Fri May 12 14:50:09 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data /usr/local/freesurfer/dev//bin/recon-all -subjid CR_t2_tra_12_SR -all -brainstem-structures -no-isrunning subjid CR_t2_tra_12_SR setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Actual FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/dev build-stamp.txt: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 44040192 kbytes descriptors 32768 memorylocked unlimited maxproc 127909 maxlocks unlimited maxsignal 127909 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 31G 633M 14G 114M 16G 30G Swap: 63G 1.3G 62G pbsjob 19716332.launchpad.nmr.mgh.harvard.edu ######################################## program versions used dev (freesurfer-linux-centos7_x86_64-dev-20230512-47dba46) dev ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:11-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:11-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:12-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:13-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:13-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:14-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:14-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:15-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:15-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:16-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:16-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:17-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:17-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:17-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:18-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:18-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:19-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:19-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:20-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:20-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:21-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:21-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:22-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:22-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:22-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:23-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:23-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:23-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:24-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:25-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:25-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:25-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:26-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:26-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 dev ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:29-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 dev ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:32-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:32-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:33-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:33-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:34-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:34-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:34-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:35-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:35-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:36-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:36-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:36-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:37-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:37-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:38-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:38-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:39-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:39-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:40-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:40-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:41-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:41-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:42-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:42-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:42-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:43-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:43-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:43-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:44-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:44-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:45-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:45-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:46-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:46-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:46-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:47-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:47-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl dev mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: dev TimeStamp: 2023/05/12-18:50:47-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.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/dev//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/dev//average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri May 12 14:50:52 EDT 2023 ERROR: no run data found in /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri. Make sure to have a volume called 001.mgz in /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CR_t2_tra_12_SR exited with ERRORS at Fri May 12 14:50:52 EDT 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #New# invocation of recon-all Fri May 12 15:00:24 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data /usr/local/freesurfer/dev//bin/recon-all -subjid CR_t2_tra_12_SR -all -brainstem-structures -no-isrunning subjid CR_t2_tra_12_SR setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Actual FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/dev build-stamp.txt: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 44040192 kbytes descriptors 32768 memorylocked unlimited maxproc 127909 maxlocks unlimited maxsignal 127909 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 31G 633M 14G 114M 16G 30G Swap: 63G 1.3G 62G pbsjob 19716339.launchpad.nmr.mgh.harvard.edu ######################################## program versions used dev (freesurfer-linux-centos7_x86_64-dev-20230512-47dba46) dev ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:26-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:27-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:28-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:28-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:29-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:29-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:30-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:30-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:31-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:31-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:32-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:32-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:33-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:33-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:34-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:34-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:34-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:35-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:35-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:35-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:36-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:36-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:36-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:37-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:37-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:38-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:38-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:38-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:39-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:39-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:39-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:39-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:40-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:40-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 dev ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:43-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 dev ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:46-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:46-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:46-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:47-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:47-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:48-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:48-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:49-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:49-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:50-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:50-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:50-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:51-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:51-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:52-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:52-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:53-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:53-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:53-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:54-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:54-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:55-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:55-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:56-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:56-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:56-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:56-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:57-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:57-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:58-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:58-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:59-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:59-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:00:59-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:01:00-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:01:00-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:01:01-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl dev mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: dev TimeStamp: 2023/05/12-19:01:01-GMT BuildTime: May 12 2023 00:22:17 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 User: wk962 Machine: compute-0-37.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.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/dev//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/dev//average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri May 12 15:01:05 EDT 2023 Found 1 runs /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri//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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri//001.mgz /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz mri_info /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz type: MGH dimensions: 164 x 201 x 153 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 201.000 dof: 1 xstart: -82.0, xend: 82.0 ystart: -100.5, yend: 100.5 zstart: -76.5, zend: 76.5 TR: 1000.00 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 = -0.9970, y_r = 0.0400, z_r = 0.0663, c_r = -1.4046 : x_a = 0.0244, y_a = 0.9748, z_a = -0.2215, c_a = -14.3056 : x_s = 0.0735, y_s = 0.2193, z_s = 0.9729, c_s = 11.2473 talairach xfm : Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -0.9970 0.0400 0.0663 71.2510 0.0244 0.9748 -0.2215 -97.3319 0.0735 0.2193 0.9729 -91.2432 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -0.9970 0.0244 0.0735 80.1219 0.0400 0.9748 0.2193 112.0360 0.0663 -0.2215 0.9729 62.4815 -0.0000 -0.0000 -0.0000 1.0000 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR mri_convert /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz --conform mri_convert /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz --conform reading from /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996994, 0.0244168, 0.0735239) j_ras = (0.0400434, 0.974846, 0.219255) k_ras = (0.0663209, -0.22154, 0.972893) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram -28.9539 177.845 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz... @#@FSTIME 2023:05:12:15:01:13 mri_convert N 3 e 4.74 S 0.02 U 3.87 P 82% M 27832 F 0 R 3180 W 0 c 3 w 194 I 8 O 6448 L 0.67 0.25 0.12 @#@FSLOADPOST 2023:05:12:15:01:17 mri_convert N 3 0.70 0.26 0.13 mri_add_xform_to_header -c /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/transforms/talairach.xfm /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2023:05:12:15:01:18 mri_add_xform_to_header N 4 e 2.00 S 0.01 U 1.38 P 70% M 19696 F 1 R 1454 W 0 c 19 w 144 I 6632 O 6448 L 0.70 0.26 0.13 @#@FSLOADPOST 2023:05:12:15:01:20 mri_add_xform_to_header N 4 0.72 0.27 0.13 mri_info /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz orig.mgz ======================================== Volume information for /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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: 1000.00 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 = -1.4046 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -14.3056 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 11.2473 talairach xfm : /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 126.5954 -0.0000 0.0000 1.0000 -142.3056 0.0000 -1.0000 0.0000 139.2473 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 126.5954 -0.0000 -0.0000 -1.0000 139.2473 -0.0000 1.0000 -0.0000 142.3056 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Fri May 12 15:01:20 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /bin/bc /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri /usr/local/freesurfer/dev//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 dev Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Fri May 12 15:01:20 EDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.26588 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.26588/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.26588/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.26588/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.26588/nu0.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.79397e-09, 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... Fri May 12 15:07:55 EDT 2023 mri_nu_correct.mni done @#@FSTIME 2023:05:12:15:01:20 mri_nu_correct.mni N 12 e 395.63 S 0.22 U 394.21 P 99% M 502576 F 1 R 29670 W 0 c 170 w 521 I 8968 O 13080 L 0.72 0.27 0.13 @#@FSLOADPOST 2023:05:12:15:07:56 mri_nu_correct.mni N 12 1.00 0.81 0.43 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Fri May 12 15:07:56 EDT 2023 Ended at Fri May 12 15:09:36 EDT 2023 talairach_avi done @#@FSTIME 2023:05:12:15:07:56 talairach_avi N 4 e 100.00 S 1.45 U 65.11 P 66% M 253920 F 6 R 44906 W 0 c 153 w 5745 I 271120 O 296064 L 1.00 0.81 0.43 @#@FSLOADPOST 2023:05:12:15:09:36 talairach_avi N 4 0.85 0.82 0.48 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/dev//average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox dev --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/dev//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 1.16698 0.00538 -0.19556 6.18156; -0.01663 1.07001 0.21135 -0.30445; 0.18568 -0.29289 1.14442 -16.44107; 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 Fri May 12 15:09:38 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6835, pval=0.4932 >= threshold=0.0050) @#@FSTIME 2023:05:12:15:09:38 talairach_afd N 4 e 0.36 S 0.00 U 0.00 P 1% M 2140 F 1 R 638 W 0 c 1 w 20 I 7360 O 0 L 0.85 0.82 0.48 @#@FSLOADPOST 2023:05:12:15:09:38 talairach_afd N 4 0.85 0.82 0.48 awk -f /usr/local/freesurfer/dev//bin/extract_talairach_avi_QA.awk /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/transforms/talairach_avi.log TalAviQA: 0.98356 z-score: 1 #-------------------------------------------- #@# Nu Intensity Correction Fri May 12 15:09:38 EDT 2023 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /bin/bc /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri /usr/local/freesurfer/dev//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 dev Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Fri May 12 15:09:39 EDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.27366 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.27366/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.27366/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.27366/ones.mgz dev cwd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.27366/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.27366/ones.mgz sysname Linux hostname compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 input ./tmp.mri_nu_correct.mni.27366/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27366/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.27366/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27366/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27366/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27366/input.mean.dat dev cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27366/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27366/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27366/input.mean.dat sysname Linux hostname compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27366/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.27366/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27366/ones.mgz --i ./tmp.mri_nu_correct.mni.27366/nu0.mgz --sum ./tmp.mri_nu_correct.mni.27366/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27366/output.mean.dat dev cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27366/ones.mgz --i ./tmp.mri_nu_correct.mni.27366/nu0.mgz --sum ./tmp.mri_nu_correct.mni.27366/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27366/output.mean.dat sysname Linux hostname compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27366/ones.mgz Loading ./tmp.mri_nu_correct.mni.27366/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.27366/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.27366/nu0.mgz ./tmp.mri_nu_correct.mni.27366/nu0.mgz mul 1.08683483919860225131 Saving result to './tmp.mri_nu_correct.mni.27366/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27366/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.27366/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.27366/nu0.