slice 200: 144684 vertices, 144776 faces slice 210: 144684 vertices, 144776 faces slice 220: 144684 vertices, 144776 faces slice 230: 144684 vertices, 144776 faces slice 240: 144684 vertices, 144776 faces slice 250: 144684 vertices, 144776 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; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 144684 voxel in cpt #1: X=-92 [v=144684,e=434328,f=289552] located at (-23.176924, -62.664371, -2.565059) For the whole surface: X=-92 [v=144684,e=434328,f=289552] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Thu Feb 12 17:33:58 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 6 found - 6 modified | TOTAL: 7 pass 2 (yz+): 0 found - 6 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 3 found - 3 modified | TOTAL: 12 pass 2 (xz+): 0 found - 3 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 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 313448: 0.004785) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.4.1 7.4.1 slice 10: 144 vertices, 179 faces slice 20: 4523 vertices, 4800 faces slice 30: 14398 vertices, 14841 faces slice 40: 26199 vertices, 26594 faces slice 50: 39695 vertices, 40187 faces slice 60: 52466 vertices, 52916 faces slice 70: 63355 vertices, 63753 faces slice 80: 74138 vertices, 74589 faces slice 90: 85103 vertices, 85549 faces slice 100: 95370 vertices, 95793 faces slice 110: 104617 vertices, 105038 faces slice 120: 113960 vertices, 114341 faces slice 130: 122779 vertices, 123162 faces slice 140: 131498 vertices, 131836 faces slice 150: 136925 vertices, 137138 faces slice 160: 140050 vertices, 140180 faces slice 170: 140392 vertices, 140468 faces slice 180: 140392 vertices, 140468 faces slice 190: 140392 vertices, 140468 faces slice 200: 140392 vertices, 140468 faces slice 210: 140392 vertices, 140468 faces slice 220: 140392 vertices, 140468 faces slice 230: 140392 vertices, 140468 faces slice 240: 140392 vertices, 140468 faces slice 250: 140392 vertices, 140468 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; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 140392 voxel in cpt #1: X=-76 [v=140392,e=421404,f=280936] located at (27.660757, -49.829597, 11.049767) For the whole surface: X=-76 [v=140392,e=421404,f=280936] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Feb 12 17:34:02 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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... #-------------------------------------------- #@# Smooth1 rh Thu Feb 12 17:34:05 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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... #-------------------------------------------- #@# Inflation1 lh Thu Feb 12 17:34:08 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 52.4 mm, total surface area = 77108 mm^2 step 000: RMS=0.154 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes inflation complete. Not saving sulc mris_inflate utimesec 20.515220 mris_inflate stimesec 1.003599 mris_inflate ru_maxrss 230508 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 563392 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 400 mris_inflate ru_oublock 10184 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 244 mris_inflate ru_nivcsw 40 #-------------------------------------------- #@# Inflation1 rh Thu Feb 12 17:34:30 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 49.2 mm, total surface area = 74582 mm^2 step 000: RMS=0.156 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.062 (target=0.015) step 030: RMS=0.057 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.050 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.047 (target=0.015) step 055: RMS=0.046 (target=0.015) step 060: RMS=0.046 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 19.787770 mris_inflate stimesec 0.917820 mris_inflate ru_maxrss 223628 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 514557 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9880 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 238 mris_inflate ru_nivcsw 38 #-------------------------------------------- #@# QSphere lh Thu Feb 12 17:34:51 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 0.347... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.59 (0.00-->6.57) (max @ vno 117811 --> 117812) face area 0.03 +- 0.04 (-0.25-->0.95) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=171.979, avgs=0 005/300: dt: 0.9000, rms radial error=171.743, avgs=0 010/300: dt: 0.9000, rms radial error=171.237, avgs=0 015/300: dt: 0.9000, rms radial error=170.573, avgs=0 020/300: dt: 0.9000, rms radial error=169.814, avgs=0 025/300: dt: 0.9000, rms radial error=169.001, avgs=0 030/300: dt: 0.9000, rms radial error=168.156, avgs=0 035/300: dt: 0.9000, rms radial error=167.293, avgs=0 040/300: dt: 0.9000, rms radial error=166.419, avgs=0 045/300: dt: 0.9000, rms radial error=165.540, avgs=0 050/300: dt: 0.9000, rms radial error=164.657, avgs=0 055/300: dt: 0.9000, rms radial error=163.775, avgs=0 060/300: dt: 0.9000, rms radial error=162.893, avgs=0 065/300: dt: 0.9000, rms radial error=162.013, avgs=0 070/300: dt: 0.9000, rms radial error=161.134, avgs=0 075/300: dt: 0.9000, rms radial error=160.258, avgs=0 080/300: dt: 0.9000, rms radial error=159.383, avgs=0 085/300: dt: 0.9000, rms radial error=158.511, avgs=0 090/300: dt: 0.9000, rms radial error=157.638, avgs=0 095/300: dt: 0.9000, rms radial error=156.761, avgs=0 100/300: dt: 0.9000, rms radial error=155.888, avgs=0 105/300: dt: 0.9000, rms radial error=155.020, avgs=0 110/300: dt: 0.9000, rms radial error=154.156, avgs=0 115/300: dt: 0.9000, rms radial error=153.296, avgs=0 120/300: dt: 0.9000, rms radial error=152.440, avgs=0 125/300: dt: 0.9000, rms radial error=151.589, avgs=0 130/300: dt: 0.9000, rms radial error=150.741, avgs=0 135/300: dt: 0.9000, rms radial error=149.898, avgs=0 140/300: dt: 0.9000, rms radial error=149.059, avgs=0 145/300: dt: 0.9000, rms radial error=148.225, avgs=0 150/300: dt: 0.9000, rms radial error=147.395, avgs=0 155/300: dt: 0.9000, rms radial error=146.569, avgs=0 160/300: dt: 0.9000, rms radial error=145.748, avgs=0 165/300: dt: 0.9000, rms radial error=144.930, avgs=0 170/300: dt: 0.9000, rms radial error=144.118, avgs=0 175/300: dt: 0.9000, rms radial error=143.310, avgs=0 180/300: dt: 0.9000, rms radial error=142.505, avgs=0 185/300: dt: 0.9000, rms radial error=141.705, avgs=0 190/300: dt: 0.9000, rms radial error=140.911, avgs=0 195/300: dt: 0.9000, rms radial error=140.122, avgs=0 200/300: dt: 0.9000, rms radial error=139.338, avgs=0 205/300: dt: 0.9000, rms radial error=138.559, avgs=0 210/300: dt: 0.9000, rms radial error=137.784, avgs=0 215/300: dt: 0.9000, rms radial error=137.013, avgs=0 220/300: dt: 0.9000, rms radial error=136.247, avgs=0 225/300: dt: 0.9000, rms radial error=135.485, avgs=0 230/300: dt: 0.9000, rms radial error=134.727, avgs=0 235/300: dt: 0.9000, rms radial error=133.973, avgs=0 240/300: dt: 0.9000, rms radial error=133.224, avgs=0 245/300: dt: 0.9000, rms radial error=132.479, avgs=0 250/300: dt: 0.9000, rms radial error=131.737, avgs=0 255/300: dt: 0.9000, rms radial error=131.000, avgs=0 260/300: dt: 0.9000, rms radial error=130.267, avgs=0 265/300: dt: 0.9000, rms radial error=129.538, avgs=0 270/300: dt: 0.9000, rms radial error=128.813, avgs=0 275/300: dt: 0.9000, rms radial error=128.091, avgs=0 280/300: dt: 0.9000, rms radial error=127.374, avgs=0 285/300: dt: 0.9000, rms radial error=126.661, avgs=0 290/300: dt: 0.9000, rms radial error=125.952, avgs=0 295/300: dt: 0.9000, rms radial error=125.246, avgs=0 300/300: dt: 0.9000, rms radial error=124.545, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16351.63 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 = 2573.54 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00061 epoch 3 (K=160.0), pass 1, starting sse = 244.68 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/14 = 0.00625 epoch 4 (K=640.0), pass 1, starting sse = 16.48 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/18 = 0.00689 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0418 hours FSRUNTIME@ mris_sphere 0.0418 hours 1 threads #VMPC# mris_sphere VmPeak 511776 mris_sphere done #-------------------------------------------- #@# QSphere rh Thu Feb 12 17:37:21 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 0.350... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.57 (0.00-->6.09) (max @ vno 65261 --> 66226) face area 0.03 +- 0.04 (-0.09-->0.79) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=173.052, avgs=0 005/300: dt: 0.9000, rms radial error=172.804, avgs=0 010/300: dt: 0.9000, rms radial error=172.270, avgs=0 015/300: dt: 0.9000, rms radial error=171.569, avgs=0 020/300: dt: 0.9000, rms radial error=170.770, avgs=0 025/300: dt: 0.9000, rms radial error=169.916, avgs=0 030/300: dt: 0.9000, rms radial error=169.030, avgs=0 035/300: dt: 0.9000, rms radial error=168.126, avgs=0 040/300: dt: 0.9000, rms radial error=167.214, avgs=0 045/300: dt: 0.9000, rms radial error=166.298, avgs=0 050/300: dt: 0.9000, rms radial error=165.384, avgs=0 055/300: dt: 0.9000, rms radial error=164.475, avgs=0 060/300: dt: 0.9000, rms radial error=163.569, avgs=0 065/300: dt: 0.9000, rms radial error=162.666, avgs=0 070/300: dt: 0.9000, rms radial error=161.766, avgs=0 075/300: dt: 0.9000, rms radial error=160.871, avgs=0 080/300: dt: 0.9000, rms radial error=159.979, avgs=0 085/300: dt: 0.9000, rms radial error=159.092, avgs=0 090/300: dt: 0.9000, rms radial error=158.209, avgs=0 095/300: dt: 0.9000, rms radial error=157.330, avgs=0 100/300: dt: 0.9000, rms radial error=156.455, avgs=0 105/300: dt: 0.9000, rms radial error=155.585, avgs=0 110/300: dt: 0.9000, rms radial error=154.719, avgs=0 115/300: dt: 0.9000, rms radial error=153.857, avgs=0 120/300: dt: 0.9000, rms radial error=153.000, avgs=0 125/300: dt: 0.9000, rms radial error=152.147, avgs=0 130/300: dt: 0.9000, rms radial error=151.299, avgs=0 135/300: dt: 0.9000, rms radial error=150.455, avgs=0 140/300: dt: 0.9000, rms radial error=149.615, avgs=0 145/300: dt: 0.9000, rms radial error=148.780, avgs=0 150/300: dt: 0.9000, rms radial error=147.949, avgs=0 155/300: dt: 0.9000, rms radial error=147.121, avgs=0 160/300: dt: 0.9000, rms radial error=146.298, avgs=0 165/300: dt: 0.9000, rms radial error=145.480, avgs=0 170/300: dt: 0.9000, rms radial error=144.665, avgs=0 175/300: dt: 0.9000, rms radial error=143.855, avgs=0 180/300: dt: 0.9000, rms radial error=143.048, avgs=0 185/300: dt: 0.9000, rms radial error=142.247, avgs=0 190/300: dt: 0.9000, rms radial error=141.450, avgs=0 195/300: dt: 0.9000, rms radial error=140.657, avgs=0 200/300: dt: 0.9000, rms radial error=139.868, avgs=0 205/300: dt: 0.9000, rms radial error=139.084, avgs=0 210/300: dt: 0.9000, rms radial error=138.304, avgs=0 215/300: dt: 0.9000, rms radial error=137.528, avgs=0 220/300: dt: 0.9000, rms radial error=136.757, avgs=0 225/300: dt: 0.9000, rms radial error=135.990, avgs=0 230/300: dt: 0.9000, rms radial error=135.227, avgs=0 235/300: dt: 0.9000, rms radial error=134.468, avgs=0 240/300: dt: 0.9000, rms radial error=133.714, avgs=0 245/300: dt: 0.9000, rms radial error=132.964, avgs=0 250/300: dt: 0.9000, rms radial error=132.217, avgs=0 255/300: dt: 0.9000, rms radial error=131.475, avgs=0 260/300: dt: 0.9000, rms radial error=130.738, avgs=0 265/300: dt: 0.9000, rms radial error=130.004, avgs=0 270/300: dt: 0.9000, rms radial error=129.274, avgs=0 275/300: dt: 0.9000, rms radial error=128.548, avgs=0 280/300: dt: 0.9000, rms radial error=127.827, avgs=0 285/300: dt: 0.9000, rms radial error=127.110, avgs=0 290/300: dt: 0.9000, rms radial error=126.396, avgs=0 295/300: dt: 0.9000, rms radial error=125.687, avgs=0 300/300: dt: 0.9000, rms radial error=124.981, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15717.60 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00032 epoch 2 (K=40.0), pass 1, starting sse = 2381.56 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00085 epoch 3 (K=160.0), pass 1, starting sse = 200.39 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/16 = 0.00902 epoch 4 (K=640.0), pass 1, starting sse = 11.46 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/17 = 0.00252 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0416 hours FSRUNTIME@ mris_sphere 0.0416 hours 1 threads #VMPC# mris_sphere VmPeak 504924 mris_sphere done #@# Fix Topology lh Thu Feb 12 17:39:51 EST 2026 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PBRHOPE_HOPE089_PETMR 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=-92 (nv=144684, nf=289552, ne=434328, g=47) 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... 5322 ambiguous faces found in tessellation segmenting defects... 55 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 55 defects to be corrected 0 vertices coincident reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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: -9.6588 (-4.8294) -vertex loglikelihood: -6.6933 (-3.3467) -normal dot loglikelihood: -3.6189 (-3.6189) -quad curv loglikelihood: -5.8191 (-2.9095) Total Loglikelihood : -25.7900 CORRECTING DEFECT 0 (vertices=102, convex hull=124, v0=326) After retessellation of defect 0 (v0=326), euler #=-51 (141329,422442,281062) : difference with theory (-52) = -1 CORRECTING DEFECT 1 (vertices=35, convex hull=83, v0=17258) After retessellation of defect 1 (v0=17258), euler #=-50 (141348,422531,281133) : difference with theory (-51) = -1 CORRECTING DEFECT 2 (vertices=60, convex hull=34, v0=18099) After retessellation of defect 2 (v0=18099), euler #=-49 (141356,422565,281160) : difference with theory (-50) = -1 CORRECTING DEFECT 3 (vertices=39, convex hull=57, v0=21086) After retessellation of defect 3 (v0=21086), euler #=-48 (141373,422638,281217) : difference with theory (-49) = -1 CORRECTING DEFECT 4 (vertices=22, convex hull=57, v0=22133) After retessellation of defect 4 (v0=22133), euler #=-47 (141385,422697,281265) : difference with theory (-48) = -1 CORRECTING DEFECT 5 (vertices=20, convex hull=49, v0=27348) After retessellation of defect 5 (v0=27348), euler #=-46 (141399,422760,281315) : difference with theory (-47) = -1 CORRECTING DEFECT 6 (vertices=75, convex hull=95, v0=27992) After retessellation of defect 6 (v0=27992), euler #=-45 (141434,422904,281425) : difference with theory (-46) = -1 CORRECTING DEFECT 7 (vertices=42, convex hull=38, v0=29577) After retessellation of defect 7 (v0=29577), euler #=-44 (141445,422954,281465) : difference with theory (-45) = -1 CORRECTING DEFECT 8 (vertices=17, convex hull=39, v0=32390) After retessellation of defect 8 (v0=32390), euler #=-43 (141447,422974,281484) : difference with theory (-44) = -1 CORRECTING DEFECT 9 (vertices=36, convex hull=60, v0=32770) After retessellation of defect 9 (v0=32770), euler #=-42 (141462,423045,281541) : difference with theory (-43) = -1 CORRECTING DEFECT 10 (vertices=101, convex hull=128, v0=37395) After retessellation of defect 10 (v0=37395), euler #=-41 (141477,423150,281632) : difference with theory (-42) = -1 CORRECTING DEFECT 11 (vertices=50, convex hull=60, v0=37474) After retessellation of defect 11 (v0=37474), euler #=-40 (141495,423229,281694) : difference with theory (-41) = -1 CORRECTING DEFECT 12 (vertices=28, convex hull=76, v0=50889) After retessellation of defect 12 (v0=50889), euler #=-39 (141508,423295,281748) : difference with theory (-40) = -1 CORRECTING DEFECT 13 (vertices=143, convex hull=201, v0=54896) After retessellation of defect 13 (v0=54896), euler #=-38 (141557,423544,281949) : difference with theory (-39) = -1 CORRECTING DEFECT 14 (vertices=48, convex hull=57, v0=57791) After retessellation of defect 14 (v0=57791), euler #=-37 (141570,423604,281997) : difference with theory (-38) = -1 CORRECTING DEFECT 15 (vertices=10, convex hull=17, v0=59073) After retessellation of defect 15 (v0=59073), euler #=-36 (141571,423613,282006) : difference with theory (-37) = -1 CORRECTING DEFECT 16 (vertices=35, convex hull=75, v0=61861) After retessellation of defect 16 (v0=61861), euler #=-35 (141594,423718,282089) : difference with theory (-36) = -1 CORRECTING DEFECT 17 (vertices=33, convex hull=43, v0=62661) After retessellation of defect 17 (v0=62661), euler #=-34 (141602,423757,282121) : difference with theory (-35) = -1 CORRECTING DEFECT 18 (vertices=43, convex hull=31, v0=62664) After retessellation of defect 18 (v0=62664), euler #=-33 (141606,423777,282138) : difference with theory (-34) = -1 CORRECTING DEFECT 19 (vertices=34, convex hull=61, v0=65376) After retessellation of defect 19 (v0=65376), euler #=-32 (141627,423863,282204) : difference with theory (-33) = -1 CORRECTING DEFECT 20 (vertices=251, convex hull=213, v0=72839) After retessellation of defect 20 (v0=72839), euler #=-31 (141646,424011,282334) : difference with theory (-32) = -1 CORRECTING DEFECT 21 (vertices=83, convex hull=76, v0=74356) After retessellation of defect 21 (v0=74356), euler #=-30 (141672,424118,282416) : difference with theory (-31) = -1 CORRECTING DEFECT 22 (vertices=16, convex hull=56, v0=77811) After retessellation of defect 22 (v0=77811), euler #=-29 (141680,424161,282452) : difference with theory (-30) = -1 CORRECTING DEFECT 23 (vertices=39, convex hull=72, v0=78272) After retessellation of defect 23 (v0=78272), euler #=-28 (141699,424244,282517) : difference with theory (-29) = -1 CORRECTING DEFECT 24 (vertices=85, convex hull=106, v0=85100) After retessellation of defect 24 (v0=85100), euler #=-28 (141747,424443,282668) : difference with theory (-28) = 0 CORRECTING DEFECT 25 (vertices=283, convex hull=283, v0=87105) After retessellation of defect 25 (v0=87105), euler #=-27 (141797,424734,282910) : difference with theory (-27) = 0 CORRECTING DEFECT 26 (vertices=11, convex hull=39, v0=87128) After retessellation of defect 26 (v0=87128), euler #=-26 (141803,424764,282935) : difference with theory (-26) = 0 CORRECTING DEFECT 27 (vertices=38, convex hull=69, v0=89816) After retessellation of defect 27 (v0=89816), euler #=-25 (141823,424851,283003) : difference with theory (-25) = 0 CORRECTING DEFECT 28 (vertices=26, convex hull=47, v0=90061) After retessellation of defect 28 (v0=90061), euler #=-24 (141839,424916,283053) : difference with theory (-24) = 0 CORRECTING DEFECT 29 (vertices=21, convex hull=55, v0=99013) After retessellation of defect 29 (v0=99013), euler #=-23 (141848,424965,283094) : difference with theory (-23) = 0 CORRECTING DEFECT 30 (vertices=27, convex hull=54, v0=99739) After retessellation of defect 30 (v0=99739), euler #=-22 (141858,425017,283137) : difference with theory (-22) = 0 CORRECTING DEFECT 31 (vertices=103, convex hull=78, v0=101732) After retessellation of defect 31 (v0=101732), euler #=-21 (141888,425139,283230) : difference with theory (-21) = 0 CORRECTING DEFECT 32 (vertices=195, convex hull=71, v0=106340) After retessellation of defect 32 (v0=106340), euler #=-20 (141904,425220,283296) : difference with theory (-20) = 0 CORRECTING DEFECT 33 (vertices=31, convex hull=59, v0=107605) After retessellation of defect 33 (v0=107605), euler #=-19 (141922,425297,283356) : difference with theory (-19) = 0 CORRECTING DEFECT 34 (vertices=22, convex hull=30, v0=111698) After retessellation of defect 34 (v0=111698), euler #=-18 (141926,425318,283374) : difference with theory (-18) = 0 CORRECTING DEFECT 35 (vertices=18, convex hull=26, v0=115271) After retessellation of defect 35 (v0=115271), euler #=-17 (141929,425334,283388) : difference with theory (-17) = 0 CORRECTING DEFECT 36 (vertices=6, convex hull=30, v0=115279) After retessellation of defect 36 (v0=115279), euler #=-16 (141932,425351,283403) : difference with theory (-16) = 0 CORRECTING DEFECT 37 (vertices=17, convex hull=33, v0=115844) After retessellation of defect 37 (v0=115844), euler #=-15 (141934,425366,283417) : difference with theory (-15) = 0 CORRECTING DEFECT 38 (vertices=13, convex hull=30, v0=116769) After retessellation of defect 38 (v0=116769), euler #=-14 (141937,425385,283434) : difference with theory (-14) = 0 CORRECTING DEFECT 39 (vertices=23, convex hull=25, v0=117726) After retessellation of defect 39 (v0=117726), euler #=-13 (141942,425406,283451) : difference with theory (-13) = 0 CORRECTING DEFECT 40 (vertices=34, convex hull=30, v0=117885) After retessellation of defect 40 (v0=117885), euler #=-12 (141951,425443,283480) : difference with theory (-12) = 0 CORRECTING DEFECT 41 (vertices=10, convex hull=26, v0=118555) After retessellation of defect 41 (v0=118555), euler #=-11 (141953,425458,283494) : difference with theory (-11) = 0 CORRECTING DEFECT 42 (vertices=30, convex hull=50, v0=119246) After retessellation of defect 42 (v0=119246), euler #=-10 (141969,425525,283546) : difference with theory (-10) = 0 CORRECTING DEFECT 43 (vertices=39, convex hull=31, v0=120459) After retessellation of defect 43 (v0=120459), euler #=-9 (141976,425557,283572) : difference with theory (-9) = 0 CORRECTING DEFECT 44 (vertices=5, convex hull=9, v0=122707) After retessellation of defect 44 (v0=122707), euler #=-8 (141976,425559,283575) : difference with theory (-8) = 0 CORRECTING DEFECT 45 (vertices=86, convex hull=68, v0=122937) After retessellation of defect 45 (v0=122937), euler #=-7 (141989,425627,283631) : difference with theory (-7) = 0 CORRECTING DEFECT 46 (vertices=246, convex hull=66, v0=125176) After retessellation of defect 46 (v0=125176), euler #=-6 (142000,425689,283683) : difference with theory (-6) = 0 CORRECTING DEFECT 47 (vertices=11, convex hull=41, v0=125752) After retessellation of defect 47 (v0=125752), euler #=-5 (142001,425708,283702) : difference with theory (-5) = 0 CORRECTING DEFECT 48 (vertices=43, convex hull=55, v0=129185) After retessellation of defect 48 (v0=129185), euler #=-4 (142030,425815,283781) : difference with theory (-4) = 0 CORRECTING DEFECT 49 (vertices=111, convex hull=106, v0=131575) first tangent vector of length zero at vertex 144119 second tangent vector of length zero at vertex 144119 first tangent vector of length zero at vertex 144119 second tangent vector of length zero at vertex 144119 first tangent vector of length zero at vertex 144119 second tangent vector of length zero at vertex 144119 After retessellation of defect 49 (v0=131575), euler #=-3 (142059,425950,283888) : difference with theory (-3) = 0 CORRECTING DEFECT 50 (vertices=40, convex hull=51, v0=132272) After retessellation of defect 50 (v0=132272), euler #=-2 (142076,426023,283945) : difference with theory (-2) = 0 CORRECTING DEFECT 51 (vertices=109, convex hull=82, v0=138076) After retessellation of defect 51 (v0=138076), euler #=-1 (142093,426110,284016) : difference with theory (-1) = 0 CORRECTING DEFECT 52 (vertices=73, convex hull=121, v0=140510) After retessellation of defect 52 (v0=140510), euler #=0 (142128,426267,284139) : difference with theory (0) = 0 CORRECTING DEFECT 53 (vertices=167, convex hull=154, v0=140600) After retessellation of defect 53 (v0=140600), euler #=1 (142185,426511,284327) : difference with theory (1) = 0 CORRECTING DEFECT 54 (vertices=116, convex hull=87, v0=141930) After retessellation of defect 54 (v0=141930), euler #=2 (142205,426609,284406) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.09-->8.36) (max @ vno 135592 --> 137536) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.09-->8.36) (max @ vno 135592 --> 137536) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 179 mutations (33.5%), 355 crossovers (66.5%), 342 vertices were eliminated building final representation... 2479 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=142205, nf=284406, ne=426609, g=0) writing corrected surface to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 395 intersecting 001: 50 intersecting 002: 2 intersecting terminating search with 0 intersecting topology fixing took 4.4 minutes FSRUNTIME@ mris_fix_topology lh 0.0739 hours 1 threads #VMPC# mris_fix_topology VmPeak 785672 #@# Fix Topology rh Thu Feb 12 17:44:18 EST 2026 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 PBRHOPE_HOPE089_PETMR 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=-76 (nv=140392, nf=280936, ne=421404, g=39) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 6038 ambiguous faces found in tessellation segmenting defects... 49 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 49 defects to be corrected 0 vertices coincident reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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: -9.4970 (-4.7485) -vertex loglikelihood: -6.7054 (-3.3527) -normal dot loglikelihood: -3.5919 (-3.5919) -quad curv loglikelihood: -6.2688 (-3.1344) Total Loglikelihood : -26.0630 CORRECTING DEFECT 0 (vertices=23, convex hull=66, v0=7934) After retessellation of defect 0 (v0=7934), euler #=-46 (136756,408899,272097) : difference with theory (-46) = 0 CORRECTING DEFECT 1 (vertices=23, convex hull=64, v0=16665) After retessellation of defect 1 (v0=16665), euler #=-45 (136767,408955,272143) : difference with theory (-45) = 0 CORRECTING DEFECT 2 (vertices=24, convex hull=63, v0=20523) After retessellation of defect 2 (v0=20523), euler #=-44 (136780,409021,272197) : difference with theory (-44) = 0 CORRECTING DEFECT 3 (vertices=169, convex hull=85, v0=26199) After retessellation of defect 3 (v0=26199), euler #=-43 (136809,409146,272294) : difference with theory (-43) = 0 CORRECTING DEFECT 4 (vertices=43, convex hull=29, v0=27648) After retessellation of defect 4 (v0=27648), euler #=-42 (136812,409164,272310) : difference with theory (-42) = 0 CORRECTING DEFECT 5 (vertices=203, convex hull=134, v0=32671) After retessellation of defect 5 (v0=32671), euler #=-41 (136876,409417,272500) : difference with theory (-41) = 0 CORRECTING DEFECT 6 (vertices=237, convex hull=113, v0=34192) After retessellation of defect 6 (v0=34192), euler #=-40 (136936,409652,272676) : difference with theory (-40) = 0 CORRECTING DEFECT 7 (vertices=40, convex hull=30, v0=39695) After retessellation of defect 7 (v0=39695), euler #=-39 (136943,409679,272697) : difference with theory (-39) = 0 CORRECTING DEFECT 8 (vertices=428, convex hull=322, v0=39853) After retessellation of defect 8 (v0=39853), euler #=-38 (137125,410411,273248) : difference with theory (-38) = 0 CORRECTING DEFECT 9 (vertices=28, convex hull=30, v0=42893) After retessellation of defect 9 (v0=42893), euler #=-37 (137129,410435,273269) : difference with theory (-37) = 0 CORRECTING DEFECT 10 (vertices=34, convex hull=35, v0=45836) After retessellation of defect 10 (v0=45836), euler #=-36 (137133,410459,273290) : difference with theory (-36) = 0 CORRECTING DEFECT 11 (vertices=76, convex hull=124, v0=47994) After retessellation of defect 11 (v0=47994), euler #=-35 (137174,410633,273424) : difference with theory (-35) = 0 CORRECTING DEFECT 12 (vertices=152, convex hull=42, v0=50110) After retessellation of defect 12 (v0=50110), euler #=-34 (137185,410685,273466) : difference with theory (-34) = 0 CORRECTING DEFECT 13 (vertices=118, convex hull=129, v0=50275) After retessellation of defect 13 (v0=50275), euler #=-33 (137226,410868,273609) : difference with theory (-33) = 0 CORRECTING DEFECT 14 (vertices=18, convex hull=33, v0=53794) After retessellation of defect 14 (v0=53794), euler #=-32 (137228,410884,273624) : difference with theory (-32) = 0 CORRECTING DEFECT 15 (vertices=31, convex hull=25, v0=57803) After retessellation of defect 15 (v0=57803), euler #=-31 (137236,410916,273649) : difference with theory (-31) = 0 CORRECTING DEFECT 16 (vertices=7, convex hull=23, v0=59833) After retessellation of defect 16 (v0=59833), euler #=-30 (137238,410929,273661) : difference with theory (-30) = 0 CORRECTING DEFECT 17 (vertices=257, convex hull=103, v0=62266) After retessellation of defect 17 (v0=62266), euler #=-29 (137250,411013,273734) : difference with theory (-29) = 0 CORRECTING DEFECT 18 (vertices=5, convex hull=22, v0=70244) After retessellation of defect 18 (v0=70244), euler #=-28 (137252,411025,273745) : difference with theory (-28) = 0 CORRECTING DEFECT 19 (vertices=28, convex hull=66, v0=72430) After retessellation of defect 19 (v0=72430), euler #=-27 (137266,411094,273801) : difference with theory (-27) = 0 CORRECTING DEFECT 20 (vertices=21, convex hull=26, v0=72996) After retessellation of defect 20 (v0=72996), euler #=-26 (137267,411105,273812) : difference with theory (-26) = 0 CORRECTING DEFECT 21 (vertices=47, convex hull=59, v0=74201) After retessellation of defect 21 (v0=74201), euler #=-25 (137279,411163,273859) : difference with theory (-25) = 0 CORRECTING DEFECT 22 (vertices=60, convex hull=130, v0=75252) After retessellation of defect 22 (v0=75252), euler #=-24 (137317,411330,273989) : difference with theory (-24) = 0 CORRECTING DEFECT 23 (vertices=85, convex hull=51, v0=77543) After retessellation of defect 23 (v0=77543), euler #=-23 (137327,411381,274031) : difference with theory (-23) = 0 CORRECTING DEFECT 24 (vertices=62, convex hull=60, v0=77713) After retessellation of defect 24 (v0=77713), euler #=-22 (137358,411498,274118) : difference with theory (-22) = 0 CORRECTING DEFECT 25 (vertices=55, convex hull=93, v0=78455) After retessellation of defect 25 (v0=78455), euler #=-21 (137388,411631,274222) : difference with theory (-21) = 0 CORRECTING DEFECT 26 (vertices=50, convex hull=72, v0=78459) After retessellation of defect 26 (v0=78459), euler #=-20 (137412,411732,274300) : difference with theory (-20) = 0 CORRECTING DEFECT 27 (vertices=20, convex hull=32, v0=79770) After retessellation of defect 27 (v0=79770), euler #=-19 (137420,411766,274327) : difference with theory (-19) = 0 CORRECTING DEFECT 28 (vertices=202, convex hull=110, v0=83705) After retessellation of defect 28 (v0=83705), euler #=-18 (137455,411918,274445) : difference with theory (-18) = 0 CORRECTING DEFECT 29 (vertices=22, convex hull=24, v0=84004) After retessellation of defect 29 (v0=84004), euler #=-17 (137459,411937,274461) : difference with theory (-17) = 0 CORRECTING DEFECT 30 (vertices=35, convex hull=29, v0=96117) After retessellation of defect 30 (v0=96117), euler #=-16 (137465,411965,274484) : difference with theory (-16) = 0 CORRECTING DEFECT 31 (vertices=26, convex hull=80, v0=101926) After retessellation of defect 31 (v0=101926), euler #=-15 (137476,412025,274534) : difference with theory (-15) = 0 CORRECTING DEFECT 32 (vertices=31, convex hull=70, v0=102198) After retessellation of defect 32 (v0=102198), euler #=-14 (137494,412107,274599) : difference with theory (-14) = 0 CORRECTING DEFECT 33 (vertices=39, convex hull=50, v0=102403) After retessellation of defect 33 (v0=102403), euler #=-13 (137503,412150,274634) : difference with theory (-13) = 0 CORRECTING DEFECT 34 (vertices=8, convex hull=22, v0=106110) After retessellation of defect 34 (v0=106110), euler #=-12 (137505,412163,274646) : difference with theory (-12) = 0 CORRECTING DEFECT 35 (vertices=229, convex hull=51, v0=107331) After retessellation of defect 35 (v0=107331), euler #=-11 (137519,412225,274695) : difference with theory (-11) = 0 CORRECTING DEFECT 36 (vertices=6, convex hull=17, v0=107495) After retessellation of defect 36 (v0=107495), euler #=-10 (137520,412234,274704) : difference with theory (-10) = 0 CORRECTING DEFECT 37 (vertices=22, convex hull=58, v0=108358) After retessellation of defect 37 (v0=108358), euler #=-9 (137533,412296,274754) : difference with theory (-9) = 0 CORRECTING DEFECT 38 (vertices=216, convex hull=158, v0=109177) After retessellation of defect 38 (v0=109177), euler #=-8 (137604,412580,274968) : difference with theory (-8) = 0 CORRECTING DEFECT 39 (vertices=25, convex hull=61, v0=115739) After retessellation of defect 39 (v0=115739), euler #=-7 (137619,412648,275022) : difference with theory (-7) = 0 CORRECTING DEFECT 40 (vertices=103, convex hull=71, v0=116398) After retessellation of defect 40 (v0=116398), euler #=-6 (137628,412705,275071) : difference with theory (-6) = 0 CORRECTING DEFECT 41 (vertices=9, convex hull=25, v0=116460) After retessellation of defect 41 (v0=116460), euler #=-5 (137630,412719,275084) : difference with theory (-5) = 0 CORRECTING DEFECT 42 (vertices=46, convex hull=50, v0=124528) After retessellation of defect 42 (v0=124528), euler #=-4 (137639,412763,275120) : difference with theory (-4) = 0 CORRECTING DEFECT 43 (vertices=18, convex hull=56, v0=125075) After retessellation of defect 43 (v0=125075), euler #=-3 (137649,412811,275159) : difference with theory (-3) = 0 CORRECTING DEFECT 44 (vertices=8, convex hull=21, v0=127503) After retessellation of defect 44 (v0=127503), euler #=-2 (137649,412817,275166) : difference with theory (-2) = 0 CORRECTING DEFECT 45 (vertices=23, convex hull=59, v0=128859) After retessellation of defect 45 (v0=128859), euler #=-1 (137663,412877,275213) : difference with theory (-1) = 0 CORRECTING DEFECT 46 (vertices=40, convex hull=83, v0=134314) After retessellation of defect 46 (v0=134314), euler #=0 (137687,412982,275295) : difference with theory (0) = 0 CORRECTING DEFECT 47 (vertices=96, convex hull=65, v0=139053) After retessellation of defect 47 (v0=139053), euler #=1 (137707,413067,275361) : difference with theory (1) = 0 CORRECTING DEFECT 48 (vertices=100, convex hull=106, v0=139321) After retessellation of defect 48 (v0=139321), euler #=2 (137743,413223,275482) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.04-->11.66) (max @ vno 106474 --> 116532) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.04-->11.66) (max @ vno 106474 --> 116532) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 148 mutations (33.6%), 293 crossovers (66.4%), 134 vertices were eliminated building final representation... 2649 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=137743, nf=275482, ne=413223, g=0) writing corrected surface to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 263 intersecting 001: 20 intersecting terminating search with 0 intersecting topology fixing took 3.3 minutes FSRUNTIME@ mris_fix_topology rh 0.0547 hours 1 threads #VMPC# mris_fix_topology VmPeak 781416 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 142205 - 426609 + 284406 = 2 --> 0 holes F =2V-4: 284406 = 284410-4 (0) 2E=3F: 853218 = 853218 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 137743 - 413223 + 275482 = 2 --> 0 holes F =2V-4: 275482 = 275486-4 (0) 2E=3F: 826446 = 826446 (0) total defect index = 0 Thu Feb 12 17:47:36 EST 2026 setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts /usr/local/freesurfer/stable7.4.1/bin/defect2seg --s PBRHOPE_HOPE089_PETMR --cortex freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 defect2seg 7.4.1 Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux pid 3748684 mri_label2label --label-cortex /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.orig.nofix /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/aseg.presurf.mgz 0 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 14 non-cortical segments detected only using segment with 9489 vertices erasing segment 1 (vno[0] = 110842) erasing segment 2 (vno[0] = 112653) erasing segment 3 (vno[0] = 114350) erasing segment 4 (vno[0] = 115844) erasing segment 5 (vno[0] = 115981) erasing segment 6 (vno[0] = 115986) erasing segment 7 (vno[0] = 116013) erasing segment 8 (vno[0] = 117672) erasing segment 9 (vno[0] = 117705) erasing segment 10 (vno[0] = 117720) erasing segment 11 (vno[0] = 120312) erasing segment 12 (vno[0] = 120445) erasing segment 13 (vno[0] = 130380) mri_label2vol --defects /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.orig.nofix /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.defect_labels /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz 1000 0 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/surface.defects.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/surface.defects.mgz mris_defects_pointset -s /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.orig.nofix -d /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.defect_labels -o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.defects.pointset --label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.nofix.cortex.label Reading in surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.orig.nofix Reading in defect segmentation /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.defect_labels Reading in label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 210088 mris_defects_pointset done mri_label2label --label-cortex /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.orig.nofix /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/aseg.presurf.mgz 0 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 33 non-cortical segments detected only using segment with 9121 vertices erasing segment 0 (vno[0] = 41810) erasing segment 1 (vno[0] = 41862) erasing segment 2 (vno[0] = 41874) erasing segment 3 (vno[0] = 43213) erasing segment 5 (vno[0] = 44552) erasing segment 6 (vno[0] = 45665) erasing segment 7 (vno[0] = 45848) erasing segment 8 (vno[0] = 48213) erasing segment 9 (vno[0] = 52987) erasing segment 10 (vno[0] = 53197) erasing segment 11 (vno[0] = 55468) erasing segment 12 (vno[0] = 55533) erasing segment 13 (vno[0] = 56411) erasing segment 14 (vno[0] = 57530) erasing segment 15 (vno[0] = 58817) erasing segment 16 (vno[0] = 58846) erasing segment 17 (vno[0] = 59605) erasing segment 18 (vno[0] = 62680) erasing segment 19 (vno[0] = 63737) erasing segment 20 (vno[0] = 64129) erasing segment 21 (vno[0] = 85996) erasing segment 22 (vno[0] = 92386) erasing segment 23 (vno[0] = 100535) erasing segment 24 (vno[0] = 102571) erasing segment 25 (vno[0] = 103293) erasing segment 26 (vno[0] = 105147) erasing segment 27 (vno[0] = 105198) erasing segment 28 (vno[0] = 106272) erasing segment 29 (vno[0] = 108279) erasing segment 30 (vno[0] = 119726) erasing segment 31 (vno[0] = 120544) erasing segment 32 (vno[0] = 120556) mri_label2vol --defects /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.orig.nofix /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.defect_labels /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/surface.defects.mgz 2000 1 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/surface.defects.