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.79397e-09, 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 11 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 19, i2 = 75 #mri_make_uchar# mapping 47 184 to 3 110 : b -33.9062 m 0.781713 : thresh 43.3743 maxsat 369.581 : nzero 11954858 nsat 0 Fri May 12 15:16:56 EDT 2023 mri_nu_correct.mni done @#@FSTIME 2023:05:12:15:09:39 mri_nu_correct.mni N 9 e 437.80 S 0.96 U 434.63 P 99% M 610240 F 1 R 182715 W 0 c 369 w 1025 I 6560 O 32360 L 0.79 0.80 0.47 @#@FSLOADPOST 2023:05:12:15:16:56 mri_nu_correct.mni N 9 1.00 0.95 0.67 mri_add_xform_to_header -c /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2023:05:12:15:16:56 mri_add_xform_to_header N 4 e 1.68 S 0.01 U 1.37 P 82% M 19760 F 0 R 1472 W 0 c 2 w 122 I 0 O 5656 L 1.00 0.95 0.67 @#@FSLOADPOST 2023:05:12:15:16:58 mri_add_xform_to_header N 4 1.00 0.95 0.67 #-------------------------------------------- #@# Intensity Normalization Fri May 12 15:16:58 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 1.16698 0.00538 -0.19556 6.18156; -0.01663 1.07001 0.21135 -0.30445; 0.18568 -0.29289 1.14442 -16.44107; 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 = 13 Starting OpenSpline(): npoints = 13 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 111 gm peak at 55 (55), valley at 38 (38) csf peak at 12, setting threshold to 40 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 55 (55), valley at 19 (19) csf peak at 28, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 5 minutes and 20 seconds. @#@FSTIME 2023:05:12:15:16:58 mri_normalize N 7 e 321.92 S 0.31 U 321.31 P 99% M 580732 F 0 R 13669 W 0 c 96 w 178 I 0 O 5392 L 1.00 0.95 0.67 @#@FSLOADPOST 2023:05:12:15:22:20 mri_normalize N 7 1.03 1.00 0.77 #-------------------------------------------- #@# Skull Stripping Fri May 12 15:22:20 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/dev//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/dev//average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 11 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=17.0 skull bounding box = (57, 50, 33) --> (202, 208, 221) finding center of left hemi white matter using (105, 103, 127) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (87,84,104) --> (122, 122,150) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 109 +- 4.4 after smoothing, mri peak at 109, scaling input intensities by 0.991 scaling channel 0 by 0.990826 initial log_p = -4.559 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.407421 @ (-10.526, -10.526, -10.526) max log p = -4.353146 @ (5.263, 5.263, -5.263) max log p = -4.331714 @ (2.632, -2.632, -2.632) max log p = -4.309817 @ (1.316, 1.316, -6.579) max log p = -4.293618 @ (0.658, -4.605, 8.553) max log p = -4.293618 @ (0.000, 0.000, 0.000) max log p = -4.293618 @ (0.000, 0.000, 0.000) max log p = -4.293618 @ (0.000, 0.000, 0.000) Found translation: (-0.7, -11.2, -16.4): log p = -4.294 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.803, old_max_log_p =-4.294 (thresh=-4.3) 1.22059 -0.17065 0.09668 -20.56895; 0.14816 1.13305 0.12942 -57.57586; -0.10647 -0.11619 1.13915 0.89580; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 17 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.803, old_max_log_p =-3.803 (thresh=-3.8) 1.22059 -0.17065 0.09668 -20.56895; 0.14816 1.13305 0.12942 -57.57586; -0.10647 -0.11619 1.13915 0.89580; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 2 minutes and 15 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.644, old_max_log_p =-3.803 (thresh=-3.8) 1.19707 -0.18819 0.01739 -6.98095; 0.19296 1.17324 0.25212 -80.59376; -0.04120 -0.22653 1.06188 12.32285; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 7 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.644, old_max_log_p =-3.644 (thresh=-3.6) 1.19707 -0.18819 0.01739 -6.98095; 0.19296 1.17324 0.25212 -80.59376; -0.04120 -0.22653 1.06188 12.32285; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 2 minutes and 8 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.635, old_max_log_p =-3.644 (thresh=-3.6) 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 54 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.635, old_max_log_p =-3.635 (thresh=-3.6) 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.635 (old=-4.559) transform before final EM align: 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.1 tol 0.000000 final transform: 1.19317 -0.18559 0.00873 -6.19532; 0.19329 1.17463 0.25228 -80.83504; -0.03140 -0.22845 1.06451 11.45291; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 905388 FSRUNTIME@ mri_em_register 0.2441 hours 1 threads registration took 14 minutes and 39 seconds. @#@FSTIME 2023:05:12:15:22:20 mri_em_register N 4 e 878.73 S 1.11 U 867.67 P 98% M 625224 F 0 R 114894 W 0 c 470 w 89 I 149672 O 40 L 1.03 1.00 0.77 @#@FSLOADPOST 2023:05:12:15:36:59 mri_em_register N 4 1.00 1.01 0.91 mri_watershed -T1 -brain_atlas /usr/local/freesurfer/dev//average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=114 z=123 r=71 first estimation of the main basin volume: 1526194 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=144, y=109, z=90, Imax=255 CSF=15, 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=7885984758 voxels, voxel volume =1.000 = 7885984758 mmm3 = 7885984.768 cm3 done. PostAnalyze...Basin Prior 5 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=128,y=123, z=117, r=9453 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=2, CSF_intensity=23, CSF_MAX=43 , nb = 44442 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 2970 LEFT_CER CSF_MIN=0, CSF_intensity=14, CSF_MAX=41 , nb = 2844 RIGHT_BRAIN CSF_MIN=4, CSF_intensity=23, CSF_MAX=44 , nb = 19008 LEFT_BRAIN CSF_MIN=4, CSF_intensity=27, CSF_MAX=42 , nb = 18972 OTHER CSF_MIN=1, CSF_intensity=7, CSF_MAX=31 , nb = 648 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 43, 37, 29, 58 after analyzing : 33, 37, 37, 42 RIGHT_CER before analyzing : 37, 33, 29, 58 after analyzing : 26, 33, 33, 39 LEFT_CER before analyzing : 41, 35, 29, 58 after analyzing : 29, 35, 35, 40 RIGHT_BRAIN before analyzing : 44, 37, 29, 58 after analyzing : 33, 37, 37, 42 LEFT_BRAIN before analyzing : 42, 37, 29, 58 after analyzing : 34, 37, 37, 42 OTHER before analyzing : 31, 30, 29, 58 after analyzing : 21, 30, 30, 37 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.012 curvature mean = 65.165, std = 7.136 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.12, sigma = 4.98 after rotation: sse = 3.12, sigma = 4.98 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.41, its var is 4.65 before Erosion-Dilatation 0.76% 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...28 iterations mri_strip_skull: done peeling brain Brain Size = 1344500 voxels, voxel volume = 1.000 mm3 = 1344500 mmm3 = 1344.500 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed done @#@FSTIME 2023:05:12:15:36:59 mri_watershed N 6 e 25.39 S 0.57 U 24.22 P 97% M 813084 F 0 R 188674 W 0 c 16 w 119 I 7960 O 2168 L 1.00 1.01 0.91 @#@FSLOADPOST 2023:05:12:15:37:25 mri_watershed N 6 1.00 1.01 0.91 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri May 12 15:37:26 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev//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/dev//average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 6 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=24.9 skull bounding box = (67, 72, 46) --> (189, 173, 204) finding center of left hemi white matter using (108, 106, 125) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (93,94,106) --> (122, 118,144) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 109 +- 4.1 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.195 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.121516 @ (-10.526, -10.526, -10.526) max log p = -3.934846 @ (5.263, 5.263, -5.263) max log p = -3.901098 @ (2.632, 2.632, -2.632) max log p = -3.864209 @ (1.316, -1.316, 3.947) max log p = -3.859535 @ (0.658, -0.658, -0.658) max log p = -3.853373 @ (-1.645, 0.329, -0.987) max log p = -3.853373 @ (0.000, 0.000, 0.000) max log p = -3.853373 @ (0.000, 0.000, 0.000) Found translation: (-2.3, -4.3, -16.1): log p = -3.853 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.423, old_max_log_p =-3.853 (thresh=-3.8) 1.13543 -0.15442 0.07381 -9.67745; 0.14816 1.12737 0.15062 -57.44864; -0.10647 -0.07803 0.99673 7.66726; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 0 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.423, old_max_log_p =-3.423 (thresh=-3.4) 1.13543 -0.15442 0.07381 -9.67745; 0.14816 1.12737 0.15062 -57.44864; -0.10647 -0.07803 0.99673 7.66726; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 2 minutes and 0 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.287, old_max_log_p =-3.423 (thresh=-3.4) 1.12893 -0.21711 -0.00486 8.47066; 0.21756 1.12204 0.25229 -76.11266; -0.05026 -0.20495 1.01663 17.42245; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 52 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.287, old_max_log_p =-3.287 (thresh=-3.3) 1.12893 -0.21711 -0.00486 8.47066; 0.21756 1.12204 0.25229 -76.11266; -0.05026 -0.20495 1.01663 17.42245; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 51 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.264, old_max_log_p =-3.287 (thresh=-3.3) 1.13680 -0.18045 0.00226 2.13449; 0.18256 1.13604 0.21000 -68.33422; -0.04152 -0.15823 1.02621 8.03013; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 39 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.264, old_max_log_p =-3.264 (thresh=-3.3) 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 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 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.264 (old=-4.195) transform before final EM align: 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 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 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 892836 FSRUNTIME@ mri_em_register 0.2098 hours 1 threads registration took 12 minutes and 35 seconds. @#@FSTIME 2023:05:12:15:37:26 mri_em_register N 7 e 755.12 S 1.11 U 748.97 P 99% M 614468 F 0 R 112908 W 0 c 895 w 91 I 139952 O 40 L 1.00 1.01 0.91 @#@FSLOADPOST 2023:05:12:15:50:01 mri_em_register N 7 1.00 1.00 0.95 #-------------------------------------- #@# CA Normalize Fri May 12 15:50:01 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev//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/dev//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=25.9 skull bounding box = (67, 72, 46) --> (189, 173, 204) finding center of left hemi white matter using (108, 106, 125) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (93,94,106) --> (122, 118,144) to find MRI wm before smoothing, mri peak at 111 robust fit to distribution - 109 +- 4.1 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246437 sample points... INFO: compute sample coordinates transform 1.13813 -0.18066 0.00227 1.98840; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (124, 63, 45) --> (188, 162, 205) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 7 of 6621 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (70, 68, 44) --> (130, 169, 205) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 12 of 6745 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (133, 139, 70) --> (179, 177, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 344 of 399 (86.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (98, 140, 67) --> (135, 183, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 289 of 305 (94.8%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (117, 131, 105) --> (150, 191, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 756 of 796 (95.0%) samples deleted using 14866 total control points for intensity normalization... bias field = 0.990 +- 0.037 21 of 13458 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (124, 63, 45) --> (188, 162, 205) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 9 of 6695 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (70, 68, 44) --> (130, 169, 205) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 13 of 6849 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (133, 139, 70) --> (179, 177, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 406 of 408 (99.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (98, 140, 67) --> (135, 183, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 311 of 311 (100.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (117, 131, 105) --> (150, 191, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 820 of 826 (99.3%) samples deleted using 15089 total control points for intensity normalization... bias field = 1.043 +- 0.038 9 of 13439 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (124, 63, 45) --> (188, 162, 205) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 5 of 6705 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (70, 68, 44) --> (130, 169, 205) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 12 of 6787 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (133, 139, 70) --> (179, 177, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 421 of 421 (100.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (98, 140, 67) --> (135, 183, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 314 of 314 (100.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (117, 131, 105) --> (150, 191, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 838 of 850 (98.6%) samples deleted using 15077 total control points for intensity normalization... bias field = 1.041 +- 0.036 10 of 13360 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 48 seconds. @#@FSTIME 2023:05:12:15:50:01 mri_ca_normalize N 8 e 108.05 S 0.62 U 107.16 P 99% M 890496 F 0 R 127940 W 0 c 54 w 141 I 0 O 3560 L 1.00 1.00 0.95 @#@FSLOADPOST 2023:05:12:15:51:49 mri_ca_normalize N 8 1.00 1.00 0.95 #-------------------------------------- #@# CA Reg Fri May 12 15:51:49 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/dev//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/dev//average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.882616 #GCAMreg# pass 0 level1 5 level2 1 tsec 594.858 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 0.721964 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 0.727856 #GCAMreg# pass 0 level1 4 level2 1 tsec 598.429 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 0.659554 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 0.697437 #GCAMreg# pass 0 level1 3 level2 1 tsec 92.098 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 0.697437 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 0.808387 #GCAMreg# pass 0 level1 2 level2 1 tsec 150.006 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 0.778717 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.871474 #GCAMreg# pass 0 level1 1 level2 1 tsec 336.567 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 0.833421 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 0.796041 #GCAMreg# pass 0 level1 0 level2 1 tsec 100.543 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 0.788622 GCAMregister done in 42.2204 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.12228 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (468 voxels, overlap=0.104) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (468 voxels, peak = 5), gca=6.4 gca peak = 0.17690 (16) mri peak = 0.09577 ( 5) Right_Lateral_Ventricle (43): linear fit = 0.25 x + 0.0 (258 voxels, overlap=0.298) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (258 voxels, peak = 4), gca=6.4 gca peak = 0.28275 (96) mri peak = 0.13520 (93) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (797 voxels, overlap=0.633) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (797 voxels, peak = 92), gca=91.7 gca peak = 0.18948 (93) mri peak = 0.11261 (93) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (678 voxels, overlap=0.568) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (678 voxels, peak = 89), gca=88.8 gca peak = 0.20755 (55) mri peak = 0.11389 (55) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (766 voxels, overlap=0.971) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (766 voxels, peak = 53), gca=53.1 gca peak = 0.31831 (58) mri peak = 0.11500 (60) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (641 voxels, overlap=0.995) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (641 voxels, peak = 55), gca=54.8 gca peak = 0.11957 (102) mri peak = 0.23056 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43932 voxels, overlap=0.575) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43932 voxels, peak = 103), gca=102.5 gca peak = 0.11429 (102) mri peak = 0.20615 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (44541 voxels, overlap=0.593) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (44541 voxels, peak = 103), gca=102.5 gca peak = 0.14521 (59) mri peak = 0.03374 (61) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (21304 voxels, overlap=0.883) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (21304 voxels, peak = 60), gca=60.5 gca peak = 0.14336 (58) mri peak = 0.03427 (64) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (20187 voxels, overlap=0.773) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (20187 voxels, peak = 62), gca=62.4 gca peak = 0.13305 (70) mri peak = 0.15271 (67) Right_Caudate (50): linear fit = 0.98 x + 0.0 (621 voxels, overlap=0.970) Right_Caudate (50): linear fit = 0.98 x + 0.0 (621 voxels, peak = 68), gca=68.2 gca peak = 0.15761 (71) mri peak = 0.09180 (73) Left_Caudate (11): linear fit = 1.00 x + 0.0 (673 voxels, overlap=0.933) Left_Caudate (11): linear fit = 1.00 x + 0.0 (673 voxels, peak = 71), gca=71.0 gca peak = 0.13537 (57) mri peak = 0.07807 (55) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (27510 voxels, overlap=0.900) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (27510 voxels, peak = 57), gca=57.0 gca peak = 0.13487 (56) mri peak = 0.06744 (54) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (29567 voxels, overlap=0.858) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (29567 voxels, peak = 53), gca=52.9 gca peak = 0.19040 (84) mri peak = 0.09314 (82) Left_Cerebellum_White_Matter (7): linear fit = 0.96 x + 0.0 (7505 voxels, overlap=0.530) Left_Cerebellum_White_Matter (7): linear fit = 0.96 x + 0.0 (7505 voxels, peak = 81), gca=81.1 gca peak = 0.18871 (83) mri peak = 0.09844 (80) Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (6163 voxels, overlap=0.348) Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (6163 voxels, peak = 78), gca=78.4 gca peak = 0.24248 (57) mri peak = 0.14699 (60) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (378 voxels, overlap=0.991) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (378 voxels, peak = 59), gca=59.0 gca peak = 0.35833 (56) mri peak = 0.13979 (55) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (465 voxels, overlap=0.953) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (465 voxels, peak = 56), gca=56.0 gca peak = 0.12897 (85) mri peak = 0.07094 (84) Left_Thalamus (10): linear fit = 1.04 x + 0.0 (4309 voxels, overlap=0.969) Left_Thalamus (10): linear fit = 1.04 x + 0.0 (4309 voxels, peak = 89), gca=88.8 gca peak = 0.13127 (83) mri peak = 0.08654 (83) Right_Thalamus (49): linear fit = 0.99 x + 0.0 (3560 voxels, overlap=0.905) Right_Thalamus (49): linear fit = 0.99 x + 0.0 (3560 voxels, peak = 82), gca=81.8 gca peak = 0.12974 (78) mri peak = 0.12368 (77) Left_Putamen (12): linear fit = 0.96 x + 0.0 (1940 voxels, overlap=0.967) Left_Putamen (12): linear fit = 0.96 x + 0.0 (1940 voxels, peak = 75), gca=75.3 gca peak = 0.17796 (79) mri peak = 0.09690 (77) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2010 voxels, overlap=0.987) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2010 voxels, peak = 76), gca=76.2 gca peak = 0.10999 (80) mri peak = 0.20948 (82) Brain_Stem (16): linear fit = 1.05 x + 0.0 (8924 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.05 x + 0.0 (8924 voxels, peak = 84), gca=84.4 gca peak = 0.13215 (88) mri peak = 0.08776 (88) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1021 voxels, overlap=0.674) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1021 voxels, peak = 94), gca=93.7 gca peak = 0.11941 (89) mri peak = 0.07636 (94) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1168 voxels, overlap=0.751) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1168 voxels, peak = 92), gca=92.1 gca peak = 0.20775 (25) mri peak = 0.11341 ( 9) gca peak = 0.13297 (21) mri peak = 0.08528 ( 5) Fourth_Ventricle (15): linear fit = 0.54 x + 0.0 (141 voxels, overlap=0.439) Fourth_Ventricle (15): linear fit = 0.54 x + 0.0 (141 voxels, peak = 11), gca=11.2 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) 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 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 6.39862 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 0.788345 #GCAMreg# pass 0 level1 5 level2 1 tsec 3072.17 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 0.64671 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 0.648687 #GCAMreg# pass 0 level1 4 level2 1 tsec 2552.54 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 0.534237 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 0.541226 #GCAMreg# pass 0 level1 3 level2 1 tsec 2039.69 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 0.484877 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 0.517792 #GCAMreg# pass 0 level1 2 level2 1 tsec 107.587 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 0.517792 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 0.584645 #GCAMreg# pass 0 level1 1 level2 1 tsec 102.654 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 0.578084 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 0.497361 #GCAMreg# pass 0 level1 0 level2 1 tsec 681.199 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 0.467616 GCAMregister done in 165.047 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 0.462955 #GCAMreg# pass 0 level1 5 level2 1 tsec 193.905 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 0.462226 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 0.461866 #GCAMreg# pass 0 level1 4 level2 1 tsec 318.889 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 0.454975 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 0.452087 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 = 4 after 13 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 13 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 5 after 14 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 5 after 12 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 6 after 16 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 552.807 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 0.435649 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.435973 #GCAMreg# pass 0 level1 2 level2 1 tsec 115.096 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 0.435894 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 0.441057 #GCAMreg# pass 0 level1 1 level2 1 tsec 102.279 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 0.441057 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 0.431615 iter 0, gcam->neg = 1233 after 19 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 155.552 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 0.407684 label assignment complete, 0 changed (0.00%) GCAMregister done in 40.5199 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 0.39465 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 5 level2 1 tsec 124.495 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 0.394649 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 0.394802 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 4 level2 1 tsec 180.053 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 0.394778 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 11 after 10 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.394526 iter 0, gcam->neg = 35 after 12 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 48 after 14 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 28 after 19 iterations, nbhd size=2, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 206.251 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 0.393879 iter 0, gcam->neg = 13 after 19 iterations, nbhd size=2, neg = 0 iter 0, gcam->neg = 14 after 13 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 9 after 11 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 22 after 13 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 24 after 10 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 19 after 4 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 21 after 16 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 12 after 14 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 2 after 1 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 5 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 5 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 = 5 after 13 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 0.390897 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 16 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 30 after 14 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 160.019 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 0.390336 iter 0, gcam->neg = 15 after 2 iterations, nbhd size=0, neg = 0 iter 0, gcam->neg = 54 after 15 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 14 after 12 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 46 after 17 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 111 after 18 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 136 after 17 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 141 after 20 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 194 after 19 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 23 after 13 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 36 after 15 iterations, nbhd size=1, neg = 0 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.39295 #GCAMreg# pass 0 level1 1 level2 1 tsec 109.381 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 0.39295 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 0.383262 iter 0, gcam->neg = 756 after 20 iterations, nbhd size=1, neg = 0 #GCAMreg# pass 0 level1 0 level2 1 tsec 139.917 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 0.377111 GCAMregister done in 43.1612 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4682 tmin = 36.0802 Calls to gcamLabelEnergy 3948 tmin = 2.83003 Calls to gcamJacobianEnergy 4682 tmin = 33.858 Calls to gcamSmoothnessEnergy 4682 tmin = 29.4407 Calls to gcamLogLikelihoodTerm 683 tmin = 10.8762 Calls to gcamLabelTerm 614 tmin = 15.2192 Calls to gcamJacobianTerm 683 tmin = 30.417 Calls to gcamSmoothnessTerm 683 tmin = 7.90745 Calls to gcamComputeGradient 683 tmin = 118.053 Calls to gcamComputeMetricProperties 7000 tmin = 41.3221 mri_ca_register took 4 hours, 57 minutes and 52 seconds. #VMPC# mri_ca_register VmPeak 2153308 FSRUNTIME@ mri_ca_register 4.9643 hours 1 threads @#@FSTIME 2023:05:12:15:51:49 mri_ca_register N 9 e 17871.67 S 2.29 U 17866.14 P 99% M 1356100 F 0 R 301807 W 0 c 8191 w 1118 I 0 O 62928 L 1.00 1.00 0.95 @#@FSLOADPOST 2023:05:12:20:49:41 mri_ca_register N 9 1.00 1.01 1.05 #-------------------------------------- #@# SubCort Seg Fri May 12 20:49:41 EDT 2023 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev//average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname compute-0-37.nmr.mgh.harvard.edu machine x86_64 setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev//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/dev//average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 5.73 Atlas used for the 3D morph was /usr/local/freesurfer/dev//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 = 0.09441 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.09 x + 0.0 (1298 voxels, overlap=0.225) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1298 voxels, peak = 2), gca=8.0 gca peak = 0.20380 (13) mri peak = 0.07692 ( 3) Right_Lateral_Ventricle (43): linear fit = 0.16 x + 0.0 (576 voxels, overlap=0.221) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (576 voxels, peak = 2), gca=5.2 gca peak = 0.26283 (96) mri peak = 0.12970 (93) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (532 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (532 voxels, peak = 92), gca=91.7 gca peak = 0.15814 (97) mri peak = 0.10225 (93) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (489 voxels, overlap=0.816) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (489 voxels, peak = 93), gca=92.6 gca peak = 0.27624 (56) mri peak = 0.10923 (55) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (1101 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (1101 voxels, peak = 54), gca=54.0 gca peak = 0.28723 (59) mri peak = 0.12559 (55) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (1119 voxels, overlap=1.011) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (1119 voxels, peak = 54), gca=54.0 gca peak = 0.07623 (103) mri peak = 0.27655 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (22833 voxels, overlap=0.510) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (22833 voxels, peak = 102), gca=102.5 gca peak = 0.07837 (105) mri peak = 0.22384 (104) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (26421 voxels, overlap=0.479) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (26421 voxels, peak = 103), gca=103.4 gca peak = 0.10165 (58) mri peak = 0.04552 (61) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (28146 voxels, overlap=0.961) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (28146 voxels, peak = 61), gca=60.6 gca peak = 0.11113 (58) mri peak = 0.04583 (61) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (25581 voxels, overlap=0.879) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (25581 voxels, peak = 62), gca=62.4 gca peak = 0.27796 (67) mri peak = 0.12500 (67) Right_Caudate (50): linear fit = 1.07 x + 0.0 (824 voxels, overlap=1.005) Right_Caudate (50): linear fit = 1.07 x + 0.0 (824 voxels, peak = 71), gca=71.4 gca peak = 0.14473 (69) mri peak = 0.11818 (73) Left_Caudate (11): linear fit = 1.00 x + 0.0 (777 voxels, overlap=0.999) Left_Caudate (11): linear fit = 1.00 x + 0.0 (777 voxels, peak = 69), gca=69.0 gca peak = 0.14301 (56) mri peak = 0.10482 (55) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23967 voxels, overlap=0.964) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23967 voxels, peak = 56), gca=56.0 gca peak = 0.14610 (55) mri peak = 0.10294 (54) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23147 voxels, overlap=0.899) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23147 voxels, peak = 53), gca=53.1 gca peak = 0.16309 (85) mri peak = 0.19318 (82) Left_Cerebellum_White_Matter (7): linear fit = 0.95 x + 0.0 (2766 voxels, overlap=0.557) Left_Cerebellum_White_Matter (7): linear fit = 0.95 x + 0.0 (2766 voxels, peak = 81), gca=81.2 gca peak = 0.15172 (84) mri peak = 0.19457 (80) Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (3034 voxels, overlap=0.627) Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (3034 voxels, peak = 79), gca=78.5 gca peak = 0.30461 (58) mri peak = 0.14053 (60) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (491 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (491 voxels, peak = 59), gca=58.9 gca peak = 0.32293 (57) mri peak = 0.14647 (60) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (573 voxels, overlap=1.001) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (573 voxels, peak = 60), gca=59.6 gca peak = 0.11083 (90) mri peak = 0.08897 (84) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (3209 voxels, overlap=0.973) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (3209 voxels, peak = 91), gca=91.3 gca peak = 0.11393 (83) mri peak = 0.10403 (83) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3191 voxels, overlap=0.975) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3191 voxels, peak = 83), gca=82.6 gca peak = 0.08575 (81) mri peak = 0.17191 (77) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1204 voxels, overlap=0.648) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1204 voxels, peak = 76), gca=75.7 gca peak = 0.08618 (78) mri peak = 0.12490 (72) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1241 voxels, overlap=0.892) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1241 voxels, peak = 76), gca=76.1 gca peak = 0.08005 (78) mri peak = 0.20931 (82) Brain_Stem (16): linear fit = 1.03 x + 0.0 (8177 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.03 x + 0.0 (8177 voxels, peak = 81), gca=80.7 gca peak = 0.12854 (88) mri peak = 0.08845 (88) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1022 voxels, overlap=0.791) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1022 voxels, peak = 91), gca=91.1 gca peak = 0.15703 (87) mri peak = 0.07897 (92) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1010 voxels, overlap=0.880) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1010 voxels, peak = 93), gca=92.7 gca peak = 0.17522 (25) mri peak = 0.10066 ( 9) gca peak = 0.17113 (14) mri peak = 0.19504 ( 3) Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (260 voxels, overlap=0.025) Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (260 voxels, peak = 2), gca=1.8 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) 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 1.01 x + 0.0 estimating mean wm scale to be 0.99 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31706 ( 7) mri peak = 0.09441 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1298 voxels, overlap=0.977) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1298 voxels, peak = 2), gca=2.8 gca peak = 0.29334 ( 5) mri peak = 0.07692 ( 3) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (576 voxels, overlap=0.574) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (576 voxels, peak = 2), gca=2.0 gca peak = 0.23983 (90) mri peak = 0.12970 (93) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (532 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (532 voxels, peak = 91), gca=91.3 gca peak = 0.18272 (92) mri peak = 0.10225 (93) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (489 voxels, overlap=1.002) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (489 voxels, peak = 92), gca=92.0 gca peak = 0.28284 (54) mri peak = 0.10923 (55) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1101 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1101 voxels, peak = 54), gca=54.0 gca peak = 0.29612 (54) mri peak = 0.12559 (55) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (1119 voxels, overlap=1.005) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (1119 voxels, peak = 58), gca=57.5 gca peak = 0.08103 (103) mri peak = 0.27655 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (22833 voxels, overlap=0.519) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (22833 voxels, peak = 102), gca=102.5 gca peak = 0.08327 (103) mri peak = 0.22384 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26421 voxels, overlap=0.513) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26421 voxels, peak = 102), gca=102.5 gca peak = 0.09144 (61) mri peak = 0.04552 (61) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28146 voxels, overlap=0.983) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28146 voxels, peak = 63), gca=62.5 gca peak = 0.10666 (63) mri peak = 0.04583 (61) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (25581 voxels, overlap=0.965) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (25581 