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/surface.defects.mgz mris_defects_pointset -s /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.orig.nofix -d /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.defect_labels -o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.defects.pointset --label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.nofix.cortex.label Reading in surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.orig.nofix Reading in defect segmentation /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.defect_labels Reading in label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 204980 mris_defects_pointset done Started at Thu Feb 12 17:47:36 EST 2026 Ended at Thu Feb 12 17:48:11 EST 2026 Defect2seg-Run-Time-Sec 35 Defect2seg-Run-Time-Min 0.70 Defect2seg-Run-Time-Hours 0.01 tkmeditfv PBRHOPE_HOPE089_PETMR brain.finalsurfs.mgz -defect defect2seg Done mris_remesh --remesh --iters 3 --input /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.orig.premesh --output /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.709298 remeshing to edge length 0.709298 with 3 iterations avg qual before : 0.889421 after: 0.970819 Removing intersections Remeshed surface quality stats nv0 = 142205 nv = 148275 1.04268 Area 296546 0.30111 0.03377 0.092680 0.4683 Corner 889638 60.00000 8.85687 20.213293 137.6794 Edge 444819 0.84194 0.08275 0.480637 1.2674 Hinge 444819 9.92108 10.21088 0.000024 128.2518 mris_remesh done mris_remesh --remesh --iters 3 --input /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.orig.premesh --output /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.709168 remeshing to edge length 0.709168 with 3 iterations avg qual before : 0.889124 after: 0.970903 Removing intersections Remeshed surface quality stats nv0 = 137743 nv = 143551 1.04217 Area 287098 0.30099 0.03369 0.083776 0.4523 Corner 861294 60.00000 8.84355 17.597211 144.2712 Edge 430647 0.84176 0.08255 0.457134 1.2611 Hinge 430647 10.02365 10.41609 0.000018 151.7853 mris_remesh done /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 rm -f ../surf/lh.inflated /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Thu Feb 12 17:49:20 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 284121 voxels (1.69%) border gray 293742 voxels (1.75%) 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=59589, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (96.0): 96.8 +- 8.1 [70.0 --> 110.0] CCS GM (75.0) : 74.2 +- 12.0 [30.0 --> 110.0] white_mean = 96.8455 +/- 8.1151, gray_mean = 74.1648 +/- 12.0292 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=179 nbins=180 intensity peaks found at WM=100+-6.1, GM=71+-10.4 white_mode = 100, gray_mode = 71 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70.000000) setting MAX_BORDER_WHITE to 108.1 (was 105.000000) setting MIN_BORDER_WHITE to 71.0 (was 85.000000) setting MAX_CSF to 46.9 (was 40.000000) setting MAX_GRAY to 91.9 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 59.0 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 34.9 (was 40.000000) When placing the white surface white_border_hi = 108.115; white_border_low = 71; white_outside_low = 58.9708; white_inside_hi = 120; white_outside_hi = 108.115; When placing the pial surface pial_border_hi = 58.9708; pial_border_low = 34.9125; pial_outside_low = 10; pial_inside_hi = 91.8849; pial_outside_hi = 52.9563; #VMPC# mris_autodet_gwstats VmPeak 287316 mris_autodet_gwstats done #-------------------------------------------- #@# AutoDetGWStats rh Thu Feb 12 17:49:24 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 284121 voxels (1.69%) border gray 293742 voxels (1.75%) 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=59589, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (96.0): 96.8 +- 8.1 [70.0 --> 110.0] CCS GM (75.0) : 74.2 +- 12.0 [30.0 --> 110.0] white_mean = 96.8455 +/- 8.1151, gray_mean = 74.1648 +/- 12.0292 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=179 nbins=180 intensity peaks found at WM=100+-7.0, GM=72+-8.7 white_mode = 100, gray_mode = 72 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 60.0 (was 70.000000) setting MAX_BORDER_WHITE to 108.1 (was 105.000000) setting MIN_BORDER_WHITE to 72.0 (was 85.000000) setting MAX_CSF to 47.9 (was 40.000000) setting MAX_GRAY to 91.9 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 60.0 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 35.9 (was 40.000000) When placing the white surface white_border_hi = 108.115; white_border_low = 72; white_outside_low = 59.9708; white_inside_hi = 120; white_outside_hi = 108.115; When placing the pial surface pial_border_hi = 59.9708; pial_border_low = 35.9125; pial_outside_low = 10; pial_inside_hi = 91.8849; pial_outside_hi = 53.9563; #VMPC# mris_autodet_gwstats VmPeak 281180 mris_autodet_gwstats done #-------------------------------------------- #@# WhitePreAparc lh Thu Feb 12 17:49:28 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs 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 296546 0.26605 0.06335 0.001364 0.5789 Corner 889638 60.00000 9.41765 4.269752 140.4642 Edge 444819 0.78731 0.11536 0.018170 1.3887 Hinge 444819 6.44473 6.41130 0.000005 136.2153 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=59589, wmmin=5, clip=110 MRIfindBrightNonWM(): 482 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=7962, nmarked2=16, nripped=7962 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 74138: xyz = (-43.3073,-53.5811,-22.7246) oxyz = (-43.3073,-53.5811,-22.7246) wxzy = (-43.3073,-53.5811,-22.7246) pxyz = (0,0,0) CBVO Creating mask 148275 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=7962 #FML# MRISripMidline(): nmarked=7962, nmarked2=16, nripped=7962 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 71.0000000; outside_low = 58.9708370; outside_hi = 108.1150970; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=2 had to be increased for 143 vertices, nripped=7962 mean border=82.1, 215 (215) missing vertices, mean dist 0.2 [1.1 (%35.3)->0.9 (%64.7))] %45 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2378 min Finding expansion regions mean absolute distance = 0.97 +- 1.18 5285 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=r440-, 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=3257705.5, rms=10.506 001: dt: 0.5000, sse=1759036.6, rms=7.564 (28.007%) 002: dt: 0.5000, sse=1040658.5, rms=5.618 (25.732%) 003: dt: 0.5000, sse=708553.1, rms=4.440 (20.968%) 004: dt: 0.5000, sse=557139.3, rms=3.778 (14.908%) 005: dt: 0.5000, sse=488502.7, rms=3.427 (9.273%) 006: dt: 0.5000, sse=457640.8, rms=3.252 (5.110%) 007: dt: 0.5000, sse=448685.0, rms=3.161 (2.796%) 008: dt: 0.5000, sse=435575.1, rms=3.111 (1.603%) rms = 3.0897/3.1106, sse=434276.2/435575.1, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=434276.2, rms=3.090 (0.673%) 010: dt: 0.2500, sse=293770.0, rms=2.108 (31.784%) 011: dt: 0.2500, sse=271111.2, rms=1.877 (10.940%) rms = 1.8449/1.8771, sse=267205.7/271111.1, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=267205.8, rms=1.845 (1.717%) 013: dt: 0.1250, sse=261205.8, rms=1.788 (3.069%) rms = 1.7834/1.7883, sse=259842.2/261205.8, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=259842.2, rms=1.783 (0.273%) 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=7962 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 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8193, nmarked2=21, nripped=8193 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 71.0000000; outside_low = 58.9708370; outside_hi = 108.1150970; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=1 had to be increased for 254 vertices, nripped=8193 mean border=85.1, 190 (68) missing vertices, mean dist -0.4 [0.7 (%66.6)->0.3 (%33.4))] %62 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1639 min Finding expansion regions mean absolute distance = 0.54 +- 0.83 6421 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=r440-, 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=837367.5, rms=4.666 015: dt: 0.5000, sse=505609.1, rms=3.144 (32.605%) 016: dt: 0.5000, sse=465785.7, rms=2.907 (7.558%) rms = 2.9090/2.9068, sse=480104.8/465785.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=373877.3, rms=2.258 (22.319%) 018: dt: 0.2500, sse=324809.8, rms=1.873 (17.036%) 019: dt: 0.2500, sse=313209.1, rms=1.741 (7.060%) 020: dt: 0.2500, sse=305653.3, rms=1.661 (4.605%) rms = 1.6121/1.6609, sse=301594.0/305653.3, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=301594.0, rms=1.612 (2.939%) 022: dt: 0.1250, sse=297061.4, rms=1.558 (3.378%) rms = 1.5424/1.5577, sse=295945.5/297061.4, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=295945.5, rms=1.542 (0.978%) 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=8193 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8299, nmarked2=21, nripped=8299 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 71.0000000; outside_low = 58.9708370; outside_hi = 108.1150970; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 681 vertices, nripped=8299 mean border=87.4, 193 (28) missing vertices, mean dist -0.2 [0.5 (%66.1)->0.3 (%33.9))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0857 min Finding expansion regions mean absolute distance = 0.39 +- 0.52 5540 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=r440-, 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=549459.9, rms=3.418 024: dt: 0.5000, sse=399313.0, rms=2.483 (27.358%) rms = 2.5733/2.4829, sse=412528.1/399313.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=325584.2, rms=1.881 (24.237%) 026: dt: 0.2500, sse=293855.2, rms=1.536 (18.330%) 027: dt: 0.2500, sse=287851.4, rms=1.453 (5.455%) rms = 1.4286/1.4525, sse=284817.2/287851.4, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=284817.2, rms=1.429 (1.646%) 029: dt: 0.1250, sse=280763.6, rms=1.377 (3.641%) rms = 1.3728/1.3766, sse=280663.4/280763.6, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=280663.4, rms=1.373 (0.277%) 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=8299 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8391, nmarked2=22, nripped=8391 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 71.0000000; outside_low = 58.9708370; outside_hi = 108.1150970; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 868 vertices, nripped=8391 mean border=88.3, 253 (22) missing vertices, mean dist -0.1 [0.4 (%56.3)->0.3 (%43.7))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0539 min Finding expansion regions mean absolute distance = 0.32 +- 0.42 3846 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=r440-, 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=325416.9, rms=1.891 031: dt: 0.5000, sse=310590.7, rms=1.692 (10.549%) rms = 2.2592/1.6918, sse=369628.2/310590.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=266885.6, rms=1.209 (28.541%) 033: dt: 0.2500, sse=262058.0, rms=1.151 (4.811%) 034: dt: 0.2500, sse=253969.1, rms=1.057 (8.124%) rms = 1.1019/1.0573, sse=254390.7/253969.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 1.0391/1.0573, sse=252542.3/253969.1, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=252542.3, rms=1.039 (1.718%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Removing intersections #ET# mris_place_surface 4.37 minutes Writing output to ../surf/lh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2249920 mris_place_surface done #-------------------------------------------- #@# WhitePreAparc rh Thu Feb 12 17:53:58 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs 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 287098 0.26521 0.06382 0.001161 0.5771 Corner 861294 60.00000 9.47082 4.727479 147.8820 Edge 430647 0.78597 0.11626 0.036445 1.3554 Hinge 430647 6.50590 6.55581 0.000017 159.9266 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=59589, wmmin=5, clip=110 MRIfindBrightNonWM(): 482 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=8153, nmarked2=0, nripped=8153 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 71776: xyz = (42.7329,-37.4736,33.1405) oxyz = (42.7329,-37.4736,33.1405) wxzy = (42.7329,-37.4736,33.1405) pxyz = (0,0,0) CBVO Creating mask 143551 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=8153 #FML# MRISripMidline(): nmarked=8153, nmarked2=0, nripped=8153 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 72.0000000; outside_low = 59.9708370; outside_hi = 108.1150970; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=2 had to be increased for 152 vertices, nripped=8153 mean border=82.7, 141 (141) missing vertices, mean dist 0.1 [1.0 (%38.5)->0.9 (%61.5))] %46 local maxima, %48 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2255 min Finding expansion regions mean absolute distance = 0.93 +- 1.16 4961 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=r440-, 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=3014809.8, rms=10.281 001: dt: 0.5000, sse=1626757.6, rms=7.386 (28.156%) 002: dt: 0.5000, sse=962800.7, rms=5.483 (25.764%) 003: dt: 0.5000, sse=663953.3, rms=4.350 (20.671%) 004: dt: 0.5000, sse=531477.1, rms=3.743 (13.951%) 005: dt: 0.5000, sse=469449.7, rms=3.420 (8.631%) 006: dt: 0.5000, sse=444660.7, rms=3.271 (4.360%) 007: dt: 0.5000, sse=435273.7, rms=3.193 (2.378%) rms = 3.1562/3.1929, sse=428629.4/435273.7, time step reduction 1 of 3 to 0.250 0 0 1 008: dt: 0.5000, sse=428629.4, rms=3.156 (1.149%) 009: dt: 0.2500, sse=294541.2, rms=2.168 (31.308%) 010: dt: 0.2500, sse=270655.4, rms=1.929 (11.031%) rms = 1.8884/1.9289, sse=260931.7/270655.4, time step reduction 2 of 3 to 0.125 0 0 1 011: dt: 0.2500, sse=260931.7, rms=1.888 (2.097%) 012: dt: 0.1250, sse=255057.7, rms=1.831 (3.046%) rms = 1.8231/1.8309, sse=255604.5/255057.7, time step reduction 3 of 3 to 0.062 0 1 1 013: dt: 0.1250, sse=255604.5, rms=1.823 (0.429%) maximum number of reductions reached, breaking from loop positioning took 1.3 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=8153 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8350, nmarked2=0, nripped=8350 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 72.0000000; outside_low = 59.9708370; outside_hi = 108.1150970; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=1 had to be increased for 254 vertices, nripped=8350 mean border=85.2, 121 (26) missing vertices, mean dist -0.3 [0.6 (%63.8)->0.3 (%36.2))] %61 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1516 min Finding expansion regions mean absolute distance = 0.48 +- 0.78 6009 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=r440-, 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=713641.7, rms=4.279 014: dt: 0.5000, sse=443239.9, rms=2.881 (32.668%) 015: dt: 0.5000, sse=424061.9, rms=2.794 (3.001%) rms = 2.8586/2.7944, sse=435406.7/424061.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 016: dt: 0.2500, sse=335327.7, rms=2.112 (24.407%) 017: dt: 0.2500, sse=298245.4, rms=1.742 (17.550%) 018: dt: 0.2500, sse=289820.6, rms=1.645 (5.555%) rms = 1.6024/1.6449, sse=287243.2/289820.6, time step reduction 2 of 3 to 0.125 0 0 1 019: dt: 0.2500, sse=287243.2, rms=1.602 (2.585%) 020: dt: 0.1250, sse=283242.6, rms=1.549 (3.354%) rms = 1.5382/1.5486, sse=283124.4/283242.6, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=283124.4, rms=1.538 (0.673%) maximum number of reductions reached, breaking from loop positioning took 0.8 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=8350 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8491, nmarked2=0, nripped=8491 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 72.0000000; outside_low = 59.9708370; outside_hi = 108.1150970; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 460 vertices, nripped=8491 mean border=87.3, 133 (15) missing vertices, mean dist -0.2 [0.4 (%64.3)->0.2 (%35.7))] %76 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0803 min Finding expansion regions mean absolute distance = 0.37 +- 0.52 5177 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=r440-, 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=496718.0, rms=3.228 022: dt: 0.5000, sse=383291.8, rms=2.481 (23.135%) rms = 2.5801/2.4812, sse=397455.7/383291.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 023: dt: 0.2500, sse=313104.9, rms=1.880 (24.223%) 024: dt: 0.2500, sse=282418.2, rms=1.541 (18.040%) 025: dt: 0.2500, sse=274515.7, rms=1.463 (5.068%) rms = 1.4369/1.4629, sse=273547.7/274515.7, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=273547.7, rms=1.437 (1.779%) rms = 1.3886/1.4369, sse=271310.8/273547.7, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=271310.8, rms=1.389 (3.360%) 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=8491 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=8527, nmarked2=0, nripped=8527 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 72.0000000; outside_low = 59.9708370; outside_hi = 108.1150970; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 632 vertices, nripped=8527 mean border=88.2, 198 (13) missing vertices, mean dist -0.1 [0.4 (%55.3)->0.2 (%44.7))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0496 min Finding expansion regions mean absolute distance = 0.31 +- 0.41 4626 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=r440-, 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=311278.9, rms=1.867 028: dt: 0.5000, sse=296076.3, rms=1.687 (9.671%) rms = 2.2699/1.6866, sse=356268.0/296076.