voxels, peak = 62), gca=62.1 gca peak = 0.23022 (71) mri peak = 0.12500 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (824 voxels, overlap=1.006) Right_Caudate (50): linear fit = 1.00 x + 0.0 (824 voxels, peak = 71), gca=71.0 gca peak = 0.14604 (69) mri peak = 0.11818 (73) Left_Caudate (11): linear fit = 1.00 x + 0.0 (777 voxels, overlap=0.999) Left_Caudate (11): linear fit = 1.00 x + 0.0 (777 voxels, peak = 69), gca=69.0 gca peak = 0.14257 (56) mri peak = 0.10482 (55) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23967 voxels, overlap=0.964) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23967 voxels, peak = 56), gca=56.0 gca peak = 0.14567 (53) mri peak = 0.10294 (54) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (23147 voxels, overlap=0.975) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (23147 voxels, peak = 53), gca=53.0 gca peak = 0.16679 (81) mri peak = 0.19318 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2766 voxels, overlap=0.897) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2766 voxels, peak = 81), gca=81.0 gca peak = 0.18035 (79) mri peak = 0.19457 (80) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3034 voxels, overlap=0.877) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3034 voxels, peak = 79), gca=79.0 gca peak = 0.30271 (59) mri peak = 0.14053 (60) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (491 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (491 voxels, peak = 59), gca=59.0 gca peak = 0.33570 (60) mri peak = 0.14647 (60) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (573 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (573 voxels, peak = 60), gca=60.0 gca peak = 0.10762 (90) mri peak = 0.08897 (84) Left_Thalamus (10): linear fit = 0.99 x + 0.0 (3209 voxels, overlap=0.996) Left_Thalamus (10): linear fit = 0.99 x + 0.0 (3209 voxels, peak = 89), gca=88.7 gca peak = 0.10393 (82) mri peak = 0.10403 (83) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3191 voxels, overlap=0.972) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3191 voxels, peak = 82), gca=81.6 gca peak = 0.08477 (74) mri peak = 0.17191 (77) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1204 voxels, overlap=0.898) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1204 voxels, peak = 74), gca=74.0 gca peak = 0.08745 (74) mri peak = 0.12490 (72) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1241 voxels, overlap=0.992) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1241 voxels, peak = 72), gca=72.2 gca peak = 0.08455 (81) mri peak = 0.20931 (82) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8177 voxels, overlap=0.576) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8177 voxels, peak = 81), gca=80.6 gca peak = 0.12038 (91) mri peak = 0.08845 (88) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1022 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1022 voxels, peak = 91), gca=90.5 gca peak = 0.14695 (91) mri peak = 0.07897 (92) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1010 voxels, overlap=0.955) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1010 voxels, peak = 91), gca=90.5 gca peak = 0.32031 (10) mri peak = 0.10066 ( 9) gca peak = 0.46125 ( 6) mri peak = 0.19504 ( 3) Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (260 voxels, overlap=0.868) Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (260 voxels, peak = 2), gca=2.1 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.17428 (26) gca peak Third_Ventricle = 0.32031 (10) gca peak Fourth_Ventricle = 0.46125 ( 6) gca peak CSF = 0.27810 (15) gca peak Left_Accumbens_area = 0.65865 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89919 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.24411 (22) gca peak Right_Accumbens_area = 0.29225 (69) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.92085 (13) gca peak WM_hypointensities = 0.10305 (76) gca peak non_WM_hypointensities = 0.13982 (40) gca peak Optic_Chiasm = 0.51840 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.40 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 29267 voxels changed in iteration 0 of unlikely voxel relabeling 153 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 22931 gm and wm labels changed (%34 to gray, %66 to white out of all changed labels) 337 hippocampal voxels changed. 1 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 53499 changed. image ll: -2.063, PF=0.500 pass 2: 12927 changed. image ll: -2.063, PF=0.500 pass 3: 4539 changed. 23845 voxels changed in iteration 0 of unlikely voxel relabeling 131 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5806 voxels changed in iteration 0 of unlikely voxel relabeling 62 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5485 voxels changed in iteration 0 of unlikely voxel relabeling 31 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5091 voxels changed in iteration 0 of unlikely voxel relabeling 9 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 !!!!!!!!! ventricle segment 0 with volume 7549 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 181 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 255 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 5334 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 118 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 373 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3126.870191 mri_ca_label stimesec 2.313972 mri_ca_label ru_maxrss 2125620 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 386273 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 192 mri_ca_label ru_oublock 640 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 179 mri_ca_label ru_nivcsw 1052 mri_ca_label took 52 minutes and 10 seconds. mri_ca_label done @#@FSTIME 2023:05:12:20:49:41 mri_ca_label N 10 e 3129.56 S 2.33 U 3126.87 P 99% M 2125620 F 0 R 386280 W 0 c 1053 w 180 I 192 O 648 L 1.00 1.01 1.05 @#@FSLOADPOST 2023:05:12:21:41:51 mri_ca_label N 10 1.00 1.01 1.05 #-------------------------------------- #@# CC Seg Fri May 12 21:41:51 EDT 2023 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/transforms/cc_up.lta CR_t2_tra_12_SR will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/transforms/cc_up.lta reading aseg from /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/norm.mgz 83830 voxels in left wm, 74485 in right wm, xrange [118, 137] searching rotation angles z=[ 3 17], y=[-7 7] searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.7 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.7 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.2 searching scale 1 Z rot 11.4 searching scale 1 Z rot 11.7 searching scale 1 Z rot 11.9 searching scale 1 Z rot 12.2 searching scale 1 Z rot 12.4 searching scale 1 Z rot 12.7 searching scale 1 Z rot 12.9 searching scale 1 Z rot 13.2 searching scale 1 Z rot 13.4 searching scale 1 Z rot 13.7 searching scale 1 Z rot 13.9 searching scale 1 Z rot 14.2 searching scale 1 Z rot 14.4 searching scale 1 Z rot 14.7 searching scale 1 Z rot 14.9 searching scale 1 Z rot 15.2 searching scale 1 Z rot 15.4 searching scale 1 Z rot 15.7 searching scale 1 Z rot 15.9 searching scale 1 Z rot 16.2 global minimum found at slice 126.0, rotations (-0.42, 9.43) final transformation (x=126.0, yr=-0.422, zr=9.427): 0.98647 -0.16379 -0.00727 21.88849; 0.16379 0.98649 -0.00121 2.93061; 0.00737 0.00000 0.99997 14.07459; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 129] in xformed coordinates best xformed slice 127 min_x_fornix = 145 min_x_fornix = 145 min_x_fornix = 146 min_x_fornix = 148 min_x_fornix = 143 cc center is found at 127 106 113 eigenvectors: -0.00210 0.00556 0.99998; -0.15238 -0.98831 0.00517; 0.98832 -0.15237 0.00292; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/aseg.auto.mgz... corpus callosum segmentation took 2.2 minutes #VMPC# mri_cc VmPeak 557828 mri_cc done @#@FSTIME 2023:05:12:21:41:51 mri_cc N 7 e 132.90 S 0.24 U 132.52 P 99% M 340232 F 0 R 15630 W 0 c 43 w 65 I 0 O 632 L 1.00 1.01 1.05 @#@FSLOADPOST 2023:05:12:21:44:04 mri_cc N 7 1.00 1.01 1.05 #-------------------------------------- #@# Merge ASeg Fri May 12 21:44:04 EDT 2023 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri May 12 21:44:04 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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... 511 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 61 (61), valley at 39 (39) csf peak at 31, setting threshold to 51 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 65 (65), valley at 39 (39) csf peak at 33, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 7 minutes and 43 seconds. @#@FSTIME 2023:05:12:21:44:04 mri_normalize N 9 e 472.08 S 1.14 U 470.74 P 99% M 1232508 F 0 R 220116 W 0 c 217 w 113 I 0 O 2184 L 1.00 1.01 1.05 @#@FSLOADPOST 2023:05:12:21:51:56 mri_normalize N 9 1.00 1.01 1.05 #-------------------------------------------- #@# Mask BFS Fri May 12 21:51:56 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1334863 voxels in mask (pct= 7.96) maskval=0, outval=0 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2023:05:12:21:51:56 mri_mask N 5 e 3.15 S 0.02 U 2.97 P 94% M 70576 F 0 R 3448 W 0 c 5 w 88 I 0 O 2168 L 1.00 1.01 1.05 @#@FSLOADPOST 2023:05:12:21:51:59 mri_mask N 5 1.00 1.01 1.05 cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #-------------------------------------------- #@# WM Segmentation Fri May 12 21:52:00 EDT 2023 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2023:05:12:21:52:00 AntsDenoiseImageFs N 4 e 61.80 S 0.11 U 61.17 P 99% M 347436 F 1 R 4279 W 0 c 31 w 70 I 8432 O 2232 L 1.00 1.01 1.05 @#@FSLOADPOST 2023:05:12:21:53:01 AntsDenoiseImageFs N 4 1.06 1.04 1.05 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 = 294847, nonwhite = 16255543, ambig = 226826, nmask = 0 Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (104.0): 104.0 +- 5.8 [79.0 --> 125.0] CCS GM (71.0) : 69.5 +- 10.3 [30.0 --> 95.0] white_mean 103.964 white_sigma 5.82245 gray_mean 69.4738 gray_sigma 10.319 setting bottom of white matter range wm_low to 79.8 setting top of gray matter range gray_hi to 90.1 wm_low 79.7928 wm_hi 125 gray_low 30 gray_hi 90.1118 Redoing initial intensity segmentation... MRIintensitySegmentation() wm_low=79.7928, wm_hi=125, gray_hi=90.1118 white = 385330, nonwhite = 16268977, ambig = 122909, nmask = 0 Recomputing local statistics to label ambiguous voxels... wm_low 79.7928 wm_hi 125 gray_low 30 gray_hi 90.1118 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 90.1118, wm_low = 79.7928 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=90.1118, wmlow=79.7928 117728 voxels processed (0.70%) 52727 voxels white (0.31%) 65001 voxels non-white (0.39%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=74.7928, gray_hi=90.1118, wsize=13 195642 voxels tested (1.17%) 34930 voxels changed (0.21%) 43019 multi-scale searches (0.26%) Recovering bright white MRIrecoverBrightWhite() wm_low 79.7928 wm_hi 125 slack 5.82245 pct_thresh 0.33 intensity_thresh 130.822 nvox_thresh 8.58 681 voxels tested (0.00%) 561 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=74.7928, hithr=90.1118 smoothing input volume with sigma = 0.250 69430 voxels tested (0.41%) 15214 voxels changed (0.09%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 866 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 999 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 2057 filled MRIfindBrightNonWM(): 2414 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... @#@FSTIME 2023:05:12:21:53:02 mri_segment N 5 e 102.51 S 0.19 U 102.22 P 99% M 148204 F 0 R 41057 W 0 c 35 w 49 I 0 O 728 L 1.06 1.04 1.05 @#@FSLOADPOST 2023:05:12:21:54:44 mri_segment N 5 1.00 1.01 1.04 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 0.89 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2875 additional wm voxels added 0 additional wm voxels added SEG EDIT: 41530 voxels turned on, 24811 voxels turned off. propagating editing to output volume from wm.seg.mgz writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2023:05:12:21:54:44 mri_edit_wm_with_aseg N 5 e 53.50 S 0.19 U 53.17 P 99% M 458548 F 0 R 21274 W 0 c 20 w 63 I 0 O 672 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:21:55:38 mri_edit_wm_with_aseg N 5 1.00 1.01 1.04 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 43 found - 43 modified | TOTAL: 43 pass 2 (xy+): 0 found - 43 modified | TOTAL: 43 pass 1 (xy-): 20 found - 20 modified | TOTAL: 63 pass 2 (xy-): 0 found - 20 modified | TOTAL: 63 pass 1 (yz+): 24 found - 24 modified | TOTAL: 87 pass 2 (yz+): 0 found - 24 modified | TOTAL: 87 pass 1 (yz-): 26 found - 26 modified | TOTAL: 113 pass 2 (yz-): 0 found - 26 modified | TOTAL: 113 pass 1 (xz+): 21 found - 21 modified | TOTAL: 134 pass 2 (xz+): 0 found - 21 modified | TOTAL: 134 pass 1 (xz-): 23 found - 23 modified | TOTAL: 157 pass 2 (xz-): 0 found - 23 modified | TOTAL: 157 Iteration Number : 1 pass 1 (+++): 5 found - 5 modified | TOTAL: 5 pass 2 (+++): 0 found - 5 modified | TOTAL: 5 pass 1 (+++): 13 found - 13 modified | TOTAL: 18 pass 2 (+++): 0 found - 13 modified | TOTAL: 18 pass 1 (+++): 9 found - 9 modified | TOTAL: 27 pass 2 (+++): 0 found - 9 modified | TOTAL: 27 pass 1 (+++): 9 found - 9 modified | TOTAL: 36 pass 2 (+++): 0 found - 9 modified | TOTAL: 36 Iteration Number : 1 pass 1 (++): 11 found - 11 modified | TOTAL: 11 pass 2 (++): 0 found - 11 modified | TOTAL: 11 pass 1 (+-): 14 found - 14 modified | TOTAL: 25 pass 2 (+-): 0 found - 14 modified | TOTAL: 25 pass 1 (--): 34 found - 34 modified | TOTAL: 59 pass 2 (--): 0 found - 34 modified | TOTAL: 59 pass 1 (-+): 22 found - 22 modified | TOTAL: 81 pass 2 (-+): 0 found - 22 modified | TOTAL: 81 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 3 found - 3 modified | TOTAL: 5 pass 2 (xy-): 0 found - 3 modified | TOTAL: 5 pass 1 (yz+): 5 found - 5 modified | TOTAL: 10 pass 2 (yz+): 0 found - 5 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 1 found - 1 modified | TOTAL: 13 pass 2 (xz+): 0 found - 1 modified | TOTAL: 13 pass 1 (xz-): 0 found - 0 modified | TOTAL: 13 Iteration Number : 2 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 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 1 found - 1 modified | TOTAL: 3 pass 2 (+-): 0 found - 1 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 293 (out of 446938: 0.065557) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:05:12:21:55:38 mri_pretess N 4 e 6.70 S 0.02 U 6.26 P 93% M 53296 F 1 R 2787 W 0 c 8 w 50 I 7296 O 672 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:21:55:44 mri_pretess N 4 1.00 1.01 1.04 #-------------------------------------------- #@# Fill Fri May 12 21:55:44 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/dev//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 1.13813 -0.18066 0.00227 1.98841; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 0.00000 0.00000 0.00000 1.00000; reading input volume... wm.mgzvoxel to talairach voxel transform 1.13813 -0.18066 0.00227 1.98841; 0.18235 1.13471 0.20975 -68.11435; -0.04147 -0.15805 1.02500 8.14426; 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] = 126 (min = 350, max = 1400), aspect = 0.88 (min = 0.10, max = 0.75) need search nearby using seed (125, 116, 92), TAL = (3.0, -36.0, 12.0) talairach voxel to voxel transform 0.85638 0.13231 -0.02897 7.54543; -0.14003 0.83522 -0.17061 58.55858; 0.01305 0.13414 0.94813 1.38890; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 116, 92) --> (3.0, -36.0, 12.0) done. filling took 2.0 minutes talairach cc position changed to (3.00, -36.