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=258114.0, rms=1.214 (28.012%) 030: dt: 0.2500, sse=249243.4, rms=1.151 (5.227%) 031: dt: 0.2500, sse=243974.6, rms=1.064 (7.541%) rms = 1.1028/1.0639, sse=245583.6/243974.6, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 1.0456/1.0639, sse=242710.1/243974.6, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=242710.1, rms=1.046 (1.719%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Removing intersections #ET# mris_place_surface 3.92 minutes Writing output to ../surf/rh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2211368 mris_place_surface done #-------------------------------------------- #@# CortexLabel lh Thu Feb 12 17:58:01 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 2 non-cortical segments detected only using segment with 10168 vertices erasing segment 1 (vno[0] = 121527) #-------------------------------------------- #@# CortexLabel+HipAmyg lh Thu Feb 12 17:58:17 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 3 non-cortical segments detected only using segment with 7778 vertices erasing segment 1 (vno[0] = 96086) erasing segment 2 (vno[0] = 129203) #-------------------------------------------- #@# CortexLabel rh Thu Feb 12 17:58:34 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 10019 vertices erasing segment 0 (vno[0] = 35090) erasing segment 1 (vno[0] = 36143) erasing segment 3 (vno[0] = 44340) erasing segment 4 (vno[0] = 45046) erasing segment 5 (vno[0] = 46192) erasing segment 6 (vno[0] = 90288) erasing segment 7 (vno[0] = 122490) #-------------------------------------------- #@# CortexLabel+HipAmyg rh Thu Feb 12 17:58:50 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 8229 vertices erasing segment 0 (vno[0] = 35090) erasing segment 1 (vno[0] = 36143) erasing segment 3 (vno[0] = 44340) erasing segment 4 (vno[0] = 45046) erasing segment 5 (vno[0] = 46192) erasing segment 6 (vno[0] = 73121) erasing segment 7 (vno[0] = 74994) erasing segment 8 (vno[0] = 90288) erasing segment 9 (vno[0] = 122490) #-------------------------------------------- #@# Smooth2 lh Thu Feb 12 17:59:06 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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... #-------------------------------------------- #@# Smooth2 rh Thu Feb 12 17:59:10 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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... #-------------------------------------------- #@# Inflation2 lh Thu Feb 12 17:59:14 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 52.4 mm, total surface area = 89828 mm^2 step 000: RMS=0.173 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.039 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.5 minutes mris_inflate utimesec 26.088392 mris_inflate stimesec 1.045350 mris_inflate ru_maxrss 228628 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 560440 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11592 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 264 mris_inflate ru_nivcsw 46 #-------------------------------------------- #@# Inflation2 rh Thu Feb 12 17:59:41 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.1 mm, total surface area = 87214 mm^2 step 000: RMS=0.175 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (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 25.475366 mris_inflate stimesec 1.005391 mris_inflate ru_maxrss 221420 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 509263 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11232 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 265 mris_inflate ru_nivcsw 69 #-------------------------------------------- #@# Curv .H and .K lh Thu Feb 12 18:00:08 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 25.502*4pi (320.469) --> -25 handles ICI = 250.9, FI = 1791.2, variation=30870.013 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 196 vertices thresholded to be in k1 ~ [-0.59 0.42], k2 ~ [-0.14 0.08] total integrated curvature = 0.506*4pi (6.353) --> 0 handles ICI = 1.5, FI = 10.0, variation=170.629 135 vertices thresholded to be in [-0.02 0.04] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 134 vertices thresholded to be in [-0.24 0.20] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done. #-------------------------------------------- #@# Curv .H and .K rh Thu Feb 12 18:01:05 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 31.444*4pi (395.140) --> -30 handles ICI = 247.5, FI = 1778.5, variation=30465.146 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 193 vertices thresholded to be in k1 ~ [-0.89 0.47], k2 ~ [-0.11 0.12] total integrated curvature = 0.572*4pi (7.182) --> 0 handles ICI = 1.5, FI = 9.3, variation=159.314 136 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 121 vertices thresholded to be in [-0.27 0.23] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done. #-------------------------------------------- #@# Sphere lh Thu Feb 12 18:02:02 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 0.319... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=r440-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.55 pass 1: epoch 2 of 3 starting distance error %19.52 unfolding complete - removing small folds... starting distance error %19.48 removing remaining folds... final distance error %19.52 MRISunfold() return, current seed 1234 -01: dt=0.0000, 23 negative triangles VmPeak 581568 169: dt=0.9900, 23 negative triangles 170: dt=0.9900, 11 negative triangles 171: dt=0.9900, 9 negative triangles 172: dt=0.9900, 5 negative triangles 173: dt=0.9900, 1 negative triangles 174: dt=0.9900, 1 negative triangles 175: dt=0.9900, 1 negative triangles 176: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1998 hours FSRUNTIME@ mris_sphere 0.1998 hours 1 threads #VMPC# mris_sphere VmPeak 581568 mris_sphere done #-------------------------------------------- #@# Sphere rh Thu Feb 12 18:14:01 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 0.321... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=r440-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.75 pass 1: epoch 2 of 3 starting distance error %19.71 unfolding complete - removing small folds... starting distance error %19.62 removing remaining folds... final distance error %19.66 MRISunfold() return, current seed 1234 -01: dt=0.0000, 29 negative triangles VmPeak 572124 210: dt=0.9900, 29 negative triangles 211: dt=0.9900, 8 negative triangles 212: dt=0.9900, 7 negative triangles 213: dt=0.9900, 7 negative triangles 214: dt=0.9900, 4 negative triangles 215: dt=0.9900, 4 negative triangles 216: dt=0.9900, 4 negative triangles 217: dt=0.9900, 4 negative triangles 218: dt=0.9900, 4 negative triangles 219: dt=0.9900, 4 negative triangles 220: dt=0.9900, 4 negative triangles 221: dt=0.9900, 3 negative triangles 222: dt=0.9900, 3 negative triangles 223: dt=0.9900, 3 negative triangles 224: dt=0.9900, 3 negative triangles 225: dt=0.9900, 3 negative triangles 226: dt=0.9900, 2 negative triangles 227: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.2345 hours FSRUNTIME@ mris_sphere 0.2345 hours 1 threads #VMPC# mris_sphere VmPeak 572124 mris_sphere done #-------------------------------------------- #@# Surf Reg lh Thu Feb 12 18:28:06 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/stable7.4.1/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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=r440-, 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=r440-, 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=r440-, 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 = 5.317 curvature mean = 0.050, std = 0.823 curvature mean = 0.018, std = 0.860 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (16.50, -9.00, -27.50) sse = 238862.1, elapsed since starting=0.4206 min MRISrigidBodyAlignGlobal() done 0.42 min curvature mean = 0.010, std = 0.833 curvature mean = 0.005, std = 0.947 curvature mean = 0.004, std = 0.842 curvature mean = 0.002, std = 0.979 curvature mean = 0.001, std = 0.843 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.020, std = 0.260 curvature mean = 0.041, std = 0.252 curvature mean = 0.057, std = 0.369 curvature mean = 0.036, std = 0.310 curvature mean = 0.031, std = 0.567 curvature mean = 0.035, std = 0.338 curvature mean = 0.017, std = 0.715 curvature mean = 0.034, std = 0.351 curvature mean = 0.005, std = 0.825 MRISregister() return, current seed 0 -01: dt=0.0000, 19 negative triangles VmPeak 560028 114: dt=0.9900, 19 negative triangles expanding nbhd size to 1 115: dt=0.9900, 24 negative triangles 116: dt=0.9900, 17 negative triangles 117: dt=0.9900, 16 negative triangles 118: dt=0.9900, 14 negative triangles 119: dt=0.9900, 11 negative triangles 120: dt=0.9900, 10 negative triangles 121: dt=0.9900, 10 negative triangles 122: dt=0.9900, 10 negative triangles 123: dt=0.9900, 11 negative triangles 124: dt=0.9900, 11 negative triangles 125: dt=0.9900, 8 negative triangles 126: dt=0.9900, 7 negative triangles 127: dt=0.9900, 1 negative triangles 128: dt=0.9900, 1 negative triangles 129: dt=0.9900, 3 negative triangles 130: dt=0.9900, 2 negative triangles 131: dt=0.9900, 1 negative triangles 132: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.16 hours #VMPC# mris_register VmPeak 560028 FSRUNTIME@ mris_register 0.1635 hours 1 threads ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Thu Feb 12 18:37:55 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/stable7.4.1/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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=r440-, 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=r440-, 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=r440-, 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 = 5.387 curvature mean = 0.041, std = 0.812 curvature mean = 0.015, std = 0.861 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (18.50, -14.50, -29.50) sse = 333914.9, elapsed since starting=0.4068 min MRISrigidBodyAlignGlobal() done 0.41 min curvature mean = 0.015, std = 0.818 curvature mean = 0.004, std = 0.947 curvature mean = 0.011, std = 0.827 curvature mean = 0.001, std = 0.979 curvature mean = 0.009, std = 0.827 curvature mean = -0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.020, std = 0.273 curvature mean = 0.038, std = 0.241 curvature mean = 0.050, std = 0.355 curvature mean = 0.032, std = 0.300 curvature mean = 0.031, std = 0.545 curvature mean = 0.031, std = 0.327 curvature mean = 0.016, std = 0.690 curvature mean = 0.031, std = 0.339 curvature mean = 0.005, std = 0.801 MRISregister() return, current seed 0 -01: dt=0.0000, 54 negative triangles VmPeak 550744 125: dt=0.9900, 54 negative triangles 126: dt=0.9900, 48 negative triangles 127: dt=0.9900, 45 negative triangles 128: dt=0.9900, 41 negative triangles 129: dt=0.9900, 41 negative triangles 130: dt=0.9900, 35 negative triangles 131: dt=0.9900, 26 negative triangles 132: dt=0.9900, 26 negative triangles 133: dt=0.9900, 23 negative triangles 134: dt=0.9900, 24 negative triangles 135: dt=0.9900, 25 negative triangles 136: dt=0.9900, 24 negative triangles 137: dt=0.9900, 21 negative triangles 138: dt=0.9900, 19 negative triangles 139: dt=0.9900, 18 negative triangles 140: dt=0.9900, 20 negative triangles 141: dt=0.9900, 19 negative triangles 142: dt=0.9900, 17 negative triangles 143: dt=0.9900, 14 negative triangles 144: dt=0.9900, 9 negative triangles 145: dt=0.9900, 11 negative triangles 146: dt=0.9900, 10 negative triangles 147: dt=0.9900, 8 negative triangles 148: dt=0.9900, 6 negative triangles 149: dt=0.9900, 4 negative triangles 150: dt=0.9900, 5 negative triangles 151: dt=0.9900, 4 negative triangles 152: dt=0.9900, 4 negative triangles 153: dt=0.9900, 3 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.18 hours #VMPC# mris_register VmPeak 550744 FSRUNTIME@ mris_register 0.1817 hours 1 threads ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Thu Feb 12 18:48:49 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 #-------------------------------------------- #@# Jacobian white rh Thu Feb 12 18:48:50 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 #-------------------------------------------- #@# AvgCurv lh Thu Feb 12 18:48:52 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Thu Feb 12 18:48:53 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Feb 12 18:48:53 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PBRHOPE_HOPE089_PETMR lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1895 labels changed using aseg relabeling using gibbs priors... 000: 3315 changed, 148275 examined... 001: 765 changed, 13992 examined... 002: 172 changed, 4338 examined... 003: 66 changed, 1076 examined... 004: 25 changed, 395 examined... 005: 10 changed, 150 examined... 006: 6 changed, 53 examined... 007: 1 changed, 33 examined... 008: 0 changed, 7 examined... 362 labels changed using aseg 000: 147 total segments, 109 labels (337 vertices) changed 001: 42 total segments, 4 labels (13 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2291 vertices marked for relabeling... 2291 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Cortical Parc rh Thu Feb 12 18:49:05 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PBRHOPE_HOPE089_PETMR rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1737 labels changed using aseg relabeling using gibbs priors... 000: 3089 changed, 143551 examined... 001: 696 changed, 13208 examined... 002: 190 changed, 3931 examined... 003: 57 changed, 1126 examined... 004: 24 changed, 351 examined... 005: 9 changed, 146 examined... 006: 2 changed, 58 examined... 007: 0 changed, 10 examined... 297 labels changed using aseg 000: 105 total segments, 61 labels (249 vertices) changed 001: 46 total segments, 2 labels (2 vertices) changed 002: 44 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... 1817 vertices marked for relabeling... 1817 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 11 seconds. #-------------------------------------------- #@# WhiteSurfs lh Thu Feb 12 18:49:17 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs 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 296546 0.34280 0.12346 0.000588 1.6525 Corner 889638 60.00000 15.33407 0.067896 179.8286 Edge 444819 0.90435 0.20710 0.014708 3.5283 Hinge 444819 14.41084 14.95986 0.000018 179.9395 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=59589, wmmin=5, clip=110 MRIfindBrightNonWM(): 482 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 10514/148275 vertices (137761 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 346 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 74138: xyz = (-43.9168,-52.9297,-23.5577) oxyz = (-43.9168,-52.9297,-23.5577) wxzy = (-43.9168,-52.9297,-23.5577) pxyz = (0,0,0) CBVO Creating mask 148275 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 71.0000000; outside_low = 58.9708370; outside_hi = 108.1150970; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=2 had to be increased for 212 vertices, nripped=10860 mean border=82.2, 222 (222) missing vertices, mean dist 0.3 [1.8 (%15.6)->0.7 (%84.4))] %44 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2265 min Finding expansion regions mean absolute distance = 0.89 +- 1.10 4695 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=r440-, 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=1809169.5, rms=7.614 001: dt: 0.5000, sse=797367.9, rms=4.625 (39.255%) 002: dt: 0.5000, sse=534511.1, rms=3.444 (25.546%) 003: dt: 0.5000, sse=476229.1, rms=3.126 (9.219%) 004: dt: 0.5000, sse=450164.0, rms=2.962 (5.261%) rms = 2.9819/2.9617, sse=454044.9/450164.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=357377.7, rms=2.303 (22.255%) 006: dt: 0.2500, sse=318089.0, rms=1.955 (15.099%) 007: dt: 0.2500, sse=308046.7, rms=1.855 (5.096%) rms = 1.8187/1.8553, sse=305025.5/308046.7, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=305025.5, rms=1.819 (1.969%) rms = 1.7717/1.8187, sse=300834.1/305025.5, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=300834.1, rms=1.772 (2.589%) 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 = 108.1150970; border_low = 71.0000000; outside_low = 58.9708370; outside_hi = 108.1150970; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=1 had to be increased for 217 vertices, nripped=10860 mean border=85.0, 138 (58) missing vertices, mean dist -0.3 [0.7 (%64.8)->0.3 (%35.2))] %60 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1614 min Finding expansion regions mean absolute distance = 0.52 +- 0.81 6151 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=r440-, 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=734509.6, rms=4.306 010: dt: 0.5000, sse=462525.8, rms=2.934 (31.850%) 011: dt: 0.5000, sse=425401.7, rms=2.704 (7.867%) rms = 2.7502/2.7036, sse=434176.1/425401.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 012: dt: 0.2500, sse=343845.0, rms=2.066 (23.590%) 013: dt: 0.2500, sse=306461.4, rms=1.685 (18.413%) 014: dt: 0.2500, sse=296486.9, rms=1.570 (6.859%) 015: dt: 0.2500, sse=294690.2, rms=1.517 (3.352%) rms = 1.4924/1.5172, sse=291061.8/294690.1, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=291061.8, rms=1.492 (1.633%) rms = 1.4505/1.4924, sse=289635.9/291061.8, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=289635.9, rms=1.450 (2.812%) maximum number of reductions reached, breaking from loop positioning took 0.8 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 = 108.1150970; border_low = 71.0000000; outside_low = 58.9708370; outside_hi = 108.1150970; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 544 vertices, nripped=10860 mean border=87.4, 162 (42) missing vertices, mean dist -0.2 [0.5 (%66.1)->0.3 (%33.9))] %75 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0845 min Finding expansion regions mean absolute distance = 0.39 +- 0.53 5656 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=r440-, 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=542873.3, rms=3.397 018: dt: 0.5000, sse=396620.0, rms=2.452 (27.823%) rms = 2.5154/2.4516, sse=403805.3/396620.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=325283.4, rms=1.850 (24.557%) 020: dt: 0.2500, sse=293438.5, rms=1.496 (19.095%) 021: dt: 0.2500, sse=289248.1, rms=1.402 (6.315%) rms = 1.3799/1.4019, sse=287644.4/289248.1, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=287644.4, rms=1.380 (1.567%) rms = 1.3310/1.3799, sse=282355.4/287644.4, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=282355.4, rms=1.331 (3.542%) 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 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 71.0000000; outside_low = 58.9708370; outside_hi = 108.1150970; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 751 vertices, nripped=10860 mean border=88.2, 224 (33) missing vertices, mean dist -0.1 [0.4 (%56.1)->0.3 (%43.9))] %81 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0525 min Finding expansion regions mean absolute distance = 0.32 +- 0.41 4585 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=r440-, 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=324955.5, rms=1.847 024: dt: 0.5000, sse=310377.1, rms=1.669 (9.651%) rms = 2.2239/1.6692, sse=361796.2/310377.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=269232.6, rms=1.188 (28.839%) 026: dt: 0.2500, sse=265647.8, rms=1.133 (4.652%) 027: dt: 0.2500, sse=257505.9, rms=1.039 (8.262%) rms = 1.0820/1.0390, sse=258553.5/257505.9, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 1.0208/1.0390, sse=255847.5/257505.9, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=255847.5, rms=1.021 (1.749%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Removing intersections #ET# mris_place_surface 3.69 minutes Writing output to ../surf/lh.white #VMPC# mris_place_surfaces VmPeak 2160400 mris_place_surface done #-------------------------------------------- #@# WhiteSurfs rh Thu Feb 12 18:53:07 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs 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 287098 0.34427 0.12221 0.001209 1.8075 Corner 861294 60.00000 14.90473 0.301707 177.6942 Edge 430647 0.90554 0.20415 0.005641 2.9534 Hinge 430647 14.29431 14.57248 0.000031 179.9721 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=59589, wmmin=5, clip=110 MRIfindBrightNonWM(): 482 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 10464/143551 vertices (133087 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 407 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 71776: xyz = (42.7422,-37.8827,33.9405) oxyz = (42.7422,-37.8827,33.9405) wxzy = (42.7422,-37.8827,33.9405) pxyz = (0,0,0) CBVO Creating mask 143551 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 72.0000000; outside_low = 59.9708370; outside_hi = 108.1150970; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=2 had to be increased for 218 vertices, nripped=10871 mean border=82.7, 173 (173) missing vertices, mean dist 0.3 [1.6 (%17.5)->0.6 (%82.5))] %44 local maxima, %48 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2121 min Finding expansion regions mean absolute distance = 0.80 +- 1.09 4475 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=r440-, 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=1486159.9, rms=6.942 001: dt: 0.5000, sse=672111.4, rms=4.166 (39.993%) 002: dt: 0.5000, sse=479092.3, rms=3.225 (22.589%) 003: dt: 0.5000, sse=454801.8, rms=3.068 (4.879%) 004: dt: 0.5000, sse=432616.3, rms=2.936 (4.290%) rms = 3.0091/2.9359, sse=447254.1/432616.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=339859.1, rms=2.243 (23.608%) 006: dt: 0.2500, sse=305822.9, rms=1.897 (15.410%) 007: dt: 0.2500, sse=301806.5, rms=1.810 (4.615%) rms = 1.7911/1.8097, sse=296343.9/301806.5, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=296343.9, rms=1.791 (1.025%) rms = 1.7482/1.7911, sse=291699.1/296343.9, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=291699.1, rms=1.748 (2.397%) 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 = 108.1150970; border_low = 72.0000000; outside_low = 59.9708370; outside_hi = 108.1150970; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=1 had to be increased for 214 vertices, nripped=10871 mean border=85.1, 117 (24) missing vertices, mean dist -0.3 [0.6 (%61.6)->0.3 (%38.4))] %59 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1528 min Finding expansion regions mean absolute distance = 0.47 +- 0.78 5557 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=r440-, 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=615936.6, rms=3.868 010: dt: 0.5000, sse=405698.9, rms=2.656 (31.326%) 011: dt: 0.5000, sse=396085.2, rms=2.602 (2.053%) rms = 2.7326/2.6018, sse=416641.4/396085.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 012: dt: 0.2500, sse=318232.1, rms=1.929 (25.857%) 013: dt: 0.2500, sse=286092.4, rms=1.579 (18.169%) 014: dt: 0.2500, sse=280149.6, rms=1.508 (4.483%) rms = 1.4865/1.5078, sse=277788.1/280149.6, time step reduction 2 of 3 to 0.125 0 0 1 015: dt: 0.2500, sse=277788.1, rms=1.487 (1.410%) rms = 1.4463/1.4865, sse=274650.9/277788.1, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=274650.9, rms=1.446 (2.705%) maximum number of reductions reached, breaking from loop positioning took 0.8 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 = 108.1150970; border_low = 72.0000000; outside_low = 59.9708370; outside_hi = 108.1150970; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 405 vertices, nripped=10871 mean border=87.2, 141 (15) missing vertices, mean dist -0.2 [0.5 (%64.2)->0.2 (%35.8))] %74 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0821 min Finding expansion regions mean absolute distance = 0.38 +- 0.52 5244 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=r440-, 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=486513.7, rms=3.197 017: dt: 0.5000, sse=378012.1, rms=2.438 (23.739%) rms = 2.5293/2.4378, sse=393792.1/378012.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=314549.4, rms=1.834 (24.788%) 019: dt: 0.2500, sse=285733.3, rms=1.487 (18.911%) 020: dt: 0.2500, sse=280898.0, rms=1.404 (5.561%) rms = 1.3859/1.4041, sse=278204.8/280898.0, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=278204.8, rms=1.386 (1.293%) rms = 1.3390/1.3859, sse=267840.5/278204.8, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=267840.5, rms=1.339 (3.390%) 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 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 108.1150970; border_low = 72.0000000; outside_low = 59.9708370; outside_hi = 108.1150970; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 565 vertices, nripped=10871 mean border=88.1, 217 (10) missing vertices, mean dist -0.1 [0.4 (%55.2)->0.2 (%44.8))] %80 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0513 min Finding expansion regions mean absolute distance = 0.32 +- 0.42 3798 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=r440-, 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=306811.3, rms=1.828 023: dt: 0.5000, sse=306126.2, rms=1.667 (8.812%) rms = 2.2350/1.6669, sse=364280.9/306126.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=259219.1, rms=1.193 (28.413%) rms = 1.1300/1.1933, sse=263698.0/259219.1, time step reduction 2 of 3 to 0.125 0 1 0 025: dt: 0.2500, sse=263698.0, rms=1.130 (5.302%) 026: dt: 0.1250, sse=247307.3, rms=1.036 (8.286%) rms = 1.0143/1.0364, sse=246374.2/247307.3, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=246374.2, rms=1.014 (2.130%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Removing intersections #ET# mris_place_surface 3.51 minutes Writing output to ../surf/rh.white #VMPC# mris_place_surfaces VmPeak 2115468 mris_place_surface done #-------------------------------------------- #@# T1PialSurf lh Thu Feb 12 18:56:46 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs 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 296546 0.34594 0.13692 0.000618 1.9389 Corner 889638 60.00000 16.74854 0.085094 179.8293 Edge 444819 0.91083 0.22690 0.018449 3.5283 Hinge 444819 14.62208 15.17349 0.000013 179.9549 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=59589, wmmin=5, clip=110 MRIfindBrightNonWM(): 482 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 63.3987 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 8247/148275 vertices (140028 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 74138: xyz = (-43.9517,-52.9247,-23.6324) oxyz = (-43.9517,-52.9247,-23.6324) wxzy = (-43.9517,-52.9247,-23.6324) pxyz = (-43.9517,-52.9247,-23.6324) CBVO Creating mask 148275 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 91.8849030; border_hi = 58.9708370; border_low = 34.9125060; outside_low = 10.0000000; outside_hi = 52.9562530; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=2 had to be increased for 227 vertices, nripped=8247 mean border=56.1, 297 (297) missing vertices, mean dist 1.9 [0.0 (%0.0)->2.6 (%100.0))] %24 local maxima, %45 large gradients and %25 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1974 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=r440-, 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=30470616.0, rms=32.903 001: dt: 0.5000, sse=22705518.0, rms=28.368 (13.783%) 002: dt: 0.5000, sse=16857544.0, rms=24.401 (13.982%) 003: dt: 0.5000, sse=12834720.0, rms=21.246 (12.933%) 004: dt: 0.5000, sse=10126852.0, rms=18.824 (11.396%) 005: dt: 0.5000, sse=8105604.5, rms=16.791 (10.803%) 006: dt: 0.5000, sse=6376254.0, rms=14.831 (11.671%) 007: dt: 0.5000, sse=4882057.0, rms=12.900 (13.019%) 008: dt: 0.5000, sse=3653345.5, rms=11.062 (14.248%) 009: dt: 0.5000, sse=2711082.0, rms=9.412 (14.919%) 010: dt: 0.5000, sse=2064766.2, rms=8.086 (14.084%) 011: dt: 0.5000, sse=1674717.5, rms=7.167 (11.369%) 012: dt: 0.5000, sse=1445035.8, rms=6.565 (8.407%) 013: dt: 0.5000, sse=1316621.8, rms=6.200 (5.547%) 014: dt: 0.5000, sse=1229117.2, rms=5.939 (4.221%) 015: dt: 0.5000, sse=1178724.4, rms=5.781 (2.657%) 016: dt: 0.5000, sse=1138120.8, rms=5.650 (2.257%) 017: dt: 0.5000, sse=1119711.0, rms=5.588 (1.101%) 018: dt: 0.5000, sse=1097783.2, rms=5.515 (1.317%) rms = 5.4860/5.5147, sse=1089839.8/1097783.2, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=1089839.8, rms=5.486 (0.520%) 020: dt: 0.2500, sse=764238.1, rms=4.269 (22.185%) 021: dt: 0.2500, sse=691149.2, rms=3.948 (7.513%) rms = 3.9020/3.9482, sse=681594.4/691149.2, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=681594.4, rms=3.902 (1.171%) 023: dt: 0.1250, sse=606183.5, rms=3.533 (9.450%) 024: dt: 0.1250, sse=595124.5, rms=3.476 (1.621%) rms = 3.4651/3.4760, sse=593145.2/595124.5, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=593145.2, rms=3.465 (0.312%) maximum number of reductions reached, breaking from loop positioning took 2.3 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 91.8849030; border_hi = 58.9708370; border_low = 34.9125060; outside_low = 10.0000000; outside_hi = 52.9562530; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=1 had to be increased for 7358 vertices, nripped=8247 mean border=53.9, 1391 (45) missing vertices, mean dist 0.2 [0.1 (%41.1)->0.4 (%58.9))] %37 local maxima, %36 large gradients and %21 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0605 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=r440-, 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=960795.1, rms=4.885 rms = 5.1909/4.8848, sse=1047684.7/960795.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=783278.1, rms=4.182 (14.378%) 027: dt: 0.2500, sse=693690.4, rms=3.778 (9.676%) 028: dt: 0.2500, sse=675601.2, rms=3.695 (2.203%) rms = 3.6858/3.6945, sse=673709.4/675601.2, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=673709.4, rms=3.686 (0.238%) 030: dt: 0.1250, sse=619805.6, rms=3.410 (7.488%) 031: dt: 0.1250, sse=608627.6, rms=3.350 (1.742%) rms = 3.3366/3.3504, sse=606088.6/608627.7, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=606088.6, rms=3.337 (0.412%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 91.8849030; border_hi = 58.9708370; border_low = 34.9125060; outside_low = 10.0000000; outside_hi = 52.9562530; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 7896 vertices, nripped=8247 mean border=52.9, 1592 (23) missing vertices, mean dist 0.1 [0.1 (%46.6)->0.4 (%53.4))] %46 local maxima, %26 large gradients and %21 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0336 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=r440-, 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=695985.8, rms=3.776 rms = 4.8136/3.7764, sse=944614.7/695985.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=628311.7, rms=3.439 (8.926%) rms = 3.4081/3.4393, sse=621993.7/628311.7, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=621993.7, rms=3.408 (0.906%) 035: dt: 0.1250, sse=602490.0, rms=3.303 (3.090%) rms = 3.2731/3.3028, sse=596890.7/602490.0, time step reduction 3 of 3 to 0.062 0 0 1 036: dt: 0.1250, sse=596890.7, rms=3.273 (0.899%) 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 = 91.8849030; border_hi = 58.9708370; border_low = 34.9125060; outside_low = 10.0000000; outside_hi = 52.9562530; 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=148275 Gdiag_no=-1 vno start=0, stop=148275 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 6697 vertices, nripped=8247 mean border=52.2, 3164 (18) missing vertices, mean dist 0.1 [0.1 (%49.6)->0.3 (%50.4))] %48 local maxima, %23 large gradients and %21 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0212 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning 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=r440-, 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=628380.9, rms=3.443 rms = 4.2792/3.4426, sse=807059.4/628380.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 037: dt: 0.2500, sse=596544.4, rms=3.273 (4.938%) rms = 3.2347/3.2726, sse=588565.6/596544.4, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=588565.6, rms=3.235 (1.157%) 039: dt: 0.1250, sse=572315.9, rms=3.143 (2.848%) rms = 3.1028/3.1426, sse=565052.5/572315.9, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=565052.5, rms=3.103 (1.267%) 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: 8 intersecting 001: 4 intersecting step 1 with no progress (num=10, old_num=4) 002: 10 intersecting 003: 4 intersecting terminating search with 0 intersecting #ET# mris_place_surface 4.40 minutes Writing output to ../surf/lh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1431588 mris_place_surface done #-------------------------------------------- #@# T1PialSurf rh Thu Feb 12 19:01:18 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs 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 287098 0.34784 0.13774 0.000240 1.8075 Corner 861294 60.00000 16.48623 0.349785 178.4548 Edge 430647 0.91258 0.22636 0.013802 3.1283 Hinge 430647 14.45615 15.08822 0.000031 179.9784 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=59589, wmmin=5, clip=110 MRIfindBrightNonWM(): 482 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 63.8987 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 8849/143551 vertices (134702 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 71776: xyz = (42.7729,-37.8248,33.7719) oxyz = (42.7729,-37.8248,33.7719) wxzy = (42.7729,-37.8248,33.7719) pxyz = (42.7729,-37.8248,33.7719) CBVO Creating mask 143551 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 91.8849030; border_hi = 59.9708370; border_low = 35.9125060; outside_low = 10.0000000; outside_hi = 53.9562530; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=2 had to be increased for 278 vertices, nripped=8849 mean border=57.0, 234 (234) missing vertices, mean dist 1.9 [0.0 (%0.0)->2.6 (%100.0))] %25 local maxima, %44 large gradients and %25 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1859 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=r440-, 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=27413138.0, rms=31.805 001: dt: 0.5000, sse=20184174.0, rms=27.253 (14.311%) 002: dt: 0.5000, sse=14771599.0, rms=23.269 (14.621%) 003: dt: 0.5000, sse=11081704.0, rms=20.103 (13.606%) 004: dt: 0.5000, sse=8625849.0, rms=17.683 (12.037%) 005: dt: 0.5000, sse=6850519.5, rms=15.703 (11.198%) 006: dt: 0.5000, sse=5397362.5, rms=13.873 (11.652%) 007: dt: 0.5000, sse=4185978.5, rms=12.138 (12.504%) 008: dt: 0.5000, sse=3222296.5, rms=10.556 (13.037%) 009: dt: 0.5000, sse=2503586.0, rms=9.199 (12.853%) 010: dt: 0.5000, sse=1993478.4, rms=8.098 (11.970%) 011: dt: 0.5000, sse=1670246.2, rms=7.313 (9.689%) 012: dt: 0.5000, sse=1456904.6, rms=6.744 (7.785%) 013: dt: 0.5000, sse=1328412.5, rms=6.375 (5.470%) 014: dt: 0.5000, sse=1241990.8, rms=6.113 (4.106%) 015: dt: 0.5000, sse=1192131.6, rms=5.955 (2.588%) 016: dt: 0.5000, sse=1150081.0, rms=5.818 (2.295%) 017: dt: 0.5000, sse=1125150.1, rms=5.734 (1.450%) 018: dt: 0.5000, sse=1097713.6, rms=5.641 (1.617%) 019: dt: 0.5000, sse=1081402.5, rms=5.584 (1.020%) 020: dt: 0.5000, sse=1064121.1, rms=5.524 (1.073%) rms = 5.4825/5.5239, sse=1052835.0/1064121.1, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=1052835.0, rms=5.483 (0.750%) 022: dt: 0.2500, sse=764699.8, rms=4.374 (20.217%) 023: dt: 0.2500, sse=698773.9, rms=4.082 (6.677%) 024: dt: 0.2500, sse=688292.5, rms=4.031 (1.247%) rms = 3.9906/4.0312, sse=679676.7/688292.5, time step reduction 2 of 3 to 0.125 0 0 1 025: dt: 0.2500, sse=679676.8, rms=3.991 (1.006%) 026: dt: 0.1250, sse=625117.8, rms=3.723 (6.716%) rms = 3.6737/3.7226, sse=615564.2/625117.8, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=615564.2, rms=3.674 (1.313%) maximum number of reductions reached, breaking from loop positioning took 2.4 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 91.8849030; border_hi = 59.9708370; border_low = 35.9125060; outside_low = 10.0000000; outside_hi = 53.9562530; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=1 had to be increased for 7001 vertices, nripped=8849 mean border=54.5, 1329 (21) missing vertices, mean dist 0.2 [0.1 (%38.3)->0.5 (%61.7))] %38 local maxima, %34 large gradients and %21 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0582 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=r440-, 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=1049567.5, rms=5.308 rms = 5.2643/5.3081, sse=1037391.4/1049567.5, time step reduction 1 of 3 to 0.250 0 0 1 028: dt: 0.5000, sse=1037391.4, rms=5.264 (0.825%) 029: dt: 0.2500, sse=747609.8, rms=4.118 (21.775%) 030: dt: 0.2500, sse=702729.9, rms=3.911 (5.027%) rms = 3.9155/3.9110, sse=703883.4/702729.9, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 031: dt: 0.1250, sse=678718.4, rms=3.793 (3.010%) 032: dt: 0.1250, sse=645377.4, rms=3.623 (4.493%) 033: dt: 0.1250, sse=635090.0, rms=3.569 (1.495%) rms = 3.5461/3.5687, sse=630811.1/635090.0, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=630811.1, rms=3.546 (0.633%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 91.8849030; border_hi = 59.9708370; border_low = 35.9125060; outside_low = 10.0000000; outside_hi = 53.9562530; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 7581 vertices, nripped=8849 mean border=53.3, 1712 (13) missing vertices, mean dist 0.1 [0.1 (%42.7)->0.4 (%57.3))] %46 local maxima, %25 large gradients and %21 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0327 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=r440-, 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=740207.2, rms=4.067 rms = 4.9590/4.0673, sse=956126.9/740207.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=658541.2, rms=3.674 (9.676%) 036: dt: 0.2500, sse=640618.6, rms=3.584 (2.454%) rms = 3.5730/3.5836, sse=637870.1/640618.5, time step reduction 2 of 3 to 0.125 0 0 1 037: dt: 0.2500, sse=637870.1, rms=3.573 (0.298%) 038: dt: 0.1250, sse=609696.6, rms=3.421 (4.253%) rms = 3.3859/3.4210, sse=603193.9/609696.6, time step reduction 3 of 3 to 0.062 0 0 1 039: dt: 0.1250, sse=603193.9, rms=3.386 (1.027%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 91.8849030; border_hi = 59.9708370; border_low = 35.9125060; outside_low = 10.0000000; outside_hi = 53.9562530; 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=143551 Gdiag_no=-1 vno start=0, stop=143551 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 6387 vertices, nripped=8849 mean border=52.6, 3294 (10) missing vertices, mean dist 0.1 [0.2 (%46.9)->0.3 (%53.1))] %49 local maxima, %22 large gradients and %21 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0208 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=r440-, 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=634358.8, rms=3.555 rms = 4.2994/3.5549, sse=789605.0/634358.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 040: dt: 0.2500, sse=602638.4, rms=3.385 (4.790%) rms = 3.3348/3.3846, sse=592572.7/602638.5, time step reduction 2 of 3 to 0.125 0 0 1 041: dt: 0.2500, sse=592572.7, rms=3.335 (1.473%) 042: dt: 0.1250, sse=578283.2, rms=3.253 (2.444%) rms = 3.2123/3.2533, sse=570850.8/578283.2, time step reduction 3 of 3 to 0.062 0 0 1 043: dt: 0.1250, sse=570850.8, rms=3.212 (1.260%) 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: 21 intersecting 001: 2 intersecting terminating search with 0 intersecting #ET# mris_place_surface 4.45 minutes Writing output to ../surf/rh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1449252 mris_place_surface done #@# white curv lh Thu Feb 12 19:05:53 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 #@# white area lh Thu Feb 12 19:05:55 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area #@# pial curv lh Thu Feb 12 19:05:56 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 #@# pial area lh Thu Feb 12 19:05:58 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial #@# thickness lh Thu Feb 12 19:05:59 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 148275 vertices processed 25000 of 148275 vertices processed 50000 of 148275 vertices processed 75000 of 148275 vertices processed 100000 of 148275 vertices processed 125000 of 148275 vertices processed 0 of 148275 vertices processed 25000 of 148275 vertices processed 50000 of 148275 vertices processed 75000 of 148275 vertices processed 100000 of 148275 vertices processed 125000 of 148275 vertices processed thickness calculation complete, 28:305 truncations. 69238 vertices at 0 distance 131128 vertices at 1 distance 66745 vertices at 2 distance 20054 vertices at 3 distance 6095 vertices at 4 distance 1971 vertices at 5 distance 736 vertices at 6 distance 251 vertices at 7 distance 106 vertices at 8 distance 64 vertices at 9 distance 42 vertices at 10 distance 30 vertices at 11 distance 18 vertices at 12 distance 23 vertices at 13 distance 15 vertices at 14 distance 8 vertices at 15 distance 10 vertices at 16 distance 4 vertices at 17 distance 6 vertices at 18 distance 3 vertices at 19 distance 3 vertices at 20 distance writing curvature file ../surf/lh.thickness #@# area and vertex vol lh Thu Feb 12 19:06:35 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR lh /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.volume masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Total face volume 238034 Total vertex volume 237839 (mask=0) #@# PBRHOPE_HOPE089_PETMR lh 237839 vertexvol Done #@# white curv rh Thu Feb 12 19:06:37 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 #@# white area rh Thu Feb 12 19:06:39 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area #@# pial curv rh Thu Feb 12 19:06:40 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 #@# pial area rh Thu Feb 12 19:06:42 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial #@# thickness rh Thu Feb 12 19:06:43 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 143551 vertices processed 25000 of 143551 vertices processed 50000 of 143551 vertices processed 75000 of 143551 vertices processed 100000 of 143551 vertices processed 125000 of 143551 vertices processed 0 of 143551 vertices processed 25000 of 143551 vertices processed 50000 of 143551 vertices processed 75000 of 143551 vertices processed 100000 of 143551 vertices processed 125000 of 143551 vertices processed thickness calculation complete, 102:640 truncations. 