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -36.00, 12.00) SRC: (111.86, 124.77, 105.57) search lh wm seed point around talairach space (-15.00, -36.00, 12.00), SRC: (142.69, 119.72, 106.04) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... Embedding colortable mri_fill done, writing output to filled.mgz... @#@FSTIME 2023:05:12:21:55:45 mri_fill N 10 e 123.98 S 1.15 U 122.71 P 99% M 982664 F 0 R 299858 W 0 c 130 w 51 I 8 O 232 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:21:57:49 mri_fill N 10 0.96 1.00 1.04 cp filled.mgz filled.auto.mgz #-------------------------------------------- #@# Tessellate lh Fri May 12 21:57:49 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 2 found - 2 modified | TOTAL: 8 pass 2 (xz+): 0 found - 2 modified | TOTAL: 8 pass 1 (xz-): 0 found - 0 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 4 found - 4 modified | TOTAL: 4 pass 2 (+-): 0 found - 4 modified | TOTAL: 4 pass 1 (--): 0 found - 0 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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 = 12 (out of 218338: 0.005496) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:05:12:21:57:49 mri_pretess N 4 e 3.68 S 0.01 U 3.58 P 97% M 36884 F 0 R 2210 W 0 c 6 w 38 I 0 O 224 L 0.96 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:57:52 mri_pretess N 4 0.96 1.00 1.04 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix dev dev slice 50: 459 vertices, 533 faces slice 60: 5292 vertices, 5522 faces slice 70: 11993 vertices, 12239 faces slice 80: 20023 vertices, 20340 faces slice 90: 29759 vertices, 30104 faces slice 100: 39572 vertices, 39907 faces slice 110: 49550 vertices, 49916 faces slice 120: 58925 vertices, 59268 faces slice 130: 68304 vertices, 68657 faces slice 140: 77668 vertices, 78027 faces slice 150: 86331 vertices, 86637 faces slice 160: 93255 vertices, 93487 faces slice 170: 98928 vertices, 99128 faces slice 180: 103714 vertices, 103887 faces slice 190: 107356 vertices, 107473 faces slice 200: 108810 vertices, 108832 faces slice 210: 108810 vertices, 108832 faces slice 220: 108810 vertices, 108832 faces slice 230: 108810 vertices, 108832 faces slice 240: 108810 vertices, 108832 faces slice 250: 108810 vertices, 108832 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2023:05:12:21:57:52 mri_tessellate N 3 e 3.84 S 0.01 U 3.56 P 93% M 38884 F 0 R 1724 W 0 c 5 w 151 I 0 O 5104 L 0.96 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:57:56 mri_tessellate N 3 0.96 1.00 1.04 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 108810 voxel in cpt #1: X=-22 [v=108810,e=326496,f=217664] located at (-24.404007, -12.224896, 15.529464) For the whole surface: X=-22 [v=108810,e=326496,f=217664] One single component has been found nothing to do done @#@FSTIME 2023:05:12:21:57:56 mris_extract_main_component N 2 e 2.22 S 0.13 U 1.38 P 68% M 216088 F 1 R 27130 W 0 c 3 w 158 I 7784 O 7656 L 0.96 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:57:59 mris_extract_main_component N 2 0.97 1.00 1.04 #-------------------------------------------- #@# Tessellate rh Fri May 12 21:57:59 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 7 (out of 213719: 0.003275) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2023:05:12:21:57:59 mri_pretess N 4 e 4.16 S 0.01 U 4.08 P 98% M 36880 F 0 R 2210 W 0 c 7 w 30 I 0 O 224 L 0.97 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:58:03 mri_pretess N 4 0.97 1.00 1.04 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix dev dev slice 50: 109 vertices, 135 faces slice 60: 3039 vertices, 3194 faces slice 70: 9410 vertices, 9638 faces slice 80: 17360 vertices, 17659 faces slice 90: 25841 vertices, 26199 faces slice 100: 35590 vertices, 35910 faces slice 110: 45544 vertices, 45899 faces slice 120: 55423 vertices, 55768 faces slice 130: 65053 vertices, 65410 faces slice 140: 74866 vertices, 75228 faces slice 150: 83661 vertices, 84001 faces slice 160: 91813 vertices, 92122 faces slice 170: 98400 vertices, 98636 faces slice 180: 103713 vertices, 103913 faces slice 190: 107697 vertices, 107845 faces slice 200: 109674 vertices, 109719 faces slice 210: 109708 vertices, 109736 faces slice 220: 109708 vertices, 109736 faces slice 230: 109708 vertices, 109736 faces slice 240: 109708 vertices, 109736 faces slice 250: 109708 vertices, 109736 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2023:05:12:21:58:03 mri_tessellate N 3 e 3.58 S 0.01 U 3.30 P 92% M 40096 F 0 R 2779 W 0 c 4 w 105 I 0 O 5152 L 0.97 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:58:07 mri_tessellate N 3 0.97 1.00 1.04 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 109708 voxel in cpt #1: X=-28 [v=109708,e=329208,f=219472] located at (24.967278, -8.539541, 8.422558) For the whole surface: X=-28 [v=109708,e=329208,f=219472] One single component has been found nothing to do done @#@FSTIME 2023:05:12:21:58:07 mris_extract_main_component N 2 e 1.96 S 0.12 U 1.47 P 81% M 218012 F 0 R 26649 W 0 c 5 w 143 I 0 O 7720 L 0.97 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:58:09 mris_extract_main_component N 2 0.97 1.00 1.04 #-------------------------------------------- #@# Smooth1 lh Fri May 12 21:58:09 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2023:05:12:21:58:09 mris_smooth N 5 e 4.99 S 0.12 U 4.49 P 92% M 171680 F 0 R 36060 W 0 c 5 w 229 I 0 O 7656 L 0.97 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:58:14 mris_smooth N 5 0.97 1.00 1.04 #-------------------------------------------- #@# Smooth1 rh Fri May 12 21:58:14 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2023:05:12:21:58:14 mris_smooth N 5 e 5.04 S 0.12 U 4.55 P 92% M 173260 F 0 R 37594 W 0 c 9 w 151 I 0 O 7728 L 0.97 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:58:19 mris_smooth N 5 0.98 1.00 1.04 #-------------------------------------------- #@# Inflation1 lh Fri May 12 21:58:19 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 43.7 mm, total surface area = 60568 mm^2 step 000: RMS=0.141 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.038 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.034 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes inflation complete. Not saving sulc mris_inflate utimesec 35.463587 mris_inflate stimesec 1.292948 mris_inflate ru_maxrss 172184 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 404097 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8680 mris_inflate ru_oublock 7656 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 162 mris_inflate ru_nivcsw 70 @#@FSTIME 2023:05:12:21:58:19 mris_inflate N 3 e 37.53 S 1.30 U 35.46 P 97% M 172184 F 1 R 404106 W 0 c 70 w 163 I 8680 O 7664 L 0.98 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:58:56 mris_inflate N 3 0.99 1.00 1.04 #-------------------------------------------- #@# Inflation1 rh Fri May 12 21:58:56 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 43.3 mm, total surface area = 60184 mm^2 step 000: RMS=0.144 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.033 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes inflation complete. Not saving sulc mris_inflate utimesec 35.768491 mris_inflate stimesec 1.355980 mris_inflate ru_maxrss 173776 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 440086 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7720 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 180 mris_inflate ru_nivcsw 11 @#@FSTIME 2023:05:12:21:58:57 mris_inflate N 3 e 37.51 S 1.36 U 35.76 P 98% M 173776 F 0 R 440095 W 0 c 11 w 181 I 0 O 7728 L 0.99 1.00 1.04 @#@FSLOADPOST 2023:05:12:21:59:34 mris_inflate N 3 0.99 1.00 1.04 #-------------------------------------------- #@# QSphere lh Fri May 12 21:59:34 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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: dev available threads: 1 scaling brain by 0.342... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.11 +- 0.62 (0.00-->7.52) (max @ vno 42151 --> 43115) face area 0.03 +- 0.04 (-0.11-->0.84) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.335, avgs=0 005/300: dt: 0.9000, rms radial error=176.078, avgs=0 010/300: dt: 0.9000, rms radial error=175.527, avgs=0 015/300: dt: 0.9000, rms radial error=174.802, avgs=0 020/300: dt: 0.9000, rms radial error=173.975, avgs=0 025/300: dt: 0.9000, rms radial error=173.090, avgs=0 030/300: dt: 0.9000, rms radial error=172.173, avgs=0 035/300: dt: 0.9000, rms radial error=171.240, avgs=0 040/300: dt: 0.9000, rms radial error=170.298, avgs=0 045/300: dt: 0.9000, rms radial error=169.354, avgs=0 050/300: dt: 0.9000, rms radial error=168.410, avgs=0 055/300: dt: 0.9000, rms radial error=167.467, avgs=0 060/300: dt: 0.9000, rms radial error=166.528, avgs=0 065/300: dt: 0.9000, rms radial error=165.594, avgs=0 070/300: dt: 0.9000, rms radial error=164.665, avgs=0 075/300: dt: 0.9000, rms radial error=163.740, avgs=0 080/300: dt: 0.9000, rms radial error=162.820, avgs=0 085/300: dt: 0.9000, rms radial error=161.904, avgs=0 090/300: dt: 0.9000, rms radial error=160.994, avgs=0 095/300: dt: 0.9000, rms radial error=160.089, avgs=0 100/300: dt: 0.9000, rms radial error=159.189, avgs=0 105/300: dt: 0.9000, rms radial error=158.294, avgs=0 110/300: dt: 0.9000, rms radial error=157.404, avgs=0 115/300: dt: 0.9000, rms radial error=156.518, avgs=0 120/300: dt: 0.9000, rms radial error=155.638, avgs=0 125/300: dt: 0.9000, rms radial error=154.762, avgs=0 130/300: dt: 0.9000, rms radial error=153.891, avgs=0 135/300: dt: 0.9000, rms radial error=153.024, avgs=0 140/300: dt: 0.9000, rms radial error=152.163, avgs=0 145/300: dt: 0.9000, rms radial error=151.306, avgs=0 150/300: dt: 0.9000, rms radial error=150.454, avgs=0 155/300: dt: 0.9000, rms radial error=149.606, avgs=0 160/300: dt: 0.9000, rms radial error=148.764, avgs=0 165/300: dt: 0.9000, rms radial error=147.927, avgs=0 170/300: dt: 0.9000, rms radial error=147.094, avgs=0 175/300: dt: 0.9000, rms radial error=146.266, avgs=0 180/300: dt: 0.9000, rms radial error=145.442, avgs=0 185/300: dt: 0.9000, rms radial error=144.624, avgs=0 190/300: dt: 0.9000, rms radial error=143.810, avgs=0 195/300: dt: 0.9000, rms radial error=143.000, avgs=0 200/300: dt: 0.9000, rms radial error=142.195, avgs=0 205/300: dt: 0.9000, rms radial error=141.394, avgs=0 210/300: dt: 0.9000, rms radial error=140.598, avgs=0 215/300: dt: 0.9000, rms radial error=139.806, avgs=0 220/300: dt: 0.9000, rms radial error=139.019, avgs=0 225/300: dt: 0.9000, rms radial error=138.236, avgs=0 230/300: dt: 0.9000, rms radial error=137.457, avgs=0 235/300: dt: 0.9000, rms radial error=136.683, avgs=0 240/300: dt: 0.9000, rms radial error=135.913, avgs=0 245/300: dt: 0.9000, rms radial error=135.147, avgs=0 250/300: dt: 0.9000, rms radial error=134.386, avgs=0 255/300: dt: 0.9000, rms radial error=133.629, avgs=0 260/300: dt: 0.9000, rms radial error=132.876, avgs=0 265/300: dt: 0.9000, rms radial error=132.127, avgs=0 270/300: dt: 0.9000, rms radial error=131.382, avgs=0 275/300: dt: 0.9000, rms radial error=130.642, avgs=0 280/300: dt: 0.9000, rms radial error=129.905, avgs=0 285/300: dt: 0.9000, rms radial error=129.173, avgs=0 290/300: dt: 0.9000, rms radial error=128.445, avgs=0 295/300: dt: 0.9000, rms radial error=127.721, avgs=0 300/300: dt: 0.9000, rms radial error=127.001, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12174.09 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00061 epoch 2 (K=40.0), pass 1, starting sse = 1772.92 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/13 = 0.00140 epoch 3 (K=160.0), pass 1, starting sse = 134.03 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.22/17 = 0.01289 epoch 4 (K=640.0), pass 1, starting sse = 4.87 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/21 = 0.00622 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0827 hours FSRUNTIME@ mris_sphere 0.0827 hours 1 threads #VMPC# mris_sphere VmPeak 568312 mris_sphere done @#@FSTIME 2023:05:12:21:59:34 mris_sphere N 9 e 297.79 S 14.41 U 282.99 P 99% M 178280 F 0 R 4889272 W 0 c 219 w 195 I 0 O 7664 L 0.99 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:04:32 mris_sphere N 9 1.00 1.00 1.04 #-------------------------------------------- #@# QSphere rh Fri May 12 22:04:32 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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: dev available threads: 1 scaling brain by 0.346... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.10 +- 0.63 (0.00-->6.80) (max @ vno 53038 --> 53964) face area 0.03 +- 0.04 (-0.23-->0.91) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.251, avgs=0 005/300: dt: 0.9000, rms radial error=175.993, avgs=0 010/300: dt: 0.9000, rms radial error=175.440, avgs=0 015/300: dt: 0.9000, rms radial error=174.716, avgs=0 020/300: dt: 0.9000, rms radial error=173.892, avgs=0 025/300: dt: 0.9000, rms radial error=173.012, avgs=0 030/300: dt: 0.9000, rms radial error=172.102, avgs=0 035/300: dt: 0.9000, rms radial error=171.175, avgs=0 040/300: dt: 0.9000, rms radial error=170.240, avgs=0 045/300: dt: 0.9000, rms radial error=169.302, avgs=0 050/300: dt: 0.9000, rms radial error=168.365, avgs=0 055/300: dt: 0.9000, rms radial error=167.430, avgs=0 060/300: dt: 0.9000, rms radial error=166.498, avgs=0 065/300: dt: 0.9000, rms radial error=165.570, avgs=0 070/300: dt: 0.9000, rms radial error=164.647, avgs=0 075/300: dt: 0.9000, rms radial error=163.728, avgs=0 080/300: dt: 0.9000, rms radial error=162.813, avgs=0 085/300: dt: 0.9000, rms radial error=161.903, avgs=0 090/300: dt: 0.9000, rms radial error=160.997, avgs=0 095/300: dt: 0.9000, rms radial error=160.096, avgs=0 100/300: dt: 0.9000, rms radial error=159.200, avgs=0 105/300: dt: 0.9000, rms radial error=158.308, avgs=0 110/300: dt: 0.9000, rms radial error=157.421, avgs=0 115/300: dt: 0.9000, rms radial error=156.539, avgs=0 120/300: dt: 0.9000, rms radial error=155.661, avgs=0 125/300: dt: 0.9000, rms radial error=154.788, avgs=0 130/300: dt: 0.9000, rms radial error=153.919, avgs=0 135/300: dt: 0.9000, rms radial error=153.055, avgs=0 140/300: dt: 0.9000, rms radial error=152.196, avgs=0 145/300: dt: 0.9000, rms radial error=151.341, avgs=0 150/300: dt: 0.9000, rms radial error=150.491, avgs=0 155/300: dt: 0.9000, rms radial error=149.645, avgs=0 160/300: dt: 0.9000, rms radial error=148.804, avgs=0 165/300: dt: 0.9000, rms radial error=147.968, avgs=0 170/300: dt: 0.9000, rms radial error=147.136, avgs=0 175/300: dt: 0.9000, rms radial error=146.308, avgs=0 180/300: dt: 0.9000, rms radial error=145.485, avgs=0 185/300: dt: 0.9000, rms radial error=144.666, avgs=0 190/300: dt: 0.9000, rms radial error=143.852, avgs=0 195/300: dt: 0.9000, rms radial error=143.042, avgs=0 200/300: dt: 0.9000, rms radial error=142.237, avgs=0 205/300: dt: 0.9000, rms radial error=141.436, avgs=0 210/300: dt: 0.9000, rms radial error=140.640, avgs=0 215/300: dt: 0.9000, rms radial error=139.848, avgs=0 220/300: dt: 0.9000, rms radial error=139.061, avgs=0 225/300: dt: 0.9000, rms radial error=138.278, avgs=0 230/300: dt: 0.9000, rms radial error=137.499, avgs=0 235/300: dt: 0.9000, rms radial error=136.725, avgs=0 240/300: dt: 0.9000, rms radial error=135.955, avgs=0 245/300: dt: 0.9000, rms radial error=135.189, avgs=0 250/300: dt: 0.9000, rms radial error=134.427, avgs=0 255/300: dt: 0.9000, rms radial error=133.670, avgs=0 260/300: dt: 0.9000, rms radial error=132.916, avgs=0 265/300: dt: 0.9000, rms radial error=132.167, avgs=0 270/300: dt: 0.9000, rms radial error=131.422, avgs=0 275/300: dt: 0.9000, rms radial error=130.682, avgs=0 280/300: dt: 0.9000, rms radial error=129.945, avgs=0 285/300: dt: 0.9000, rms radial error=129.213, avgs=0 290/300: dt: 0.9000, rms radial error=128.484, avgs=0 295/300: dt: 0.9000, rms radial error=127.760, avgs=0 300/300: dt: 0.9000, rms radial error=127.040, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12270.79 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00041 epoch 2 (K=40.0), pass 1, starting sse = 1826.07 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00107 epoch 3 (K=160.0), pass 1, starting sse = 143.79 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/16 = 0.01126 epoch 4 (K=640.0), pass 1, starting sse = 7.33 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/19 = 0.00688 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0804 hours FSRUNTIME@ mris_sphere 0.0804 hours 1 threads #VMPC# mris_sphere VmPeak 569988 mris_sphere done @#@FSTIME 2023:05:12:22:04:32 mris_sphere N 9 e 289.32 S 14.06 U 274.82 P 99% M 180108 F 0 R 5003548 W 0 c 134 w 203 I 0 O 7728 L 1.00 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:09:21 mris_sphere N 9 1.00 1.00 1.04 #@# Fix Topology lh Fri May 12 22:09:21 EDT 2023 mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 CR_t2_tra_12_SR lh Setting OMP_NUM_THREADS=1 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' dev dev before topology correction, eno=-22 (nv=108810, nf=217664, ne=326496, g=12) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 2121 ambiguous faces found in tessellation segmenting defects... 14 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 14 defects to be corrected 0 vertices coincident reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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: -9.4503 (-4.7251) -vertex loglikelihood: -6.5687 (-3.2844) -normal dot loglikelihood: -3.6442 (-3.6442) -quad curv loglikelihood: -6.0137 (-3.0069) Total Loglikelihood : -25.6769 CORRECTING DEFECT 0 (vertices=86, convex hull=128, v0=1941) After retessellation of defect 0 (v0=1941), euler #=-11 (107485,321818,214322) : difference with theory (-11) = 0 CORRECTING DEFECT 1 (vertices=186, convex hull=199, v0=3696) After retessellation of defect 1 (v0=3696), euler #=-10 (107544,322087,214533) : difference with theory (-10) = 0 CORRECTING DEFECT 2 (vertices=32, convex hull=73, v0=4533) After retessellation of defect 2 (v0=4533), euler #=-9 (107558,322159,214592) : difference with theory (-9) = 0 CORRECTING DEFECT 3 (vertices=72, convex hull=83, v0=5448) After retessellation of defect 3 (v0=5448), euler #=-8 (107586,322279,214685) : difference with theory (-8) = 0 CORRECTING DEFECT 4 (vertices=159, convex hull=178, v0=6287) After retessellation of defect 4 (v0=6287), euler #=-7 (107671,322622,214944) : difference with theory (-7) = 0 CORRECTING DEFECT 5 (vertices=175, convex hull=115, v0=7034) After retessellation of defect 5 (v0=7034), euler #=-6 (107717,322811,215088) : difference with theory (-6) = 0 CORRECTING DEFECT 6 (vertices=86, convex hull=133, v0=15185) After retessellation of defect 6 (v0=15185), euler #=-5 (107768,323020,215247) : difference with theory (-5) = 0 CORRECTING DEFECT 7 (vertices=103, convex hull=142, v0=16564) After retessellation of defect 7 (v0=16564), euler #=-4 (107817,323232,215411) : difference with theory (-4) = 0 CORRECTING DEFECT 8 (vertices=122, convex hull=146, v0=36359) normal vector of length zero at vertex 108368 with 5 faces normal vector of length zero at vertex 108368 with 3 faces normal vector of length zero at vertex 108417 with 3 faces After retessellation of defect 8 (v0=36359), euler #=-3 (107896,323541,215642) : difference with theory (-3) = 0 CORRECTING DEFECT 9 (vertices=46, convex hull=79, v0=47152) After retessellation of defect 9 (v0=47152), euler #=-2 (107906,323601,215693) : difference with theory (-2) = 0 CORRECTING DEFECT 10 (vertices=40, convex hull=55, v0=77338) After retessellation of defect 10 (v0=77338), euler #=-1 (107917,323655,215737) : difference with theory (-1) = 0 CORRECTING DEFECT 11 (vertices=35, convex hull=35, v0=77392) After retessellation of defect 11 (v0=77392), euler #=0 (107925,323689,215764) : difference with theory (0) = 0 CORRECTING DEFECT 12 (vertices=173, convex hull=74, v0=82721) After retessellation of defect 12 (v0=82721), euler #=1 (107950,323804,215855) : difference with theory (1) = 0 CORRECTING DEFECT 13 (vertices=56, convex hull=95, v0=104572) After retessellation of defect 13 (v0=104572), euler #=2 (107973,323913,215942) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.14-->7.56) (max @ vno 102830 --> 105399) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.14-->7.56) (max @ vno 102830 --> 105399) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 33 mutations (31.1%), 73 crossovers (68.9%), 83 vertices were eliminated building final representation... 837 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=107973, nf=215942, ne=323913, g=0) writing corrected surface to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 159 intersecting 001: 5 intersecting terminating search with 0 intersecting topology fixing took 2.3 minutes FSRUNTIME@ mris_fix_topology lh 0.0388 hours 1 threads #VMPC# mris_fix_topology VmPeak 861348 @#@FSTIME 2023:05:12:22:09:22 mris_fix_topology N 16 e 139.73 S 0.57 U 138.55 P 99% M 705648 F 0 R 177334 W 0 c 51 w 293 I 0 O 10176 L 1.00 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:11:41 mris_fix_topology N 16 1.00 1.00 1.04 #@# Fix Topology rh Fri May 12 22:11:41 EDT 2023 mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 CR_t2_tra_12_SR rh Setting OMP_NUM_THREADS=1 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' dev dev before topology correction, eno=-28 (nv=109708, nf=219472, ne=329208, g=15) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 3825 ambiguous faces found in tessellation segmenting defects... 