67940 vertices at 0 distance 123679 vertices at 1 distance 64742 vertices at 2 distance 20600 vertices at 3 distance 6504 vertices at 4 distance 2093 vertices at 5 distance 781 vertices at 6 distance 312 vertices at 7 distance 143 vertices at 8 distance 82 vertices at 9 distance 55 vertices at 10 distance 31 vertices at 11 distance 28 vertices at 12 distance 22 vertices at 13 distance 16 vertices at 14 distance 12 vertices at 15 distance 19 vertices at 16 distance 9 vertices at 17 distance 9 vertices at 18 distance 8 vertices at 19 distance 17 vertices at 20 distance writing curvature file ../surf/rh.thickness #@# area and vertex vol rh Thu Feb 12 19:07:17 EST 2026 cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR rh /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.volume masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Total face volume 232183 Total vertex volume 231983 (mask=0) #@# PBRHOPE_HOPE089_PETMR rh 231983 vertexvol Done #----------------------------------------- #@# Curvature Stats lh Thu Feb 12 19:07:19 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PBRHOPE_HOPE089_PETMR 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 [ PBRHOPE_HOPE089_PETMR/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 [ 287 ] Gb_filter = 0 WARN: S lookup min: -0.023208 WARN: S explicit min: 0.000000 vertex = 215 #----------------------------------------- #@# Curvature Stats rh Thu Feb 12 19:07:22 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PBRHOPE_HOPE089_PETMR 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 [ PBRHOPE_HOPE089_PETMR/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 [ 258 ] Gb_filter = 0 WARN: S lookup min: -0.340715 WARN: S explicit min: 0.000000 vertex = 75 #-------------------------------------------- #@# Cortical ribbon mask Thu Feb 12 19:07:25 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR SUBJECTS_DIR is /autofs/space/hope_002/users/PBR28_HOPE/data/fs 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 = 85 writing volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/ribbon.mgz mris_volmask took 5.46 minutes writing ribbon files #----------------------------------------- #@# Cortical Parc 2 lh Thu Feb 12 19:12:53 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PBRHOPE_HOPE089_PETMR lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 50 labels changed using aseg relabeling using gibbs priors... 000: 9706 changed, 148275 examined... 001: 2286 changed, 37772 examined... 002: 673 changed, 12093 examined... 003: 298 changed, 3851 examined... 004: 141 changed, 1704 examined... 005: 77 changed, 806 examined... 006: 46 changed, 450 examined... 007: 18 changed, 250 examined... 008: 10 changed, 109 examined... 009: 4 changed, 63 examined... 010: 2 changed, 29 examined... 011: 0 changed, 9 examined... 4 labels changed using aseg 000: 218 total segments, 137 labels (1806 vertices) changed 001: 87 total segments, 6 labels (23 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1524 vertices marked for relabeling... 1524 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Thu Feb 12 19:13:08 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PBRHOPE_HOPE089_PETMR rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 48 labels changed using aseg relabeling using gibbs priors... 000: 9506 changed, 143551 examined... 001: 2170 changed, 37129 examined... 002: 652 changed, 11518 examined... 003: 259 changed, 3757 examined... 004: 125 changed, 1489 examined... 005: 62 changed, 743 examined... 006: 34 changed, 373 examined... 007: 14 changed, 199 examined... 008: 5 changed, 88 examined... 009: 0 changed, 29 examined... 20 labels changed using aseg 000: 245 total segments, 159 labels (2534 vertices) changed 001: 88 total segments, 3 labels (11 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 31 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 1303 vertices marked for relabeling... 1303 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Cortical Parc 3 lh Thu Feb 12 19:13:23 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PBRHOPE_HOPE089_PETMR lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1325 labels changed using aseg relabeling using gibbs priors... 000: 2085 changed, 148275 examined... 001: 464 changed, 9680 examined... 002: 156 changed, 2630 examined... 003: 85 changed, 863 examined... 004: 38 changed, 446 examined... 005: 29 changed, 212 examined... 006: 21 changed, 156 examined... 007: 11 changed, 126 examined... 008: 10 changed, 57 examined... 009: 11 changed, 58 examined... 010: 8 changed, 56 examined... 011: 7 changed, 43 examined... 012: 6 changed, 33 examined... 013: 10 changed, 35 examined... 014: 8 changed, 47 examined... 015: 9 changed, 44 examined... 016: 5 changed, 45 examined... 017: 2 changed, 25 examined... 018: 4 changed, 13 examined... 019: 4 changed, 20 examined... 020: 2 changed, 26 examined... 021: 0 changed, 14 examined... 458 labels changed using aseg 000: 52 total segments, 19 labels (168 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1297 vertices marked for relabeling... 1297 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Thu Feb 12 19:13:35 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 PBRHOPE_HOPE089_PETMR rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1833 labels changed using aseg relabeling using gibbs priors... 000: 2116 changed, 143551 examined... 001: 519 changed, 9841 examined... 002: 156 changed, 2826 examined... 003: 79 changed, 850 examined... 004: 57 changed, 416 examined... 005: 56 changed, 270 examined... 006: 39 changed, 259 examined... 007: 21 changed, 194 examined... 008: 15 changed, 116 examined... 009: 13 changed, 90 examined... 010: 5 changed, 64 examined... 011: 6 changed, 32 examined... 012: 3 changed, 26 examined... 013: 4 changed, 17 examined... 014: 0 changed, 19 examined... 538 labels changed using aseg 000: 62 total segments, 29 labels (568 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 835 vertices marked for relabeling... 835 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. #----------------------------------------- #@# WM/GM Contrast lh Thu Feb 12 19:13:46 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts pctsurfcon --s PBRHOPE_HOPE089_PETMR --lh-only Log file is /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts/pctsurfcon.log Thu Feb 12 19:13:46 EST 2026 setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts /usr/local/freesurfer/stable7.4.1/bin/pctsurfcon pctsurfcon 7.4.1 Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 mri_vol2surf --mov /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3840865/lh.wm.mgh --regheader PBRHOPE_HOPE089_PETMR --cortex srcvol = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Reading surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 = 85827 Masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3840865/lh.wm.mgh Dim: 148275 1 1 mri_vol2surf done mri_vol2surf --mov /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3840865/lh.gm.mgh --projfrac 0.3 --regheader PBRHOPE_HOPE089_PETMR --cortex srcvol = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Reading surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Done reading source surface Reading thickness /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 = 101553 Masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3840865/lh.gm.mgh Dim: 148275 1 1 mri_vol2surf done mri_concat /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3840865/lh.wm.mgh /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3840865/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.w-g.pct.mgh --annot PBRHOPE_HOPE089_PETMR lh aparc --sum /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/stats/lh.w-g.pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.w-g.pct.mgh --annot PBRHOPE_HOPE089_PETMR lh aparc --sum /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/stats/lh.w-g.pct.stats --snr sysname Linux hostname r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.annot Seg base 1000 MRISannot2seg(): nhits = 137761 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.w-g.pct.mgh Vertex Area is 0.691871 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 #----------------------------------------- #@# WM/GM Contrast rh Thu Feb 12 19:13:50 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts pctsurfcon --s PBRHOPE_HOPE089_PETMR --rh-only Log file is /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts/pctsurfcon.log Thu Feb 12 19:13:50 EST 2026 setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/scripts /usr/local/freesurfer/stable7.4.1/bin/pctsurfcon pctsurfcon 7.4.1 Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 mri_vol2surf --mov /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3841018/rh.wm.mgh --regheader PBRHOPE_HOPE089_PETMR --cortex srcvol = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Reading surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 = 83718 Masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3841018/rh.wm.mgh Dim: 143551 1 1 mri_vol2surf done mri_vol2surf --mov /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3841018/rh.gm.mgh --projfrac 0.3 --regheader PBRHOPE_HOPE089_PETMR --cortex srcvol = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Reading surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Done reading source surface Reading thickness /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 = 98701 Masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3841018/rh.gm.mgh Dim: 143551 1 1 mri_vol2surf done mri_concat /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3841018/rh.wm.mgh /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/tmp.pctsurfcon.3841018/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.w-g.pct.mgh --annot PBRHOPE_HOPE089_PETMR rh aparc --sum /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/stats/rh.w-g.pct.stats --snr 7.4.1 cwd cmdline mri_segstats --in /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.w-g.pct.mgh --annot PBRHOPE_HOPE089_PETMR rh aparc --sum /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/stats/rh.w-g.pct.stats --snr sysname Linux hostname r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.aparc.annot Seg base 2000 MRISannot2seg(): nhits = 133087 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.w-g.pct.mgh Vertex Area is 0.695663 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 #----------------------------------------- #@# Relabel Hypointensities Thu Feb 12 19:13:54 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3614 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 7056 voxels changed to hypointensity... 10162 hypointense voxels neighboring cortex changed #----------------------------------------- #@# APas-to-ASeg Thu Feb 12 19:14:11 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/ribbon.mgz --threads 1 --lh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label --lh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white --lh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial --rh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label --rh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white --rh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs outvol aseg.mgz 6 avail.processors, using 1 Loading aseg.presurf.hypos.mgz Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/ribbon.mgz Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 985364 mri_surf2volseg done mri_brainvol_stats --subject PBRHOPE_HOPE089_PETMR ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1745438.0 #CBVS2 BrainSegVol 1239671.0 #CBVS2 BrainSegVolNotVent 1174488.0 #CBVS2 SupraTentVol 1105648.0 #CBVS2 SupraTentVolNotVent 1040465.0 #CBVS2 lhCtxGM 237490.3 #CBVS2 rhCtxGM 231662.1 #CBVS2 lhCerebralWM 260742.0 #CBVS2 rhCerebralWM 252656.0 #CBVS2 SubCortGMVol 60046.0 #CBVS2 CerebellumVol 134023.0 #CBVS2 CerebellumGMVol 107858.0 #CBVS2 VentChorVol 58180.0 #CBVS2 3rd4th5thCSF 7003.0 #CBVS2 AllCSF 65183.0 #CBVS2 CCVol 4228.0 #----------------------------------------- #@# AParc-to-ASeg aparc Thu Feb 12 19:14:28 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.annot 1000 --lh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label --lh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white --lh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial --rh-annot /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.aparc.annot 2000 --rh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label --rh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white --rh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs outvol aparc+aseg.mgz 6 avail.processors, using 1 Loading aseg.mgz Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10514 vertices from lh hemi Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.annot Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10464 vertices from rh hemi Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 = 21064 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 968512 mri_surf2volseg done #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Thu Feb 12 19:16:50 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label --lh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white --lh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial --rh-annot /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label --rh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white --rh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs outvol aparc.a2009s+aseg.mgz 6 avail.processors, using 1 Loading aseg.mgz Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10514 vertices from lh hemi Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.a2009s.annot Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10464 vertices from rh hemi Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 = 21064 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 968596 mri_surf2volseg done #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Thu Feb 12 19:19:13 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label --lh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white --lh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial --rh-annot /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label --rh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white --rh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs outvol aparc.DKTatlas+aseg.mgz 6 avail.processors, using 1 Loading aseg.mgz Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10514 vertices from lh hemi Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.DKTatlas.annot Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10464 vertices from rh hemi Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 = 21064 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 968512 mri_surf2volseg done #----------------------------------------- #@# WMParc Thu Feb 12 19:21:36 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 1 --lh-annot /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.annot 3000 --lh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label --lh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white --lh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial --rh-annot /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.aparc.annot 4000 --rh-cortex-mask /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label --rh-white /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white --rh-pial /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs outvol wmparc.mgz 6 avail.processors, using 1 Loading aparc+aseg.mgz Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 10514 vertices from lh hemi Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.aparc.annot Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 10464 vertices from rh hemi Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 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--in-intensity-units MR --subject PBRHOPE_HOPE089_PETMR --surf-wm-vol --ctab /usr/local/freesurfer/stable7.4.1/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 PBRHOPE_HOPE089_PETMR --surf-wm-vol --ctab /usr/local/freesurfer/stable7.4.1/WMParcStatsLUT.txt --etiv sysname Linux hostname r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1825641 mm^3 (det: 1.067080 ) 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 #----------------------------------------- #@# Parcellation Stats lh Thu Feb 12 19:27:42 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 238034 Total vertex volume 237839 (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) = 1825641 mm^3 (det: 1.067080 ) 1310 878 1981 2.412 0.400 0.101 0.023 8 1.2 bankssts 1326 889 1797 1.848 0.670 0.138 0.033 18 1.8 caudalanteriorcingulate 3170 2262 6220 2.534 0.547 0.133 0.039 31 5.0 caudalmiddlefrontal 2896 1995 3551 1.723 0.426 0.155 0.046 45 5.6 cuneus 641 425 1734 3.017 0.862 0.128 0.035 6 1.0 entorhinal 4606 3321 9647 2.514 0.574 0.139 0.039 60 6.9 fusiform 7059 4770 12222 2.378 0.466 0.129 0.036 79 9.5 inferiorparietal 5333 3700 11096 2.688 0.634 0.126 0.034 61 7.2 inferiortemporal 2440 1696 3671 1.990 0.700 0.135 0.042 33 3.9 isthmuscingulate 8355 5718 12435 2.030 0.491 0.144 0.042 115 13.9 lateraloccipital 3822 2856 7759 2.500 0.654 0.157 0.052 56 8.1 lateralorbitofrontal 5195 3719 7172 1.835 0.519 0.155 0.049 76 10.0 lingual 3284 2394 5495 2.111 0.579 0.144 0.046 54 5.8 medialorbitofrontal 5327 3671 11612 2.724 0.530 0.126 0.036 61 7.5 middletemporal 1026 634 1529 2.103 0.651 0.099 0.027 9 1.0 parahippocampal 2028 1440 3413 2.193 0.552 0.139 0.049 24 4.2 paracentral 2582 1763 4371 2.306 0.464 0.138 0.050 36 5.0 parsopercularis 1080 791 2246 2.348 0.581 0.145 0.047 14 1.7 parsorbitalis 1986 1376 2987 2.151 0.522 0.151 0.054 28 4.4 parstriangularis 2324 1718 2273 1.523 0.350 0.151 0.043 26 4.5 pericalcarine 6662 4519 9429 1.976 0.593 0.138 0.046 95 12.2 postcentral 2219 1527 3140 1.904 0.701 0.125 0.030 26 2.7 posteriorcingulate 8408 5963 14256 2.332 0.700 0.155 0.054 121 20.1 precentral 6356 4519 10454 2.188 0.489 0.136 0.040 75 9.7 precuneus 1335 952 2433 2.385 0.590 0.141 0.037 22 2.3 rostralanteriorcingulate 8759 6381 16147 2.315 0.534 0.141 0.042 116 14.6 rostralmiddlefrontal 11405 8334 22906 2.406 0.573 0.136 0.041 133 19.8 superiorfrontal 9014 5917 13305 2.137 0.518 0.133 0.040 105 14.4 superiorparietal 6205 4072 10974 2.484 0.509 0.110 0.030 60 7.5 superiortemporal 5873 4038 10130 2.338 0.518 0.130 0.032 62 7.7 supramarginal 412 373 1116 2.505 0.416 0.209 0.064 12 1.2 frontalpole 683 531 2327 3.066 0.728 0.156 0.052 11 1.3 temporalpole 749 471 1018 2.050 0.628 0.151 0.052 12 1.7 transversetemporal 3891 2679 6996 2.604 0.775 0.132 0.044 41 7.