16 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 16 defects to be corrected 0 vertices coincident reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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: -9.4020 (-4.7010) -vertex loglikelihood: -6.5900 (-3.2950) -normal dot loglikelihood: -3.7196 (-3.7196) -quad curv loglikelihood: -6.0558 (-3.0279) Total Loglikelihood : -25.7674 CORRECTING DEFECT 0 (vertices=49, convex hull=91, v0=386) After retessellation of defect 0 (v0=386), euler #=-13 (107500,321803,214290) : difference with theory (-13) = 0 CORRECTING DEFECT 1 (vertices=24, convex hull=68, v0=1785) After retessellation of defect 1 (v0=1785), euler #=-12 (107510,321855,214333) : difference with theory (-12) = 0 CORRECTING DEFECT 2 (vertices=216, convex hull=208, v0=3872) After retessellation of defect 2 (v0=3872), euler #=-11 (107577,322159,214571) : difference with theory (-11) = 0 CORRECTING DEFECT 3 (vertices=72, convex hull=89, v0=7507) After retessellation of defect 3 (v0=7507), euler #=-10 (107611,322296,214675) : difference with theory (-10) = 0 CORRECTING DEFECT 4 (vertices=573, convex hull=240, v0=11983) After retessellation of defect 4 (v0=11983), euler #=-9 (107686,322642,214947) : difference with theory (-9) = 0 CORRECTING DEFECT 5 (vertices=50, convex hull=87, v0=18841) After retessellation of defect 5 (v0=18841), euler #=-8 (107717,322773,215048) : difference with theory (-8) = 0 CORRECTING DEFECT 6 (vertices=61, convex hull=81, v0=27267) After retessellation of defect 6 (v0=27267), euler #=-7 (107734,322857,215116) : difference with theory (-7) = 0 CORRECTING DEFECT 7 (vertices=13, convex hull=37, v0=39369) After retessellation of defect 7 (v0=39369), euler #=-6 (107739,322885,215140) : difference with theory (-6) = 0 CORRECTING DEFECT 8 (vertices=6, convex hull=27, v0=48531) After retessellation of defect 8 (v0=48531), euler #=-5 (107741,322900,215154) : difference with theory (-5) = 0 CORRECTING DEFECT 9 (vertices=38, convex hull=41, v0=49529) After retessellation of defect 9 (v0=49529), euler #=-4 (107756,322961,215201) : difference with theory (-4) = 0 CORRECTING DEFECT 10 (vertices=193, convex hull=227, v0=53484) After retessellation of defect 10 (v0=53484), euler #=-3 (107850,323348,215495) : difference with theory (-3) = 0 CORRECTING DEFECT 11 (vertices=99, convex hull=141, v0=55854) After retessellation of defect 11 (v0=55854), euler #=-2 (107901,323568,215665) : difference with theory (-2) = 0 CORRECTING DEFECT 12 (vertices=83, convex hull=94, v0=63762) After retessellation of defect 12 (v0=63762), euler #=-1 (107943,323737,215793) : difference with theory (-1) = 0 CORRECTING DEFECT 13 (vertices=725, convex hull=100, v0=78895) After retessellation of defect 13 (v0=78895), euler #=0 (107966,323852,215886) : difference with theory (0) = 0 CORRECTING DEFECT 14 (vertices=22, convex hull=39, v0=85881) After retessellation of defect 14 (v0=85881), euler #=1 (107978,323902,215925) : difference with theory (1) = 0 CORRECTING DEFECT 15 (vertices=17, convex hull=62, v0=95360) After retessellation of defect 15 (v0=95360), euler #=2 (107987,323955,215970) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.06-->10.05) (max @ vno 3788 --> 7415) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.06-->10.05) (max @ vno 3788 --> 7415) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 60 mutations (33.7%), 118 crossovers (66.3%), 160 vertices were eliminated building final representation... 1721 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=107987, nf=215970, ne=323955, g=0) writing corrected surface to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 281 intersecting 001: 19 intersecting terminating search with 0 intersecting topology fixing took 3.9 minutes FSRUNTIME@ mris_fix_topology rh 0.0643 hours 1 threads #VMPC# mris_fix_topology VmPeak 862292 @#@FSTIME 2023:05:12:22:11:41 mris_fix_topology N 16 e 231.47 S 0.56 U 230.26 P 99% M 704624 F 0 R 179011 W 0 c 76 w 305 I 0 O 10192 L 1.00 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:15:33 mris_fix_topology N 16 1.00 1.00 1.04 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 107973 - 323913 + 215942 = 2 --> 0 holes F =2V-4: 215942 = 215946-4 (0) 2E=3F: 647826 = 647826 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 107987 - 323955 + 215970 = 2 --> 0 holes F =2V-4: 215970 = 215974-4 (0) 2E=3F: 647910 = 647910 (0) total defect index = 0 Fri May 12 22:15:35 EDT 2023 setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts /usr/local/freesurfer/dev//bin/defect2seg --s CR_t2_tra_12_SR --cortex freesurfer-linux-centos7_x86_64-dev-20230512-47dba46 defect2seg dev Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux pid 27059 mri_label2label --label-cortex /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig.nofix /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/aseg.presurf.mgz 0 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 12 non-cortical segments detected only using segment with 6156 vertices erasing segment 1 (vno[0] = 40354) erasing segment 2 (vno[0] = 73730) erasing segment 3 (vno[0] = 73748) erasing segment 4 (vno[0] = 79324) erasing segment 5 (vno[0] = 80239) erasing segment 6 (vno[0] = 81027) erasing segment 7 (vno[0] = 81105) erasing segment 8 (vno[0] = 82760) erasing segment 9 (vno[0] = 83705) erasing segment 10 (vno[0] = 84601) erasing segment 11 (vno[0] = 86835) mri_label2vol --defects /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig.nofix /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.defect_labels /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz 1000 0 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/surface.defects.mgz /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.nofix.cortex.label Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/surface.defects.mgz mris_defects_pointset -s /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig.nofix -d /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.defect_labels -o /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.defects.pointset --label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.nofix.cortex.label Reading in surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig.nofix Reading in defect segmentation /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.defect_labels Reading in label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.nofix.cortex.label #VMPC# mris_defects_pointset 167864 mris_defects_pointset done mri_label2label --label-cortex /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.orig.nofix /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/aseg.presurf.mgz 0 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.nofix.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 21 non-cortical segments detected only using segment with 6303 vertices erasing segment 0 (vno[0] = 37195) erasing segment 2 (vno[0] = 38185) erasing segment 3 (vno[0] = 39142) erasing segment 4 (vno[0] = 43943) erasing segment 5 (vno[0] = 45005) erasing segment 6 (vno[0] = 49419) erasing segment 7 (vno[0] = 67472) erasing segment 8 (vno[0] = 68560) erasing segment 9 (vno[0] = 78044) erasing segment 10 (vno[0] = 78061) erasing segment 11 (vno[0] = 78896) erasing segment 12 (vno[0] = 78914) erasing segment 13 (vno[0] = 78933) erasing segment 14 (vno[0] = 79793) erasing segment 15 (vno[0] = 80798) erasing segment 16 (vno[0] = 81517) erasing segment 17 (vno[0] = 81800) erasing segment 18 (vno[0] = 82600) erasing segment 19 (vno[0] = 83321) erasing segment 20 (vno[0] = 94376) mri_label2vol --defects /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.orig.nofix /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.defect_labels /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/surface.defects.mgz 2000 1 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/surface.defects.mgz /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.nofix.cortex.label mri_label2vol supposed to be reproducible but seed not set Contraining to label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.nofix.cortex.label Converting defects to volume: offset=2000, merge=1 Writing to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/surface.defects.mgz mris_defects_pointset -s /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.orig.nofix -d /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.defect_labels -o /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.defects.pointset --label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.nofix.cortex.label Reading in surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.orig.nofix Reading in defect segmentation /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.defect_labels Reading in label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.nofix.cortex.label #VMPC# mris_defects_pointset 169080 mris_defects_pointset done Started at Fri May 12 22:15:35 EDT 2023 Ended at Fri May 12 22:16:35 EDT 2023 Defect2seg-Run-Time-Sec 59 Defect2seg-Run-Time-Min 1.18 Defect2seg-Run-Time-Hours 0.02 tkmeditfv CR_t2_tra_12_SR brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2023:05:12:22:15:35 defect2seg N 3 e 59.77 S 0.86 U 57.07 P 96% M 346824 F 1 R 187318 W 0 c 116 w 981 I 7272 O 18224 L 1.00 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:16:35 defect2seg N 3 0.95 0.98 1.03 mris_remesh --remesh --iters 3 --input /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig.premesh --output /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.714277 remeshing to edge length 0.714277 with 3 iterations avg qual before : 0.890661 after: 0.971274 Removing intersections Remeshed surface quality stats nv0 = 107973 nv = 113073 1.04723 Area 226142 0.30540 0.03392 0.084823 0.4763 Corner 678426 60.00000 8.79327 15.579581 148.5243 Edge 339213 0.84779 0.08253 0.411014 1.2223 Hinge 339213 8.78726 8.70997 0.000040 170.9642 mris_remesh done @#@FSTIME 2023:05:12:22:16:35 mris_remesh N 7 e 35.65 S 0.44 U 34.48 P 97% M 613380 F 1 R 116953 W 0 c 26 w 159 I 7536 O 7960 L 0.95 0.98 1.03 @#@FSLOADPOST 2023:05:12:22:17:10 mris_remesh N 7 0.97 0.99 1.03 mris_remesh --remesh --iters 3 --input /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.orig.premesh --output /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.712886 remeshing to edge length 0.712886 with 3 iterations avg qual before : 0.888234 after: 0.971646 Removing intersections Remeshed surface quality stats nv0 = 107987 nv = 112490 1.0417 Area 224976 0.30446 0.03348 0.096721 0.4602 Corner 674928 60.00000 8.73163 19.629963 140.2604 Edge 337464 0.84640 0.08188 0.462137 1.2328 Hinge 337464 8.95178 8.81658 0.000088 147.6386 mris_remesh done @#@FSTIME 2023:05:12:22:17:10 mris_remesh N 7 e 35.13 S 0.44 U 34.28 P 98% M 606444 F 0 R 116341 W 0 c 12 w 192 I 0 O 7920 L 0.97 0.99 1.03 @#@FSLOADPOST 2023:05:12:22:17:45 mris_remesh N 7 1.06 1.00 1.04 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/lh.orig @#@FSTIME 2023:05:12:22:17:46 mris_remove_intersection N 2 e 5.96 S 0.30 U 4.91 P 87% M 292648 F 1 R 89483 W 0 c 6 w 168 I 7912 O 7968 L 1.06 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:17:51 mris_remove_intersection N 2 1.06 1.00 1.04 rm -f ../surf/lh.inflated /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours Found 0 intersections writing corrected surface to ../surf/rh.orig @#@FSTIME 2023:05:12:22:17:52 mris_remove_intersection N 2 e 5.49 S 0.21 U 4.89 P 92% M 283896 F 0 R 61406 W 0 c 4 w 163 I 0 O 7920 L 1.06 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:17:57 mris_remove_intersection N 2 1.05 1.00 1.04 rm -f ../surf/rh.inflated #-------------------------------------------- #@# AutoDetGWStats lh Fri May 12 22:17:57 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh dev cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 210580 voxels (1.26%) border gray 229245 voxels (1.37%) 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=11523, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (98.0): 98.0 +- 8.5 [70.0 --> 110.0] CCS GM (72.0) : 70.6 +- 11.7 [30.0 --> 110.0] white_mean = 97.9654 +/- 8.50438, gray_mean = 70.6173 +/- 11.7184 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=177 nbins=178 intensity peaks found at WM=103+-5.2, GM=61+-16.5 white_mode = 103, gray_mode = 61 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 49.3 (was 70.000000) setting MAX_BORDER_WHITE to 111.5 (was 105.000000) setting MIN_BORDER_WHITE to 61.0 (was 85.000000) setting MAX_CSF to 37.6 (was 40.000000) setting MAX_GRAY to 94.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 25.8 (was 40.000000) When placing the white surface white_border_hi = 111.504; white_border_low = 61; white_outside_low = 49.2816; white_inside_hi = 120; white_outside_hi = 111.504; When placing the pial surface pial_border_hi = 49.2816; pial_border_low = 25.8448; pial_outside_low = 10; pial_inside_hi = 94.4956; pial_outside_hi = 43.4224; #VMPC# mris_autodet_gwstats VmPeak 340920 mris_autodet_gwstats done @#@FSTIME 2023:05:12:22:17:57 mris_autodet_gwstats N 8 e 8.02 S 0.12 U 7.51 P 95% M 200616 F 1 R 30401 W 0 c 13 w 37 I 7064 O 16 L 1.05 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:18:05 mris_autodet_gwstats N 8 1.05 1.00 1.04 #-------------------------------------------- #@# AutoDetGWStats rh Fri May 12 22:18:05 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh dev cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 210580 voxels (1.26%) border gray 229245 voxels (1.37%) 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=11523, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (98.0): 98.0 +- 8.5 [70.0 --> 110.0] CCS GM (72.0) : 70.6 +- 11.7 [30.0 --> 110.0] white_mean = 97.9654 +/- 8.50438, gray_mean = 70.6173 +/- 11.7184 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=177 nbins=178 intensity peaks found at WM=103+-6.1, GM=61+-16.5 white_mode = 103, gray_mode = 61 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 49.3 (was 70.000000) setting MAX_BORDER_WHITE to 111.5 (was 105.000000) setting MIN_BORDER_WHITE to 61.0 (was 85.000000) setting MAX_CSF to 37.6 (was 40.000000) setting MAX_GRAY to 94.5 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 25.8 (was 40.000000) When placing the white surface white_border_hi = 111.504; white_border_low = 61; white_outside_low = 49.2816; white_inside_hi = 120; white_outside_hi = 111.504; When placing the pial surface pial_border_hi = 49.2816; pial_border_low = 25.8448; pial_outside_low = 10; pial_inside_hi = 94.4956; pial_outside_hi = 43.4224; #VMPC# mris_autodet_gwstats VmPeak 341124 mris_autodet_gwstats done @#@FSTIME 2023:05:12:22:18:05 mris_autodet_gwstats N 8 e 7.70 S 0.11 U 7.52 P 99% M 200680 F 0 R 28922 W 0 c 13 w 28 I 0 O 16 L 1.05 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:18:13 mris_autodet_gwstats N 8 1.04 1.00 1.04 #-------------------------------------------- #@# WhitePreAparc lh Fri May 12 22:18:13 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 dev dev cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data 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 226142 0.27520 0.06111 0.000983 0.5609 Corner 678426 60.00000 8.85210 9.744099 137.5656 Edge 339213 0.80060 0.10927 0.045848 1.2730 Hinge 339213 6.06148 5.84201 0.000002 128.1085 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=11523, wmmin=5, clip=110 MRIfindBrightNonWM(): 3692 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=5562, nmarked2=1, nripped=5562 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56537: xyz = (-10.0341,-1.87502,-16.8828) oxyz = (-10.0341,-1.87502,-16.8828) wxzy = (-10.0341,-1.87502,-16.8828) pxyz = (0,0,0) CBVO Creating mask 113073 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=5562 #FML# MRISripMidline(): nmarked=5562, nmarked2=1, nripped=5562 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=2 had to be increased for 38 vertices, nripped=5562 mean border=77.0, 33 (33) missing vertices, mean dist 0.5 [0.5 (%32.1)->0.9 (%67.9))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.4326 min Finding expansion regions mean absolute distance = 0.78 +- 1.00 4784 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=compu, 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=3093777.0, rms=11.750 001: dt: 0.5000, sse=1761222.8, rms=8.727 (25.724%) 002: dt: 0.5000, sse=1132795.1, rms=6.852 (21.486%) 003: dt: 0.5000, sse=792927.0, rms=5.579 (18.586%) 004: dt: 0.5000, sse=599135.2, rms=4.697 (15.798%) 005: dt: 0.5000, sse=491501.8, rms=4.125 (12.189%) 006: dt: 0.5000, sse=428377.9, rms=3.744 (9.236%) 007: dt: 0.5000, sse=395610.2, rms=3.528 (5.765%) 008: dt: 0.5000, sse=375807.3, rms=3.385 (4.056%) 009: dt: 0.5000, sse=366926.2, rms=3.324 (1.813%) rms = 3.2743/3.3235, sse=360810.1/366926.2, time step reduction 1 of 3 to 0.250 0 0 1 010: dt: 0.5000, sse=360810.1, rms=3.274 (1.482%) 011: dt: 0.2500, sse=184893.3, rms=1.555 (52.510%) 012: dt: 0.2500, sse=162978.1, rms=1.108 (28.720%) 013: dt: 0.2500, sse=155624.4, rms=0.956 (13.758%) 014: dt: 0.2500, sse=149934.0, rms=0.888 (7.123%) rms = 0.8630/0.8878, sse=149083.3/149934.0, time step reduction 2 of 3 to 0.125 0 0 1 015: dt: 0.2500, sse=149083.3, rms=0.863 (2.790%) 016: dt: 0.1250, sse=147094.4, rms=0.810 (6.179%) rms = 0.8049/0.8097, sse=147057.9/147094.4, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=147057.9, rms=0.805 (0.588%) maximum number of reductions reached, breaking from loop positioning took 2.3 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=5562 #FML# MRISripMidline(): nmarked=5647, nmarked2=1, nripped=5647 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=1 had to be increased for 16 vertices, nripped=5647 mean border=79.1, 15 (4) missing vertices, mean dist -0.2 [0.4 (%65.5)->0.3 (%34.5))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3084 min Finding expansion regions mean absolute distance = 0.39 +- 0.78 3634 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=compu, 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=574661.7, rms=4.296 018: dt: 0.5000, sse=370445.1, rms=2.996 (30.259%) rms = 3.0452/2.9962, sse=376142.6/370445.