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PBRHOPE_HOPE089_PETMR lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 238034 Total vertex volume 237839 (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) = 1825641 mm^3 (det: 1.067080 ) 1310 745 1981 2.412 0.400 0.095 0.026 17 1.2 bankssts 1326 1012 1797 1.848 0.670 0.171 0.048 541 1.9 caudalanteriorcingulate 3170 2490 6220 2.534 0.547 0.123 0.030 29 3.9 caudalmiddlefrontal 2896 2279 3551 1.723 0.426 0.141 0.038 51 4.1 cuneus 641 729 1734 3.017 0.862 0.220 0.062 21 1.9 entorhinal 4606 4319 9647 2.514 0.574 0.184 0.050 124 9.6 fusiform 7059 5493 12222 2.378 0.466 0.150 0.055 23968 8.9 inferiorparietal 5333 4442 11096 2.688 0.634 0.151 0.042 100 9.0 inferiortemporal 2440 2064 3671 1.990 0.700 0.169 0.052 56 4.8 isthmuscingulate 8355 6679 12435 2.030 0.491 0.144 0.044 346 12.4 lateraloccipital 3822 3354 7759 2.500 0.654 0.171 0.045 99 7.3 lateralorbitofrontal 5195 4305 7172 1.835 0.519 0.151 0.044 95 8.6 lingual 3284 2789 5495 2.111 0.579 0.154 0.044 101 5.2 medialorbitofrontal 5327 4698 11612 2.724 0.530 0.133 0.030 66 6.4 middletemporal 1026 853 1529 2.103 0.651 0.160 0.046 18 1.9 parahippocampal 2028 1641 3413 2.193 0.552 0.129 0.033 26 2.5 paracentral 2582 1979 4371 2.306 0.464 0.118 0.026 19 2.8 parsopercularis 1080 1072 2246 2.348 0.581 0.158 0.038 15 1.7 parsorbitalis 1986 1417 2987 2.151 0.522 0.124 0.030 32 2.5 parstriangularis 2324 1394 2273 1.523 0.350 0.114 0.031 33 2.7 pericalcarine 6662 5048 9429 1.976 0.593 0.114 0.025 52 6.6 postcentral 2219 1747 3140 1.904 0.701 0.151 0.039 70 3.5 posteriorcingulate 8408 5949 14256 2.332 0.700 0.105 0.025 92 8.1 precentral 6356 5076 10454 2.188 0.489 0.146 0.039 125 9.5 precuneus 1335 1142 2433 2.385 0.590 0.175 0.052 76 2.2 rostralanteriorcingulate 8759 7410 16147 2.315 0.534 0.141 0.035 112 12.1 rostralmiddlefrontal 11405 10163 22906 2.406 0.573 0.142 0.032 152 15.0 superiorfrontal 9014 6521 13305 2.137 0.518 0.128 0.034 171 11.8 superiorparietal 6205 4615 10974 2.484 0.509 0.113 0.024 82 5.7 superiortemporal 5873 4491 10130 2.338 0.518 0.127 0.029 97 6.3 supramarginal 412 533 1116 2.505 0.416 0.213 0.040 7 0.6 frontalpole 683 957 2327 3.066 0.728 0.197 0.032 10 1.1 temporalpole 749 527 1018 2.050 0.628 0.091 0.015 3 0.4 transversetemporal 3891 2530 6996 2.604 0.775 0.135 0.044 92 6.3 insula #----------------------------------------- #@# Parcellation Stats rh Thu Feb 12 19:28:18 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 232183 Total vertex volume 231983 (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) = 1825641 mm^3 (det: 1.067080 ) 1639 1137 2601 2.373 0.425 0.121 0.031 14 2.1 bankssts 1349 860 1786 1.856 0.737 0.114 0.026 16 1.3 caudalanteriorcingulate 2982 2168 6038 2.434 0.567 0.134 0.038 33 4.8 caudalmiddlefrontal 2761 1863 3409 1.723 0.491 0.145 0.046 40 4.8 cuneus 569 417 1627 2.995 0.821 0.149 0.043 7 1.2 entorhinal 5329 3696 10449 2.482 0.643 0.132 0.039 64 7.7 fusiform 8095 5472 12834 2.271 0.482 0.125 0.033 96 10.5 inferiorparietal 4638 3252 8221 2.432 0.659 0.136 0.040 50 7.7 inferiortemporal 1427 938 2314 2.256 0.624 0.137 0.044 19 2.2 isthmuscingulate 8775 5864 11454 1.897 0.490 0.144 0.044 116 14.5 lateraloccipital 3716 2775 7203 2.456 0.641 0.159 0.053 58 8.1 lateralorbitofrontal 5208 3584 6512 1.763 0.542 0.146 0.046 69 9.5 lingual 3037 2218 5891 2.396 0.662 0.137 0.041 43 4.8 medialorbitofrontal 5243 3731 11844 2.684 0.552 0.128 0.037 63 7.6 middletemporal 1115 670 1636 2.125 0.695 0.095 0.022 8 0.9 parahippocampal 2594 1875 4027 2.121 0.547 0.165 0.061 38 6.7 paracentral 1300 941 2438 2.403 0.471 0.121 0.031 11 1.7 parsopercularis 1120 879 2918 2.602 0.524 0.155 0.046 17 2.0 parsorbitalis 1590 1213 3446 2.379 0.556 0.139 0.038 17 2.5 parstriangularis 2359 1758 2283 1.488 0.361 0.153 0.042 28 4.7 pericalcarine 6851 4708 9695 1.918 0.531 0.131 0.042 82 11.5 postcentral 1738 1240 2880 2.126 0.750 0.133 0.036 24 2.6 posteriorcingulate 7908 5689 15477 2.403 0.731 0.143 0.044 94 15.0 precentral 6456 4475 10590 2.309 0.538 0.135 0.038 71 9.9 precuneus 1069 775 2038 2.384 0.647 0.135 0.039 19 1.6 rostralanteriorcingulate 8017 6092 16743 2.351 0.568 0.151 0.048 125 15.5 rostralmiddlefrontal 9506 6980 20345 2.488 0.621 0.146 0.045 130 17.8 superiorfrontal 8613 5743 11763 1.985 0.449 0.126 0.036 93 11.8 superiorparietal 5776 4000 11062 2.478 0.511 0.113 0.028 58 6.6 superiortemporal 6391 4437 10740 2.323 0.479 0.132 0.038 75 9.6 supramarginal 479 394 1325 2.711 0.583 0.211 0.084 19 2.1 frontalpole 659 526 2306 3.329 0.563 0.172 0.054 11 1.6 temporalpole 723 419 1022 2.199 0.549 0.135 0.052 10 1.4 transversetemporal 4055 2798 7066 2.487 0.771 0.131 0.044 45 6.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PBRHOPE_HOPE089_PETMR rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 232183 Total vertex volume 231983 (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) = 1825641 mm^3 (det: 1.067080 ) 1639 1010 2601 2.373 0.425 0.114 0.030 27 2.0 bankssts 1349 1045 1786 1.856 0.737 0.150 0.043 44 2.4 caudalanteriorcingulate 2982 2677 6038 2.434 0.567 0.139 0.029 44 3.2 caudalmiddlefrontal 2761 2170 3409 1.723 0.491 0.133 0.035 64 3.6 cuneus 569 695 1627 2.995 0.821 0.287 0.078 21 2.0 entorhinal 5329 4753 10449 2.482 0.643 0.161 0.044 133 9.7 fusiform 8095 5903 12834 2.271 0.482 0.118 0.028 123 8.8 inferiorparietal 4638 3515 8221 2.432 0.659 0.146 0.046 111 8.1 inferiortemporal 1427 1156 2314 2.256 0.624 0.159 0.054 49 3.1 isthmuscingulate 8775 6506 11454 1.897 0.490 0.130 0.035 172 11.9 lateraloccipital 3716 3088 7203 2.456 0.641 0.165 0.046 92 6.9 lateralorbitofrontal 5208 4105 6512 1.763 0.542 0.144 0.040 147 8.0 lingual 3037 2684 5891 2.396 0.662 0.150 0.040 57 4.6 medialorbitofrontal 5243 4961 11844 2.684 0.552 0.147 0.030 70 6.8 middletemporal 1115 886 1636 2.125 0.695 0.157 0.046 19 2.2 parahippocampal 2594 1917 4027 2.121 0.547 0.137 0.047 60 4.5 paracentral 1300 1052 2438 2.403 0.471 0.135 0.030 16 1.5 parsopercularis 1120 1338 2918 2.602 0.524 0.195 0.045 18 1.9 parsorbitalis 1590 1602 3446 2.379 0.556 0.164 0.030 20 2.2 parstriangularis 2359 1430 2283 1.488 0.361 0.112 0.032 46 2.7 pericalcarine 6851 5336 9695 1.918 0.531 0.117 0.024 59 6.6 postcentral 1738 1500 2880 2.126 0.750 0.161 0.043 85 2.9 posteriorcingulate 7908 6545 15477 2.403 0.731 0.131 0.031 108 9.6 precentral 6456 4746 10590 2.309 0.538 0.143 0.042 207 9.9 precuneus 1069 960 2038 2.384 0.647 0.169 0.049 39 2.0 rostralanteriorcingulate 8017 7897 16743 2.351 0.568 0.174 0.042 143 13.1 rostralmiddlefrontal 9506 8921 20345 2.488 0.621 0.162 0.040 195 15.0 superiorfrontal 8613 6227 11763 1.985 0.449 0.121 0.032 115 10.4 superiorparietal 5776 4705 11062 2.478 0.511 0.118 0.023 78 5.3 superiortemporal 6391 4739 10740 2.323 0.479 0.127 0.031 88 7.3 supramarginal 479 560 1325 2.711 0.583 0.199 0.039 6 0.8 frontalpole 659 847 2306 3.329 0.563 0.202 0.044 11 1.4 temporalpole 723 509 1022 2.199 0.549 0.102 0.021 10 0.6 transversetemporal 4055 2683 7066 2.487 0.771 0.126 0.034 61 5.9 insula #----------------------------------------- #@# Parcellation Stats 2 lh Thu Feb 12 19:28:53 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 238034 Total vertex volume 237839 (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) = 1825641 mm^3 (det: 1.067080 ) 1307 1022 2402 2.333 0.543 0.173 0.052 25 2.8 G_and_S_frontomargin 1506 1091 2775 2.237 0.486 0.143 0.048 24 2.8 G_and_S_occipital_inf 1648 1196 3117 2.227 0.607 0.160 0.061 27 4.2 G_and_S_paracentral 1674 1151 3516 2.602 0.525 0.134 0.041 20 2.7 G_and_S_subcentral 898 708 2002 2.349 0.475 0.174 0.053 21 2.1 G_and_S_transv_frontopol 2433 1737 4130 2.324 0.414 0.121 0.029 26 3.2 G_and_S_cingul-Ant 1464 1018 2263 2.143 0.542 0.127 0.032 14 2.0 G_and_S_cingul-Mid-Ant 1400 989 2173 2.164 0.479 0.117 0.028 13 1.6 G_and_S_cingul-Mid-Post 940 667 1966 2.470 0.604 0.153 0.047 15 1.5 G_cingul-Post-dorsal 484 335 981 2.400 0.659 0.142 0.049 8 0.9 G_cingul-Post-ventral 2783 1908 3510 1.707 0.426 0.158 0.047 45 5.3 G_cuneus 1533 1031 2901 2.396 0.554 0.147 0.058 24 3.3 G_front_inf-Opercular 507 355 1163 2.542 0.607 0.143 0.047 7 1.0 G_front_inf-Orbital 1246 825 2228 2.266 0.548 0.161 0.068 24 3.1 G_front_inf-Triangul 4565 3348 10752 2.514 0.575 0.152 0.051 74 8.8 G_front_middle 7613 5728 17789 2.504 0.602 0.147 0.048 111 15.0 G_front_sup 816 517 1430 2.762 0.657 0.125 0.042 10 1.2 G_Ins_lg_and_S_cent_ins 857 621 2467 3.206 0.780 0.166 0.066 14 2.0 G_insular_short 2984 1896 5332 2.319 0.484 0.144 0.046 46 4.8 G_occipital_middle 1902 1269 2932 2.047 0.562 0.149 0.049 29 3.4 G_occipital_sup 2124 1495 5122 2.599 0.536 0.145 0.045 36 3.3 G_oc-temp_lat-fusifor 3505 2509 5313 1.858 0.546 0.165 0.056 62 7.4 G_oc-temp_med-Lingual 1323 836 2959 2.645 0.881 0.124 0.038 17 1.9 G_oc-temp_med-Parahip 2404 1839 5724 2.429 0.667 0.162 0.057 42 4.8 G_orbital 2642 1779 5558 2.456 0.479 0.135 0.038 40 3.6 G_pariet_inf-Angular 2914 1969 5764 2.447 0.494 0.132 0.035 37 3.7 G_pariet_inf-Supramar 3570 2303 5891 2.206 0.571 0.142 0.047 52 6.6 G_parietal_sup 2610 1698 3829 1.960 0.573 0.150 0.058 52 5.8 G_postcentral 3137 2162 6165 2.359 0.775 0.157 0.057 49 7.2 G_precentral 2856 2029 5790 2.333 0.508 0.138 0.043 39 4.5 G_precuneus 1039 786 2341 2.302 0.567 0.158 0.056 23 2.1 G_rectus 675 458 908 1.935 0.765 0.156 0.068 15 2.1 G_subcallosal 585 329 911 2.313 0.651 0.146 0.055 10 1.5 G_temp_sup-G_T_transv 2230 1439 5065 2.663 0.491 0.126 0.043 33 3.6 G_temp_sup-Lateral 744 516 1387 2.476 0.551 0.085 0.019 2 0.7 G_temp_sup-Plan_polar 1118 727 2107 2.617 0.510 0.102 0.026 10 1.2 G_temp_sup-Plan_tempo 2721 1939 6770 2.750 0.634 0.137 0.044 43 4.3 G_temporal_inf 2996 2057 7455 2.827 0.537 0.138 0.045 47 4.9 G_temporal_middle 299 216 376 2.086 0.416 0.128 0.036 2 0.5 Lat_Fis-ant-Horizont 284 208 356 2.157 0.354 0.147 0.046 3 0.6 Lat_Fis-ant-Vertical 1227 882 1463 1.938 0.471 0.129 0.030 9 1.7 Lat_Fis-post 2462 1763 3451 1.798 0.457 0.159 0.047 37 4.7 Pole_occipital 1529 1193 5144 3.148 0.670 0.164 0.053 26 3.1 Pole_temporal 3250 2385 3396 1.670 0.464 0.144 0.042 32 6.0 S_calcarine 3691 2694 4358 1.960 0.690 0.152 0.048 46 8.2 S_central 1231 853 1693 2.045 0.416 0.112 0.031 8 1.6 S_cingul-Marginalis 547 382 887 2.620 0.607 0.122 0.034 3 0.9 S_circular_insula_ant 1561 1049 1942 2.219 0.554 0.097 0.020 7 1.4 S_circular_insula_inf 1938 1340 2441 2.188 0.451 0.122 0.035 12 3.4 S_circular_insula_sup 825 564 1552 2.990 0.530 0.118 0.027 7 0.9 S_collat_transv_ant 534 374 525 1.763 0.434 0.127 0.030 4 0.7 S_collat_transv_post 2303 1600 3433 2.309 0.518 0.126 0.034 18 3.1 S_front_inf 1715 1201 2334 2.143 0.403 0.117 0.028 14 2.2 S_front_middle 2921 2097 4741 2.357 0.433 0.118 0.030 21 3.8 S_front_sup 333 241 360 1.936 0.396 0.129 0.026 2 0.5 S_interm_prim-Jensen 3176 2125 4022 2.136 0.460 0.117 0.029 21 3.8 S_intrapariet_and_P_trans 1338 900 1620 2.106 0.451 0.133 0.032 11 2.0 S_oc_middle_and_Lunatus 1724 1162 2115 2.065 0.491 0.124 0.033 13 2.3 S_oc_sup_and_transversal 501 331 668 2.083 0.351 0.099 0.019 3 0.5 S_occipital_ant 1125 775 1632 2.409 0.401 0.108 0.023 6 1.2 S_oc-temp_lat 1939 1385 2626 2.008 0.465 0.123 0.028 13 2.5 S_oc-temp_med_and_Lingual 419 319 477 1.814 0.383 0.150 0.043 3 0.9 S_orbital_lateral 707 482 830 2.056 0.621 0.126 0.035 6 1.0 S_orbital_med-olfact 1342 1021 2544 2.521 0.683 0.156 0.048 17 2.9 S_orbital-H_Shaped 2642 1829 3303 1.983 0.426 0.133 0.035 29 4.1 S_parieto_occipital 2384 1511 1739 1.403 0.554 0.123 0.032 32 3.1 S_pericallosal 2798 1950 3978 2.209 0.511 0.131 0.033 28 4.0 S_postcentral 1566 1115 2239 2.207 0.491 0.138 0.044 18 3.3 S_precentral-inf-part 1667 1166 2306 2.251 0.648 0.147 0.046 20 3.9 S_precentral-sup-part 767 554 954 2.014 0.457 0.134 0.033 7 1.1 S_suborbital 1254 905 1889 2.204 0.399 0.131 0.034 13 1.8 S_subparietal 1898 1273 2657 2.427 0.417 0.107 0.021 11 2.0 S_temporal_inf 5779 3923 8469 2.407 0.431 0.108 0.024 39 6.0 S_temporal_sup 332 248 432 2.176 0.439 0.134 0.027 2 0.5 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Thu Feb 12 19:29:11 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 232183 Total vertex volume 231983 (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) = 1825641 mm^3 (det: 1.067080 ) 981 788 2239 2.558 0.669 0.183 0.068 25 3.2 G_and_S_frontomargin 1361 960 2163 2.010 0.581 0.148 0.045 19 2.2 G_and_S_occipital_inf 1665 1228 3216 2.193 0.740 0.165 0.062 27 3.9 G_and_S_paracentral 1414 1001 2866 2.436 0.462 0.137 0.036 18 2.1 G_and_S_subcentral 1236 977 2844 2.313 0.592 0.175 0.059 26 3.0 G_and_S_transv_frontopol 3229 2287 5544 2.352 0.498 0.121 0.031 38 4.0 G_and_S_cingul-Ant 1284 877 2172 2.390 0.557 0.129 0.034 14 1.7 G_and_S_cingul-Mid-Ant 1327 939 2263 2.338 0.549 0.128 0.035 13 1.8 G_and_S_cingul-Mid-Post 533 353 1201 2.612 0.500 0.134 0.045 8 0.8 G_cingul-Post-dorsal 425 235 676 2.367 0.510 0.124 0.044 6 0.6 G_cingul-Post-ventral 2683 1771 3202 1.655 0.512 0.149 0.047 43 4.7 G_cuneus 872 643 2167 2.698 0.364 0.122 0.031 9 1.1 G_front_inf-Opercular 361 278 1096 2.819 0.450 0.179 0.060 7 0.8 G_front_inf-Orbital 704 566 1988 2.591 0.534 0.153 0.043 10 1.3 G_front_inf-Triangul 3444 2688 8647 2.501 0.572 0.163 0.053 63 7.4 G_front_middle 6244 4781 15896 2.590 0.706 0.169 0.060 113 15.8 G_front_sup 619 410 1184 2.902 0.568 0.141 0.051 8 1.2 G_Ins_lg_and_S_cent_ins 932 668 2284 2.788 0.867 0.153 0.060 18 2.0 G_insular_short 2582 1690 4507 2.205 0.515 0.140 0.049 43 4.1 G_occipital_middle 1997 1251 2682 1.881 0.517 0.130 0.046 27 3.3 G_occipital_sup 2655 1772 5881 2.578 0.649 0.131 0.044 38 3.9 G_oc-temp_lat-fusifor 3352 2297 4486 1.785 0.582 0.156 0.053 52 6.7 G_oc-temp_med-Lingual 1452 947 3480 2.746 0.912 0.127 0.037 16 2.1 G_oc-temp_med-Parahip 2492 1968 6951 2.722 0.651 0.164 0.055 47 5.3 G_orbital 2912 1936 5333 2.415 0.556 0.131 0.039 45 4.0 G_pariet_inf-Angular 3051 2123 6150 2.413 0.466 0.141 0.042 46 4.8 G_pariet_inf-Supramar 2735 1860 4351 2.031 0.471 0.132 0.038 35 3.9 G_parietal_sup 2441 1614 3728 1.893 0.525 0.138 0.052 41 4.5 G_postcentral 2986 2187 7471 2.571 0.808 0.154 0.051 44 6.1 G_precentral 2651 1784 5218 2.420 0.525 0.134 0.039 35 3.8 G_precuneus 888 671 2325 2.621 0.624 0.167 0.060 21 1.8 G_rectus 648 415 1031 2.387 0.840 0.123 0.049 8 1.2 G_subcallosal 572 327 883 2.226 0.517 0.145 0.059 10 1.3 G_temp_sup-G_T_transv 2178 1569 5501 2.732 0.465 0.135 0.038 36 3.1 G_temp_sup-Lateral 681 492 1414 2.698 0.592 0.104 0.025 4 0.8 G_temp_sup-Plan_polar 744 518 1236 2.295 0.369 0.083 0.018 2 0.6 G_temp_sup-Plan_tempo 2064 1449 4920 2.638 0.736 0.139 0.048 28 3.7 G_temporal_inf 3001 2202 7814 2.762 0.561 0.142 0.046 49 4.9 G_temporal_middle 347 242 434 2.169 0.433 0.108 0.027 2 0.4 Lat_Fis-ant-Horizont 101 83 178 2.201 0.401 0.132 0.030 1 0.1 Lat_Fis-ant-Vertical 1579 1073 1907 2.058 0.444 0.117 0.030 10 2.2 Lat_Fis-post 3945 2603 4838 1.803 0.477 0.150 0.045 57 7.0 Pole_occipital 1848 1404 5160 2.881 0.690 0.159 0.052 28 3.8 Pole_temporal 2611 1936 2778 1.657 0.487 0.144 0.039 26 4.7 S_calcarine 3339 2392 3649 1.816 0.540 0.134 0.040 30 6.4 S_central 1305 905 1849 2.178 0.420 0.118 0.029 8 1.7 S_cingul-Marginalis 538 395 886 2.582 0.565 0.149 0.047 5 1.2 S_circular_insula_ant 1357 913 1631 2.033 0.523 0.090 0.019 5 1.2 S_circular_insula_inf 1448 971 1823 2.312 0.383 0.109 0.026 7 1.8 S_circular_insula_sup 1010 681 1493 2.486 0.440 0.106 0.022 7 1.0 S_collat_transv_ant 653 478 672 1.782 0.445 0.152 0.041 6 1.2 S_collat_transv_post 1270 907 1834 2.136 0.441 0.134 0.041 12 2.1 S_front_inf 2582 1860 4133 2.183 0.507 0.131 0.036 26 3.8 S_front_middle 2897 2078 5640 2.419 0.575 0.126 0.034 30 3.9 S_front_sup 579 395 700 2.280 0.417 0.119 0.024 3 0.8 S_interm_prim-Jensen 3209 2159 3925 1.981 0.401 0.115 0.027 25 3.7 S_intrapariet_and_P_trans 1142 795 1285 1.906 0.327 0.137 0.035 8 1.9 S_oc_middle_and_Lunatus 1889 1307 2178 1.940 0.465 0.137 0.035 19 2.8 S_oc_sup_and_transversal 863 610 940 1.956 0.391 0.142 0.039 8 1.4 S_occipital_ant 1472 1040 1756 2.038 0.508 0.125 0.029 10 2.0 S_oc-temp_lat 2141 1493 2804 2.093 0.515 0.121 0.028 16 2.6 S_oc-temp_med_and_Lingual 400 290 549 2.140 0.414 0.138 0.040 3 0.6 S_orbital_lateral 744 520 1001 2.222 0.638 0.111 0.023 4 0.8 S_orbital_med-olfact 1412 1044 2082 2.189 0.447 0.160 0.052 18 3.3 S_orbital-H_Shaped 2819 1953 3442 1.986 0.459 0.126 0.031 23 4.0 S_parieto_occipital 1615 1072 1139 1.402 0.486 0.129 0.032 24 2.1 S_pericallosal 3297 2282 4108 2.041 0.451 0.132 0.038 32 5.4 S_postcentral 1246 844 1716 2.259 0.338 0.111 0.024 7 1.4 S_precentral-inf-part 1815 1255 2726 2.212 0.596 0.133 0.041 21 3.2 S_precentral-sup-part 385 302 705 2.303 0.878 0.172 0.047 6 0.8 S_suborbital 1399 1031 2450 2.578 0.509 0.154 0.046 16 2.6 S_subparietal 1310 923 1806 2.480 0.483 0.134 0.032 10 2.4 S_temporal_inf 6685 4510 10135 2.359 0.418 0.107 0.025 48 7.0 S_temporal_sup 439 317 623 2.354 0.540 0.137 0.030 5 0.6 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 3 lh Thu Feb 12 19:29:29 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 238034 Total vertex volume 237839 (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) = 1825641 mm^3 (det: 1.067080 ) 2122 1426 2965 1.982 0.641 0.136 0.034 26 3.2 caudalanteriorcingulate 3434 2447 6799 2.544 0.561 0.134 0.039 34 5.5 caudalmiddlefrontal 3707 2531 4637 1.785 0.449 0.149 0.044 54 6.8 cuneus 547 368 1607 3.117 0.834 0.120 0.033 4 0.7 entorhinal 4208 2980 8443 2.482 0.573 0.135 0.037 53 5.9 fusiform 7288 4908 12572 2.369 0.476 0.130 0.036 83 9.8 inferiorparietal 5242 3718 11278 2.685 0.627 0.130 0.036 62 7.5 inferiortemporal 2421 1686 3695 2.021 0.693 0.135 0.042 33 3.8 isthmuscingulate 8472 5810 12772 2.050 0.502 0.145 0.043 117 14.2 lateraloccipital 4135 3080 8305 2.445 0.677 0.160 0.055 70 9.4 lateralorbitofrontal 5291 3786 7273 1.826 0.519 0.155 0.049 77 10.2 lingual 2565 1912 4600 2.140 0.585 0.151 0.050 46 4.9 medialorbitofrontal 6733 4609 13949 2.680 0.541 0.122 0.034 73 9.0 middletemporal 1102 683 1639 2.091 0.665 0.102 0.028 11 1.2 parahippocampal 2416 1707 4218 2.258 0.554 0.139 0.049 29 5.0 paracentral 2407 1663 4042 2.296 0.472 0.139 0.050 33 4.7 parsopercularis 1029 736 2086 2.441 0.523 0.137 0.047 12 1.7 parsorbitalis 2460 1702 3691 2.164 0.513 0.152 0.056 36 5.5 parstriangularis 2328 1721 2275 1.520 0.350 0.150 0.043 26 4.4 pericalcarine 7597 5174 10920 2.008 0.592 0.137 0.044 104 13.7 postcentral 2448 1680 3481 1.947 0.700 0.126 0.031 29 3.1 posteriorcingulate 8300 5873 13914 2.322 0.692 0.154 0.054 119 19.9 precentral 6250 4429 10425 2.202 0.491 0.138 0.041 77 10.1 precuneus 1872 1309 3146 2.316 0.614 0.130 0.033 25 2.7 rostralanteriorcingulate 6076 4408 11343 2.339 0.545 0.139 0.040 74 9.8 rostralmiddlefrontal 12841 9545 26083 2.382 0.569 0.140 0.042 166 22.8 superiorfrontal 7199 4689 10375 2.125 0.511 0.130 0.038 81 11.0 superiorparietal 7900 5287 14943 2.536 0.550 0.114 0.031 78 10.0 superiortemporal 5328 3693 9135 2.323 0.518 0.132 0.033 57 7.1 supramarginal 736 462 998 2.048 0.627 0.151 0.053 12 1.7 transversetemporal 3307 2270 6230 2.675 0.764 0.127 0.040 31 5.3 insula #----------------------------------------- #@# Parcellation Stats 3 rh Thu Feb 12 19:29:46 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 PBRHOPE_HOPE089_PETMR rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 232183 Total vertex volume 231983 (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) = 1825641 mm^3 (det: 1.067080 ) 1516 966 2044 1.899 0.748 0.115 0.027 18 1.5 caudalanteriorcingulate 3121 2259 6183 2.388 0.599 0.133 0.039 34 5.1 caudalmiddlefrontal 3368 2271 4169 1.744 0.481 0.139 0.045 47 5.5 cuneus 565 416 1637 3.013 0.827 0.149 0.041 6 1.1 entorhinal 4934 3396 9537 2.464 0.636 0.128 0.038 57 6.9 fusiform 8112 5489 12830 2.272 0.482 0.125 0.033 94 10.5 inferiorparietal 5017 3539 9200 2.444 0.690 0.137 0.041 56 8.3 inferiortemporal 1424 934 2310 2.260 0.608 0.137 0.044 19 2.3 isthmuscingulate 8783 5865 11361 1.887 0.489 0.145 0.044 117 14.7 lateraloccipital 4403 3306 8770 2.468 0.662 0.163 0.057 78 10.5 lateralorbitofrontal 5061 3487 6342 1.764 0.545 0.146 0.046 67 9.2 lingual 2511 1832 5122 2.448 0.694 0.149 0.051 42 4.9 medialorbitofrontal 6455 4550 13598 2.620 0.541 0.127 0.036 75 9.3 middletemporal 1156 705 1712 2.142 0.707 0.098 0.022 8 1.0 parahippocampal 2666 1933 4245 2.142 0.566 0.164 0.060 39 6.8 paracentral 1570 1134 2928 2.392 0.457 0.125 0.035 15 2.2 parsopercularis 996 757 2277 2.572 0.501 0.149 0.043 14 1.7 parsorbitalis 1449 1105 3031 2.338 0.563 0.137 0.037 14 2.2 parstriangularis 2371 1763 2299 1.491 0.361 0.153 0.042 28 4.8 pericalcarine 7575 5204 10690 1.926 0.519 0.133 0.042 91 12.8 postcentral 1780 1274 2952 2.160 0.742 0.134 0.037 24 2.7 posteriorcingulate 7549 5407 14674 2.409 0.704 0.142 0.043 91 14.0 precentral 6590 4556 10797 2.308 0.533 0.136 0.038 72 10.0 precuneus 1351 975 2495 2.343 0.651 0.132 0.038 26 2.0 rostralanteriorcingulate 5587 4219 11496 2.342 0.549 0.149 0.046 86 10.4 rostralmiddlefrontal 12535 9340 27250 2.464 0.634 0.147 0.045 172 23.8 superiorfrontal 7059 4706 9707 1.986 0.448 0.124 0.036 75 9.7 superiorparietal 7692 5411 15385 2.527 0.577 0.122 0.033 84 10.2 superiortemporal 6021 4184 10082 2.319 0.479 0.130 0.037 69 8.8 supramarginal 711 412 1013 2.204 0.551 0.137 0.053 10 1.4 transversetemporal 3159 2190 5847 2.583 0.731 0.128 0.040 32 5.1 insula #-------------------------------------------- #@# ASeg Stats Thu Feb 12 19:30:03 EST 2026 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR 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 /usr/local/freesurfer/stable7.4.1/ASegStatsLUT.txt --subject PBRHOPE_HOPE089_PETMR 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 /usr/local/freesurfer/stable7.4.1/ASegStatsLUT.txt --subject PBRHOPE_HOPE089_PETMR sysname Linux hostname r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1825641 mm^3 (det: 1.067080 ) Computing euler number orig.nofix lheno = -92, rheno = -76 orig.nofix lhholes = 47, rhholes = 39 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label INFO: fsaverage subject does not have uptodate *rhinal labels! cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs; rm -Rf fsaverage; cd - INFO: Creating symlink to fsaverage subject... cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs; ln -s /usr/local/freesurfer/stable7.4.1/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Thu Feb 12 19:32:54 EST 2026 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA1_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 255 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA2_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 273 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8182 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3a_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 132 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4209 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3b_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 237 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6220 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4a_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 454 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6238 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4p_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 320 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4390 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA6_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 1023 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14612 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA44_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 276 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4457 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA45_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 482 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3904 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V1_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 1854 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6495 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V2_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 3734 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11848 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.MT_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 244 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2262 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1355 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1242 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 520 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 833 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 2034 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 484 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2585 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 1566 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 5443 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 1602 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 4521 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 486 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1772 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 299 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1305 mri_label2label: Done mris_label2annot --s PBRHOPE_HOPE089_PETMR --ctab /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE089_PETMR --ctab /usr/local/freesurfer/stable7.4.1/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 r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE089_PETMR hemi lh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable7.4.1/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 130329 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.mpm.vpnl.annot mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1115 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2193 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1516 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2055 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2467 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1697 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 720 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7755 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2115 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 202 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1353 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 1315 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4720 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 1734 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5068 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 596 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 483 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 148275 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 470 mri_label2label: Done mris_label2annot --s PBRHOPE_HOPE089_PETMR --hemi lh --ctab /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE089_PETMR --hemi lh --ctab /usr/local/freesurfer/stable7.4.1/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 r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE089_PETMR hemi lh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable7.4.1/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 103523 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.BA_exvivo.annot mris_label2annot --s PBRHOPE_HOPE089_PETMR --hemi lh --ctab /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE089_PETMR --hemi lh --ctab /usr/local/freesurfer/stable7.4.1/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 r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE089_PETMR hemi lh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable7.4.1/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 120482 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab PBRHOPE_HOPE089_PETMR lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 238034 Total vertex volume 237839 (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) = 1825641 mm^3 (det: 1.067080 ) 1292 791 1860 1.932 0.564 0.150 0.069 29 3.3 BA1_exvivo 3822 2653 5880 2.232 0.514 0.132 0.037 43 5.7 BA2_exvivo 1120 870 1142 1.750 0.433 0.159 0.046 13 2.2 BA3a_exvivo 2530 1730 3475 1.848 0.613 0.131 0.037 31 3.7 BA3b_exvivo 1714 1259 3470 2.446 0.655 0.175 0.069 29 5.0 BA4a_exvivo 1713 1214 2339 2.255 0.735 0.178 0.070 35 5.4 BA4p_exvivo 10007 7221 20638 2.459 0.665 0.141 0.046 123 19.7 BA6_exvivo 2458 1687 4371 2.359 0.606 0.141 0.052 36 4.9 BA44_exvivo 2942 2058 4790 2.193 0.524 0.151 0.055 43 6.1 BA45_exvivo 4281 3075 4883 1.601 0.422 0.158 0.047 59 8.8 V1_exvivo 9779 6905 13350 1.842 0.498 0.153 0.048 145 18.2 V2_exvivo 1856 1210 3066 2.358 0.381 0.124 0.035 19 2.4 MT_exvivo 625 426 1161 2.671 0.882 0.134 0.041 8 0.9 perirhinal_exvivo 613 377 1495 2.635 1.047 0.112 0.034 6 0.8 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PBRHOPE_HOPE089_PETMR lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 238034 Total vertex volume 237839 (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) = 1825641 mm^3 (det: 1.067080 ) 861 499 1182 1.871 0.553 0.157 0.074 23 2.2 BA1_exvivo 1650 1127 2620 2.185 0.552 0.130 0.039 20 2.5 BA2_exvivo 911 738 908 1.688 0.388 0.160 0.045 9 1.8 BA3a_exvivo 1543 1077 1634 1.552 0.362 0.120 0.032 12 2.1 BA3b_exvivo 1737 1271 3282 2.403 0.679 0.171 0.067 30 5.0 BA4a_exvivo 1350 969 1946 2.334 0.752 0.182 0.069 26 4.3 BA4p_exvivo 6130 4367 12168 2.390 0.702 0.142 0.048 79 12.8 BA6_exvivo 1668 1131 2726 2.199 0.530 0.147 0.058 28 3.8 BA44_exvivo 1215 817 2231 2.351 0.542 0.155 0.065 21 2.8 BA45_exvivo 4577 3269 5432 1.642 0.463 0.156 0.046 62 9.2 V1_exvivo 4993 3520 6406 1.756 0.468 0.160 0.049 77 9.7 V2_exvivo 507 309 840 2.267 0.422 0.117 0.040 6 0.7 MT_exvivo 283 191 519 2.715 0.892 0.143 0.045 4 0.4 perirhinal_exvivo 368 240 957 2.905 0.744 0.097 0.027 2 0.4 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Thu Feb 12 19:36:06 EST 2026 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA1_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 266 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4228 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA2_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 420 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7107 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3a_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4060 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3b_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 218 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4740 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4a_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 381 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6128 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4p_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 228 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4701 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA6_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 902 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13158 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA44_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 6968 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA45_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 168 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5523 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V1_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 1835 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6562 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V2_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 3550 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11566 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.MT_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 451 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2383 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1114 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 815 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 275 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 816 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 390 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 1111 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 309 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1832 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 586 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 2172 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 1353 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 5020 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 1269 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3988 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 713 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1941 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 528 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1553 mri_label2label: Done mris_label2annot --s PBRHOPE_HOPE089_PETMR --ctab /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average/colortable_vpnl.txt Number of ctab entries 9 7.4.1 cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE089_PETMR --ctab /usr/local/freesurfer/stable7.4.1/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 r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE089_PETMR hemi rh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable7.4.1/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 125827 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.mpm.vpnl.annot mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 970 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2847 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1714 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2244 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 102 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1490 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1609 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 556 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7515 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 8 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1020 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1189 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 1196 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4428 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 1626 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5063 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 322 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 735 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject PBRHOPE_HOPE089_PETMR --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE089_PETMR 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable7.4.1 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 143551 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 321 mri_label2label: Done mris_label2annot --s PBRHOPE_HOPE089_PETMR --hemi rh --ctab /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE089_PETMR --hemi rh --ctab /usr/local/freesurfer/stable7.4.1/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 r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE089_PETMR hemi rh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable7.4.1/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 101727 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.BA_exvivo.annot mris_label2annot --s PBRHOPE_HOPE089_PETMR --hemi rh --ctab /usr/local/freesurfer/stable7.4.1/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 /usr/local/freesurfer/stable7.4.1/average/colortable_BA.txt Number of ctab entries 15 7.4.1 cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE089_PETMR --hemi rh --ctab /usr/local/freesurfer/stable7.4.1/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 r440-05.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE089_PETMR hemi rh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable7.4.1/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/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 119107 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab PBRHOPE_HOPE089_PETMR rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 232183 Total vertex volume 231983 (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) = 1825641 mm^3 (det: 1.067080 ) 1078 725 2001 2.088 0.568 0.158 0.060 23 2.3 BA1_exvivo 3817 2644 5175 2.031 0.447 0.131 0.041 41 6.4 BA2_exvivo 1080 803 1031 1.683 0.426 0.141 0.044 11 1.9 BA3a_exvivo 2176 1482 2564 1.641 0.444 0.124 0.036 20 3.6 BA3b_exvivo 1740 1290 3693 2.418 0.825 0.170 0.062 29 5.0 BA4a_exvivo 1493 1074 2188 2.197 0.607 0.155 0.051 19 3.5 BA4p_exvivo 7748 5682 17209 2.486 0.739 0.154 0.051 110 16.4 BA6_exvivo 2656 1901 5128 2.434 0.465 0.128 0.031 26 3.6 BA44_exvivo 2994 2302 6530 2.413 0.518 0.147 0.042 39 5.1 BA45_exvivo 4411 3033 5005 1.621 0.474 0.145 0.044 56 8.2 V1_exvivo 9343 6384 11333 1.756 0.502 0.152 0.047 132 17.3 V2_exvivo 2246 1575 3025 2.001 0.444 0.139 0.042 27 3.5 MT_exvivo 433 298 916 2.728 0.665 0.131 0.032 5 0.6 perirhinal_exvivo 609 424 1696 2.928 0.897 0.123 0.033 6 0.8 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab PBRHOPE_HOPE089_PETMR rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE089_PETMR/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 232183 Total vertex volume 231983 (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) = 1825641 mm^3 (det: 1.067080 ) 758 492 1315 2.006 0.583 0.162 0.066 17 1.5 BA1_exvivo 2163 1502 3100 2.019 0.467 0.130 0.043 23 3.8 BA2_exvivo 959 717 882 1.643 0.360 0.141 0.042 8 1.7 BA3a_exvivo 1637 1125 1662 1.517 0.335 0.110 0.029 9 2.3 BA3b_exvivo 1021 792 2322 2.455 0.940 0.198 0.079 21 3.9 BA4a_exvivo 1249 911 1766 2.177 0.628 0.164 0.055 18 3.3 BA4p_exvivo 5293 3858 11772 2.482 0.738 0.151 0.051 73 10.9 BA6_exvivo 582 445 1403 2.566 0.428 0.116 0.029 5 0.7 BA44_exvivo 734 602 1990 2.539 0.475 0.160 0.044 12 1.3 BA45_exvivo 4219 2904 4697 1.603 0.472 0.145 0.045 53 8.0 V1_exvivo 4884 3363 5443 1.654 0.492 0.160 0.049 77 9.6 V2_exvivo 296 226 511 2.068 0.535 0.150 0.050 4 0.6 MT_exvivo 40 26 89 3.050 0.517 0.122 0.026 0 0.0 perirhinal_exvivo 609 418 1530 2.981 0.742 0.114 0.026 4 0.7 entorhinal_exvivo Started at Thu Feb 12 13:37:14 EST 2026 Ended at Thu Feb 12 19:39:14 EST 2026 #@#%# recon-all-run-time-hours 6.033 recon-all -s PBRHOPE_HOPE089_PETMR finished without error at Thu Feb 12 19:39:14 EST 2026