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 019: dt: 0.2500, sse=285081.4, rms=2.236 (25.379%) 020: dt: 0.2500, sse=235471.2, rms=1.631 (27.037%) 021: dt: 0.2500, sse=213841.2, rms=1.298 (20.417%) 022: dt: 0.2500, sse=203503.7, rms=1.096 (15.541%) 023: dt: 0.2500, sse=198938.0, rms=0.961 (12.319%) 024: dt: 0.2500, sse=193792.9, rms=0.877 (8.803%) 025: dt: 0.2500, sse=192009.2, rms=0.821 (6.328%) rms = 0.7903/0.8213, sse=191555.6/192009.2, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=191555.6, rms=0.790 (3.768%) rms = 0.7562/0.7903, sse=190331.0/191555.6, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=190331.0, rms=0.756 (4.321%) maximum number of reductions reached, breaking from loop positioning took 1.4 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=5647 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5662, nmarked2=1, nripped=5662 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 26 vertices, nripped=5662 mean border=81.4, 20 (1) missing vertices, mean dist -0.2 [0.4 (%68.4)->0.2 (%31.6))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1723 min Finding expansion regions mean absolute distance = 0.35 +- 0.63 4472 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=compu, 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=427086.3, rms=3.428 028: dt: 0.5000, sse=320048.2, rms=2.576 (24.858%) rms = 2.7367/2.5756, sse=337727.1/320048.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=241898.9, rms=1.746 (32.210%) 030: dt: 0.2500, sse=206245.0, rms=1.152 (34.044%) 031: dt: 0.2500, sse=192814.3, rms=0.884 (23.210%) 032: dt: 0.2500, sse=191806.0, rms=0.773 (12.601%) rms = 0.7251/0.7729, sse=189093.0/191806.0, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=189093.0, rms=0.725 (6.186%) rms = 0.6870/0.7251, sse=188282.1/189093.0, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=188282.1, rms=0.687 (5.252%) maximum number of reductions reached, breaking from loop positioning took 1.0 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=5662 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5683, nmarked2=1, nripped=5683 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 27 vertices, nripped=5683 mean border=82.6, 25 (1) missing vertices, mean dist -0.1 [0.4 (%58.9)->0.3 (%41.1))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1079 min Finding expansion regions mean absolute distance = 0.32 +- 0.53 3948 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=compu, 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=274991.2, rms=2.184 035: dt: 0.5000, sse=231460.3, rms=1.675 (23.272%) rms = 2.0808/1.6754, sse=267348.2/231460.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=191672.3, rms=1.007 (39.873%) 037: dt: 0.2500, sse=186550.9, rms=0.676 (32.854%) 038: dt: 0.2500, sse=183412.8, rms=0.592 (12.488%) rms = 0.5888/0.5920, sse=181230.2/183412.8, time step reduction 2 of 3 to 0.125 0 0 1 039: dt: 0.2500, sse=181230.2, rms=0.589 (0.538%) rms = 0.5455/0.5888, sse=181471.3/181230.2, time step reduction 3 of 3 to 0.062 0 1 1 040: dt: 0.1250, sse=181471.3, rms=0.545 (7.357%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes done positioning surface Removing intersections #ET# mris_place_surface 6.71 minutes Writing output to ../surf/lh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2121016 mris_place_surface done @#@FSTIME 2023:05:12:22:18:13 mris_place_surface N 18 e 416.05 S 0.96 U 414.61 P 99% M 1743820 F 0 R 262543 W 0 c 212 w 218 I 0 O 7968 L 1.04 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:25:09 mris_place_surface N 18 1.01 1.06 1.06 #-------------------------------------------- #@# WhitePreAparc rh Fri May 12 22:25:09 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 dev dev cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data 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 224976 0.27373 0.06051 0.001135 0.5867 Corner 674928 60.00000 8.79059 6.390269 135.4571 Edge 337464 0.79842 0.10845 0.048858 1.3115 Hinge 337464 6.13800 5.83182 0.000054 161.1795 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=11523, wmmin=5, clip=110 MRIfindBrightNonWM(): 3692 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=5680, nmarked2=16, nripped=5680 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56245: xyz = (51.2832,2.56187,-3.24646) oxyz = (51.2832,2.56187,-3.24646) wxzy = (51.2832,2.56187,-3.24646) pxyz = (0,0,0) CBVO Creating mask 112490 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=5680 #FML# MRISripMidline(): nmarked=5680, nmarked2=16, nripped=5680 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=2 had to be increased for 53 vertices, nripped=5680 mean border=77.3, 25 (25) missing vertices, mean dist 0.4 [0.5 (%32.8)->0.9 (%67.2))] %71 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.4355 min Finding expansion regions mean absolute distance = 0.77 +- 1.01 5112 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=compu, 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=2981505.2, rms=11.566 001: dt: 0.5000, sse=1722567.6, rms=8.656 (25.164%) 002: dt: 0.5000, sse=1126161.4, rms=6.857 (20.780%) 003: dt: 0.5000, sse=797650.5, rms=5.623 (17.999%) 004: dt: 0.5000, sse=606130.2, rms=4.755 (15.434%) 005: dt: 0.5000, sse=497481.9, rms=4.181 (12.080%) 006: dt: 0.5000, sse=434089.6, rms=3.804 (9.010%) 007: dt: 0.5000, sse=399410.7, rms=3.577 (5.963%) 008: dt: 0.5000, sse=379069.0, rms=3.435 (3.984%) 009: dt: 0.5000, sse=370315.8, rms=3.368 (1.944%) rms = 3.3230/3.3680, sse=367849.4/370315.9, time step reduction 1 of 3 to 0.250 0 0 1 010: dt: 0.5000, sse=367849.4, rms=3.323 (1.336%) 011: dt: 0.2500, sse=184099.0, rms=1.585 (52.303%) 012: dt: 0.2500, sse=157749.5, rms=1.128 (28.813%) 013: dt: 0.2500, sse=151048.5, rms=0.976 (13.488%) 014: dt: 0.2500, sse=148228.7, rms=0.904 (7.366%) rms = 0.8766/0.9042, sse=147261.7/148228.7, time step reduction 2 of 3 to 0.125 0 0 1 015: dt: 0.2500, sse=147261.7, rms=0.877 (3.054%) rms = 0.8289/0.8766, sse=145698.2/147261.7, time step reduction 3 of 3 to 0.062 0 0 1 016: dt: 0.1250, sse=145698.2, rms=0.829 (5.435%) maximum number of reductions reached, breaking from loop positioning took 2.1 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=5680 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5726, nmarked2=16, nripped=5726 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=1 had to be increased for 29 vertices, nripped=5726 mean border=79.2, 44 (9) missing vertices, mean dist -0.2 [0.4 (%65.3)->0.3 (%34.7))] %71 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3066 min Finding expansion regions mean absolute distance = 0.37 +- 0.75 3147 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=compu, 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=534399.1, rms=4.095 017: dt: 0.5000, sse=352909.6, rms=2.886 (29.524%) rms = 3.0246/2.8862, sse=370323.9/352909.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 018: dt: 0.2500, sse=268519.9, rms=2.087 (27.700%) 019: dt: 0.2500, sse=223243.0, rms=1.501 (28.086%) 020: dt: 0.2500, sse=206152.0, rms=1.193 (20.473%) 021: dt: 0.2500, sse=197346.2, rms=1.014 (15.005%) 022: dt: 0.2500, sse=192774.8, rms=0.901 (11.213%) 023: dt: 0.2500, sse=190633.4, rms=0.834 (7.419%) rms = 0.7975/0.8338, sse=189811.1/190633.4, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=189811.1, rms=0.797 (4.352%) rms = 0.7694/0.7975, sse=189888.8/189811.1, time step reduction 3 of 3 to 0.062 0 1 1 025: dt: 0.1250, sse=189888.8, rms=0.769 (3.517%) maximum number of reductions reached, breaking from loop positioning took 1.3 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=5726 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5747, nmarked2=16, nripped=5747 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 20 vertices, nripped=5747 mean border=81.4, 51 (6) missing vertices, mean dist -0.2 [0.4 (%67.7)->0.2 (%32.3))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1684 min Finding expansion regions mean absolute distance = 0.34 +- 0.63 4223 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=compu, 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=417849.7, rms=3.379 026: dt: 0.5000, sse=320411.5, rms=2.591 (23.321%) rms = 2.7841/2.5912, sse=342760.2/320411.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=241947.4, rms=1.770 (31.674%) 028: dt: 0.2500, sse=204735.8, rms=1.196 (32.431%) 029: dt: 0.2500, sse=195129.5, rms=0.933 (21.987%) 030: dt: 0.2500, sse=189164.9, rms=0.824 (11.755%) 031: dt: 0.2500, sse=187610.7, rms=0.767 (6.852%) rms = 0.7443/0.7671, sse=186124.3/187610.7, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=186124.3, rms=0.744 (2.978%) rms = 0.7186/0.7443, sse=184784.2/186124.3, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=184784.2, rms=0.719 (3.452%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=5747 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=5794, nmarked2=16, nripped=5794 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 25 vertices, nripped=5794 mean border=82.5, 65 (6) missing vertices, mean dist -0.1 [0.4 (%58.0)->0.3 (%42.0))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1057 min Finding expansion regions mean absolute distance = 0.32 +- 0.53 3453 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=compu, 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=263398.4, rms=2.108 034: dt: 0.5000, sse=229656.2, rms=1.682 (20.230%) rms = 2.1345/1.6816, sse=267496.6/229656.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=191396.8, rms=1.016 (39.609%) 036: dt: 0.2500, sse=181408.3, rms=0.703 (30.725%) 037: dt: 0.2500, sse=179343.0, rms=0.616 (12.471%) rms = 0.6107/0.6158, sse=179239.7/179343.0, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=179239.7, rms=0.611 (0.825%) rms = 0.5788/0.6107, sse=178202.8/179239.7, time step reduction 3 of 3 to 0.062 0 0 1 039: dt: 0.1250, sse=178202.8, rms=0.579 (5.222%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes done positioning surface Removing intersections #ET# mris_place_surface 6.49 minutes Writing output to ../surf/rh.white.preaparc #VMPC# mris_place_surfaces VmPeak 2065012 mris_place_surface done @#@FSTIME 2023:05:12:22:25:09 mris_place_surface N 18 e 403.01 S 0.91 U 401.59 P 99% M 1687824 F 0 R 239002 W 0 c 426 w 296 I 0 O 7920 L 1.01 1.06 1.06 @#@FSLOADPOST 2023:05:12:22:31:52 mris_place_surface N 18 1.00 1.02 1.05 #-------------------------------------------- #@# CortexLabel lh Fri May 12 22:31:53 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 6721 vertices erasing segment 1 (vno[0] = 69344) @#@FSTIME 2023:05:12:22:31:53 mri_label2label N 5 e 24.35 S 0.15 U 23.74 P 98% M 273872 F 0 R 31873 W 0 c 13 w 194 I 0 O 9184 L 1.00 1.02 1.05 @#@FSLOADPOST 2023:05:12:22:32:17 mri_label2label N 5 1.00 1.02 1.05 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Fri May 12 22:32:17 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 4 non-cortical segments detected only using segment with 5029 vertices erasing segment 1 (vno[0] = 40045) erasing segment 2 (vno[0] = 53264) erasing segment 3 (vno[0] = 69344) @#@FSTIME 2023:05:12:22:32:17 mri_label2label N 5 e 24.70 S 0.15 U 24.10 P 98% M 281656 F 0 R 33329 W 0 c 17 w 241 I 0 O 9320 L 1.00 1.02 1.05 @#@FSLOADPOST 2023:05:12:22:32:42 mri_label2label N 5 1.00 1.02 1.05 #-------------------------------------------- #@# CortexLabel rh Fri May 12 22:32:42 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 6 non-cortical segments detected only using segment with 6891 vertices erasing segment 1 (vno[0] = 32804) erasing segment 2 (vno[0] = 64790) erasing segment 3 (vno[0] = 66974) erasing segment 4 (vno[0] = 67717) erasing segment 5 (vno[0] = 93134) @#@FSTIME 2023:05:12:22:32:42 mri_label2label N 5 e 24.85 S 0.16 U 24.24 P 98% M 288748 F 0 R 33470 W 0 c 17 w 186 I 0 O 8936 L 1.00 1.02 1.05 @#@FSLOADPOST 2023:05:12:22:33:07 mri_label2label N 5 1.00 1.01 1.05 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Fri May 12 22:33:07 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 7 non-cortical segments detected only using segment with 4990 vertices erasing segment 1 (vno[0] = 32804) erasing segment 2 (vno[0] = 38162) erasing segment 3 (vno[0] = 42718) erasing segment 4 (vno[0] = 42727) erasing segment 5 (vno[0] = 66974) erasing segment 6 (vno[0] = 67717) @#@FSTIME 2023:05:12:22:33:07 mri_label2label N 5 e 25.27 S 0.15 U 24.65 P 98% M 292692 F 0 R 32948 W 0 c 13 w 197 I 0 O 9104 L 1.00 1.01 1.05 @#@FSLOADPOST 2023:05:12:22:33:32 mri_label2label N 5 1.07 1.03 1.05 #-------------------------------------------- #@# Smooth2 lh Fri May 12 22:33:32 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2023:05:12:22:33:32 mris_smooth N 7 e 5.65 S 0.13 U 5.13 P 93% M 172776 F 0 R 37311 W 0 c 7 w 196 I 0 O 7960 L 1.07 1.03 1.05 @#@FSLOADPOST 2023:05:12:22:33:38 mris_smooth N 7 1.06 1.03 1.05 #-------------------------------------------- #@# Smooth2 rh Fri May 12 22:33:38 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2023:05:12:22:33:38 mris_smooth N 7 e 5.48 S 0.13 U 4.97 P 93% M 171828 F 0 R 37017 W 0 c 8 w 234 I 0 O 7920 L 1.06 1.03 1.05 @#@FSLOADPOST 2023:05:12:22:33:44 mris_smooth N 7 1.06 1.03 1.05 #-------------------------------------------- #@# Inflation2 lh Fri May 12 22:33:44 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 43.7 mm, total surface area = 71441 mm^2 step 000: RMS=0.158 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.7 minutes mris_inflate utimesec 40.557944 mris_inflate stimesec 1.245967 mris_inflate ru_maxrss 173240 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 439940 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8848 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 200 mris_inflate ru_nivcsw 14 @#@FSTIME 2023:05:12:22:33:44 mris_inflate N 2 e 42.26 S 1.25 U 40.55 P 98% M 173240 F 0 R 439949 W 0 c 14 w 201 I 0 O 8856 L 1.06 1.03 1.05 @#@FSLOADPOST 2023:05:12:22:34:26 mris_inflate N 2 0.99 1.01 1.04 #-------------------------------------------- #@# Inflation2 rh Fri May 12 22:34:26 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 43.3 mm, total surface area = 71178 mm^2 step 000: RMS=0.160 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.020 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.7 minutes mris_inflate utimesec 40.237931 mris_inflate stimesec 1.384963 mris_inflate ru_maxrss 172276 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 469612 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8800 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 192 mris_inflate ru_nivcsw 33 @#@FSTIME 2023:05:12:22:34:26 mris_inflate N 2 e 42.07 S 1.39 U 40.23 P 98% M 172276 F 0 R 469621 W 0 c 33 w 193 I 0 O 8808 L 0.99 1.01 1.04 @#@FSLOADPOST 2023:05:12:22:35:08 mris_inflate N 2 0.99 1.01 1.04 #-------------------------------------------- #@# Curv .H and .K lh Fri May 12 22:35:08 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 15.670*4pi (196.911) --> -15 handles ICI = 127.0, FI = 877.7, variation=15189.019 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done. @#@FSTIME 2023:05:12:22:35:08 mris_curvature N 4 e 2.74 S 0.08 U 2.53 P 95% M 128300 F 0 R 20772 W 0 c 3 w 55 I 0 O 1776 L 0.99 1.01 1.04 @#@FSLOADPOST 2023:05:12:22:35:11 mris_curvature N 4 0.91 1.00 1.04 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 166 vertices thresholded to be in k1 ~ [-0.28 0.48], k2 ~ [-0.16 0.11] total integrated curvature = 0.557*4pi (6.994) --> 0 handles ICI = 1.4, FI = 7.5, variation=135.762 92 vertices thresholded to be in [-0.02 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 135 vertices thresholded to be in [-0.19 0.23] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.024 mris_curvature done. @#@FSTIME 2023:05:12:22:35:11 mris_curvature N 12 e 65.29 S 0.22 U 64.87 P 99% M 305168 F 0 R 64554 W 0 c 66 w 94 I 0 O 1776 L 0.91 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:36:17 mris_curvature N 12 0.97 1.00 1.04 #-------------------------------------------- #@# Curv .H and .K rh Fri May 12 22:36:17 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 20.406*4pi (256.434) --> -19 handles ICI = 134.4, FI = 900.4, variation=15656.945 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done. @#@FSTIME 2023:05:12:22:36:17 mris_curvature N 4 e 2.73 S 0.08 U 2.48 P 94% M 127668 F 0 R 20067 W 0 c 4 w 70 I 0 O 1760 L 0.97 1.00 1.04 @#@FSLOADPOST 2023:05:12:22:36:20 mris_curvature N 4 0.89 0.98 1.03 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 168 vertices thresholded to be in k1 ~ [-0.22 0.46], k2 ~ [-0.11 0.06] total integrated curvature = 0.540*4pi (6.788) --> 0 handles ICI = 1.4, FI = 8.5, variation=146.485 97 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 128 vertices thresholded to be in [-0.14 0.23] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.025 mris_curvature done. @#@FSTIME 2023:05:12:22:36:20 mris_curvature N 12 e 64.67 S 0.21 U 64.27 P 99% M 303664 F 0 R 63110 W 0 c 58 w 93 I 0 O 1768 L 0.89 0.98 1.03 @#@FSLOADPOST 2023:05:12:22:37:25 mris_curvature N 12 0.96 0.99 1.03 #-------------------------------------------- #@# Sphere lh Fri May 12 22:37:25 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: dev available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.314... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %42.04 pass 1: epoch 2 of 3 starting distance error %21.20 unfolding complete - removing small folds... starting distance error %21.03 removing remaining folds... final distance error %21.07 MRISunfold() return, current seed 1234 -01: dt=0.0000, 3 negative triangles VmPeak 623920 150: dt=0.9900, 3 negative triangles expanding nbhd size to 1 151: dt=0.9900, 3 negative triangles 152: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.2340 hours FSRUNTIME@ mris_sphere 0.2340 hours 1 threads #VMPC# mris_sphere VmPeak 623920 mris_sphere done @#@FSTIME 2023:05:12:22:37:25 mris_sphere N 4 e 842.41 S 25.28 U 816.65 P 99% M 233840 F 0 R 8465273 W 0 c 1065 w 279 I 0 O 7968 L 0.96 0.99 1.03 @#@FSLOADPOST 2023:05:12:22:51:27 mris_sphere N 4 0.91 0.97 1.02 #-------------------------------------------- #@# Sphere rh Fri May 12 22:51:27 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: dev available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.318... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %41.45 pass 1: epoch 2 of 3 starting distance error %20.51 unfolding complete - removing small folds... starting distance error %20.47 removing remaining folds... final distance error %20.47 MRISunfold() return, current seed 1234 -01: dt=0.0000, 94 negative triangles VmPeak 622716 047: dt=0.9900, 94 negative triangles 048: dt=0.9900, 51 negative triangles 049: dt=0.9900, 40 negative triangles 050: dt=0.9900, 28 negative triangles 051: dt=0.9900, 22 negative triangles 052: dt=0.9900, 16 negative triangles 053: dt=0.9900, 14 negative triangles 054: dt=0.9900, 9 negative triangles 055: dt=0.9900, 10 negative triangles 056: dt=0.9900, 5 negative triangles 057: dt=0.9900, 9 negative triangles 058: dt=0.9900, 5 negative triangles 059: dt=0.9900, 3 negative triangles 060: dt=0.9900, 2 negative triangles 061: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1103 hours FSRUNTIME@ mris_sphere 0.1103 hours 1 threads #VMPC# mris_sphere VmPeak 622716 mris_sphere done @#@FSTIME 2023:05:12:22:51:27 mris_sphere N 4 e 397.19 S 7.49 U 389.25 P 99% M 232704 F 0 R 2479616 W 0 c 216 w 288 I 0 O 7928 L 0.91 0.97 1.02 @#@FSLOADPOST 2023:05:12:22:58:05 mris_sphere N 4 1.00 0.99 1.02 #-------------------------------------------- #@# Surf Reg lh Fri May 12 22:58:05 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/dev//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/dev//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) dev dev reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/dev//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=compu, 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=compu, 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=compu, 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 = 5.709 curvature mean = 0.046, std = 0.824 curvature mean = -0.003, std = 0.878 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (3.50, 0.50, 2.00) sse = 194986.7, elapsed since starting=0.6408 min MRISrigidBodyAlignGlobal() done 0.64 min curvature mean = 0.013, std = 0.825 curvature mean = -0.002, std = 0.953 curvature mean = 0.012, std = 0.837 curvature mean = -0.000, std = 0.982 curvature mean = 0.011, std = 0.840 curvature mean = -0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.018, std = 0.220 curvature mean = 0.044, std = 0.244 curvature mean = 0.016, std = 0.492 curvature mean = 0.041, std = 0.302 curvature mean = 0.015, std = 0.702 curvature mean = 0.041, std = 0.327 curvature mean = 0.007, std = 0.830 curvature mean = 0.041, std = 0.338 curvature mean = 0.002, std = 0.907 MRISregister() return, current seed 0 -01: dt=0.0000, 2 negative triangles VmPeak 616652 101: dt=0.9900, 2 negative triangles expanding nbhd size to 1 102: dt=0.9900, 4 negative triangles 103: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.22 hours #VMPC# mris_register VmPeak 616652 FSRUNTIME@ mris_register 0.2207 hours 1 threads @#@FSTIME 2023:05:12:22:58:05 mris_register N 4 e 794.54 S 15.63 U 778.15 P 99% M 225120 F 0 R 5034157 W 0 c 376 w 318 I 5584 O 7968 L 1.00 0.99 1.02 @#@FSLOADPOST 2023:05:12:23:11:19 mris_register N 4 1.00 0.99 1.02 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Fri May 12 23:11:19 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/dev//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/dev//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) dev dev reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/dev//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=compu, 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=compu, 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=compu, 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 = 5.694 curvature mean = 0.018, std = 0.812 curvature mean = -0.001, std = 0.880 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (9.50, 4.50, 2.50) sse = 197305.3, elapsed since starting=0.6527 min MRISrigidBodyAlignGlobal() done 0.65 min curvature mean = 0.006, std = 0.834 curvature mean = -0.000, std = 0.955 curvature mean = 0.005, std = 0.844 curvature mean = -0.000, std = 0.983 curvature mean = 0.005, std = 0.847 curvature mean = -0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.016, std = 0.219 curvature mean = 0.039, std = 0.238 curvature mean = 0.018, std = 0.495 curvature mean = 0.038, std = 0.295 curvature mean = 0.012, std = 0.715 curvature mean = 0.038, std = 0.320 curvature mean = 0.006, std = 0.843 curvature mean = 0.038, std = 0.331 curvature mean = 0.002, std = 0.917 MRISregister() return, current seed 0 -01: dt=0.0000, 1 negative triangles VmPeak 615612 104: dt=0.9900, 1 negative triangles expanding nbhd size to 1 105: dt=0.9900, 2 negative triangles 106: dt=0.9900, 1 negative triangles 107: dt=0.9900, 1 negative triangles 108: dt=0.9900, 1 negative triangles 109: dt=0.9900, 1 negative triangles 110: dt=0.9405, 1 negative triangles 111: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.22 hours #VMPC# mris_register VmPeak 615612 FSRUNTIME@ mris_register 0.2250 hours 1 threads @#@FSTIME 2023:05:12:23:11:19 mris_register N 4 e 809.98 S 16.01 U 793.21 P 99% M 223884 F 0 R 4996518 W 0 c 799 w 309 I 5584 O 7928 L 1.00 0.99 1.02 @#@FSLOADPOST 2023:05:12:23:24:49 mris_register N 4 1.01 1.02 1.04 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Fri May 12 23:24:49 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white @#@FSTIME 2023:05:12:23:24:50 mris_jacobian N 3 e 1.92 S 0.13 U 1.68 P 94% M 172200 F 0 R 37193 W 0 c 4 w 46 I 0 O 888 L 1.01 1.02 1.04 @#@FSLOADPOST 2023:05:12:23:24:51 mris_jacobian N 3 1.01 1.02 1.04 #-------------------------------------------- #@# Jacobian white rh Fri May 12 23:24:52 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white @#@FSTIME 2023:05:12:23:24:52 mris_jacobian N 3 e 1.89 S 0.12 U 1.67 P 95% M 171500 F 0 R 36902 W 0 c 4 w 37 I 0 O 880 L 1.01 1.02 1.04 @#@FSLOADPOST 2023:05:12:23:24:53 mris_jacobian N 3 1.01 1.02 1.04 #-------------------------------------------- #@# AvgCurv lh Fri May 12 23:24:53 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mrisp_paint -a 5 /usr/local/freesurfer/dev//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/dev//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2023:05:12:23:24:54 mrisp_paint N 5 e 1.45 S 0.07 U 1.29 P 94% M 133396 F 0 R 20521 W 0 c 5 w 36 I 0 O 888 L 1.01 1.02 1.04 @#@FSLOADPOST 2023:05:12:23:24:55 mrisp_paint N 5 1.01 1.02 1.04 #-------------------------------------------- #@# AvgCurv rh Fri May 12 23:24:55 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mrisp_paint -a 5 /usr/local/freesurfer/dev//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/dev//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2023:05:12:23:24:55 mrisp_paint N 5 e 1.44 S 0.09 U 1.27 P 94% M 132724 F 0 R 20318 W 0 c 2 w 33 I 0 O 880 L 1.01 1.02 1.04 @#@FSLOADPOST 2023:05:12:23:24:57 mrisp_paint N 5 1.01 1.02 1.04 #----------------------------------------- #@# Cortical Parc lh Fri May 12 23:24:57 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 CR_t2_tra_12_SR lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev//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 dev dev reading atlas from /usr/local/freesurfer/dev//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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 736 labels changed using aseg relabeling using gibbs priors... 000: 2522 changed, 113073 examined... 001: 590 changed, 10892 examined... 002: 143 changed, 3392 examined... 003: 43 changed, 845 examined... 004: 17 changed, 270 examined... 005: 8 changed, 105 examined... 006: 3 changed, 55 examined... 007: 0 changed, 21 examined... 217 labels changed using aseg 000: 91 total segments, 51 labels (134 vertices) changed 001: 41 total segments, 1 labels (1 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1345 vertices marked for relabeling... 1345 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 18 seconds. @#@FSTIME 2023:05:12:23:24:57 mris_ca_label N 11 e 18.13 S 0.73 U 15.02 P 86% M 1003352 F 0 R 190949 W 0 c 19 w 108 I 62920 O 1776 L 1.01 1.02 1.04 @#@FSLOADPOST 2023:05:12:23:25:15 mris_ca_label N 11 1.01 1.02 1.04 #----------------------------------------- #@# Cortical Parc rh Fri May 12 23:25:15 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 CR_t2_tra_12_SR rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev//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 dev dev reading atlas from /usr/local/freesurfer/dev//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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 803 labels changed using aseg relabeling using gibbs priors... 000: 2332 changed, 112490 examined... 001: 540 changed, 10149 examined... 002: 120 changed, 3086 examined... 003: 41 changed, 765 examined... 004: 19 changed, 259 examined... 005: 8 changed, 119 examined... 006: 3 changed, 51 examined... 007: 0 changed, 21 examined... 152 labels changed using aseg 000: 73 total segments, 28 labels (70 vertices) changed 001: 45 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... 1034 vertices marked for relabeling... 1034 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 16 seconds. @#@FSTIME 2023:05:12:23:25:15 mris_ca_label N 11 e 16.48 S 0.64 U 14.38 P 91% M 928696 F 0 R 163455 W 0 c 16 w 82 I 36352 O 1776 L 1.01 1.02 1.04 @#@FSLOADPOST 2023:05:12:23:25:31 mris_ca_label N 11 1.01 1.02 1.04 #-------------------------------------------- #@# WhiteSurfs lh Fri May 12 23:25:31 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 dev dev cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data 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 226142 0.34334 0.11625 0.000983 2.3488 Corner 678426 60.00000 12.47570 0.502867 178.4653 Edge 339213 0.89955 0.18849 0.034036 3.6080 Hinge 339213 8.70801 9.12219 0.000002 179.9948 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=11523, wmmin=5, clip=110 MRIfindBrightNonWM(): 3692 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 6990/113073 vertices (106083 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 446 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56537: xyz = (-10.0341,-1.87502,-16.8828) oxyz = (-10.0341,-1.87502,-16.8828) wxzy = (-10.0341,-1.87502,-16.8828) pxyz = (0,0,0) CBVO Creating mask 113073 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=2 had to be increased for 57 vertices, nripped=7436 mean border=76.4, 59 (59) missing vertices, mean dist 0.4 [0.7 (%16.7)->0.6 (%83.3))] %67 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.4040 min Finding expansion regions mean absolute distance = 0.63 +- 0.98 3641 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=compu, 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=1657920.5, rms=8.395 001: dt: 0.5000, sse=886482.2, rms=5.858 (30.219%) 002: dt: 0.5000, sse=618155.9, rms=4.646 (20.699%) 003: dt: 0.5000, sse=518765.1, rms=4.059 (12.629%) 004: dt: 0.5000, sse=441679.8, rms=3.566 (12.137%) 005: dt: 0.5000, sse=426425.2, rms=3.450 (3.255%) 006: dt: 0.5000, sse=397093.2, rms=3.197 (7.333%) rms = 3.2575/3.1973, sse=404096.2/397093.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 007: dt: 0.2500, sse=276649.9, rms=2.055 (35.714%) 008: dt: 0.2500, sse=225695.1, rms=1.423 (30.753%) 009: dt: 0.2500, sse=205781.2, rms=1.192 (16.254%) 010: dt: 0.2500, sse=202989.6, rms=1.099 (7.758%) 011: dt: 0.2500, sse=192915.1, rms=1.036 (5.786%) rms = 1.0075/1.0359, sse=195334.8/192915.1, time step reduction 2 of 3 to 0.125 0 1 1 012: dt: 0.2500, sse=195334.8, rms=1.008 (2.735%) rms = 0.9727/1.0075, sse=200276.3/195334.8, time step reduction 3 of 3 to 0.062 0 1 1 013: dt: 0.1250, sse=200276.2, rms=0.973 (3.461%) maximum number of reductions reached, breaking from loop positioning took 1.9 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=1 had to be increased for 43 vertices, nripped=7436 mean border=78.9, 61 (37) missing vertices, mean dist -0.3 [0.5 (%65.8)->0.3 (%34.2))] %70 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3025 min Finding expansion regions mean absolute distance = 0.43 +- 0.87 3966 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=compu, 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=630558.5, rms=4.515 014: dt: 0.5000, sse=407820.6, rms=3.185 (29.461%) 015: dt: 0.5000, sse=395343.6, rms=3.100 (2.663%) 016: dt: 0.5000, sse=385284.4, rms=3.049 (1.653%) rms = 3.1388/3.0486, sse=394433.2/385284.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 017: dt: 0.2500, sse=268013.7, rms=1.944 (36.236%) 018: dt: 0.2500, sse=226439.8, rms=1.344 (30.865%) 019: dt: 0.2500, sse=215787.6, rms=1.089 (18.933%) 020: dt: 0.2500, sse=209783.2, rms=0.975 (10.478%) 021: dt: 0.2500, sse=207113.9, rms=0.894 (8.364%) rms = 0.8504/0.8937, sse=215758.8/207113.9, time step reduction 2 of 3 to 0.125 0 1 1 022: dt: 0.2500, sse=215758.8, rms=0.850 (4.853%) rms = 0.8102/0.8504, sse=202488.4/215758.8, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=202488.4, rms=0.810 (4.719%) maximum number of reductions reached, breaking from loop positioning took 1.4 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 52 vertices, nripped=7436 mean border=81.4, 67 (28) missing vertices, mean dist -0.2 [0.4 (%69.3)->0.3 (%30.7))] %77 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1693 min Finding expansion regions mean absolute distance = 0.39 +- 0.68 4028 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=compu, 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=466402.4, rms=3.677 024: dt: 0.5000, sse=337419.1, rms=2.719 (26.063%) rms = 2.7804/2.7188, sse=343707.6/337419.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=258939.7, rms=1.920 (29.372%) 026: dt: 0.2500, sse=218835.2, rms=1.290 (32.834%) 027: dt: 0.2500, sse=202084.0, rms=0.991 (23.198%) 028: dt: 0.2500, sse=196834.2, rms=0.858 (13.358%) 029: dt: 0.2500, sse=193510.8, rms=0.793 (7.581%) rms = 0.7670/0.7932, sse=193716.8/193510.8, time step reduction 2 of 3 to 0.125 0 1 1 030: dt: 0.2500, sse=193716.8, rms=0.767 (3.296%) rms = 0.7366/0.7670, sse=192403.2/193716.8, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=192403.2, rms=0.737 (3.968%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 50 vertices, nripped=7436 mean border=82.6, 61 (18) missing vertices, mean dist -0.1 [0.4 (%59.3)->0.3 (%40.7))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1055 min Finding expansion regions mean absolute distance = 0.34 +- 0.57 3685 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=compu, 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=279610.7, rms=2.235 032: dt: 0.5000, sse=240507.7, rms=1.725 (22.835%) rms = 2.0959/1.7247, sse=271180.3/240507.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 033: dt: 0.2500, sse=201770.3, rms=1.067 (38.120%) 034: dt: 0.2500, sse=190293.9, rms=0.736 (31.063%) 035: dt: 0.2500, sse=187211.2, rms=0.653 (11.187%) rms = 0.6312/0.6534, sse=183821.0/187211.2, time step reduction 2 of 3 to 0.125 0 0 1 036: dt: 0.2500, sse=183821.0, rms=0.631 (3.397%) 037: dt: 0.1250, sse=183030.8, rms=0.578 (8.411%) rms = 0.5709/0.5781, sse=183275.9/183030.8, time step reduction 3 of 3 to 0.062 0 1 1 038: dt: 0.1250, sse=183275.9, rms=0.571 (1.243%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes done positioning surface Removing intersections #ET# mris_place_surface 6.41 minutes Writing output to ../surf/lh.white #VMPC# mris_place_surfaces VmPeak 2099852 mris_place_surface done @#@FSTIME 2023:05:12:23:25:31 mris_place_surface N 25 e 398.79 S 1.01 U 397.25 P 99% M 1722672 F 0 R 259172 W 0 c 176 w 311 I 0 O 7968 L 1.01 1.02 1.04 @#@FSLOADPOST 2023:05:12:23:32:10 mris_place_surface N 25 1.00 1.01 1.04 #-------------------------------------------- #@# WhiteSurfs rh Fri May 12 23:32:10 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 dev dev cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data 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 224976 0.34527 0.11767 0.003965 2.4577 Corner 674928 60.00000 12.40663 1.189832 177.0344 Edge 337464 0.90216 0.18991 0.047514 3.3828 Hinge 337464 8.84987 9.42811 0.000003 179.0158 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=11523, wmmin=5, clip=110 MRIfindBrightNonWM(): 3692 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 7154/112490 vertices (105336 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 435 Ripping segs (eg, WMSA, BG, frozen) Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 56245: xyz = (51.6471,2.81604,-2.59619) oxyz = (51.6471,2.81604,-2.59619) wxzy = (51.6471,2.81604,-2.59619) pxyz = (0,0,0) CBVO Creating mask 112490 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=2 had to be increased for 82 vertices, nripped=7589 mean border=76.5, 51 (51) missing vertices, mean dist 0.4 [0.7 (%17.5)->0.6 (%82.5))] %67 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.4037 min Finding expansion regions mean absolute distance = 0.60 +- 0.98 3602 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=compu, 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=1533069.2, rms=8.076 001: dt: 0.5000, sse=824893.1, rms=5.617 (30.445%) 002: dt: 0.5000, sse=592128.2, rms=4.525 (19.442%) 003: dt: 0.5000, sse=498599.8, rms=3.996 (11.685%) 004: dt: 0.5000, sse=431856.8, rms=3.553 (11.082%) 005: dt: 0.5000, sse=412662.1, rms=3.438 (3.257%) 006: dt: 0.5000, sse=381719.3, rms=3.211 (6.586%) rms = 3.2619/3.2112, sse=390961.7/381719.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 007: dt: 0.2500, sse=253217.2, rms=2.031 (36.747%) 008: dt: 0.2500, sse=206542.3, rms=1.373 (32.400%) 009: dt: 0.2500, sse=194175.7, rms=1.137 (17.162%) 010: dt: 0.2500, sse=191579.5, rms=1.054 (7.351%) rms = 1.0095/1.0538, sse=189845.4/191579.5, time step reduction 2 of 3 to 0.125 0 0 1 011: dt: 0.2500, sse=189845.4, rms=1.009 (4.206%) rms = 0.9782/1.0095, sse=189472.2/189845.4, time step reduction 3 of 3 to 0.062 0 0 1 012: dt: 0.1250, sse=189472.2, rms=0.978 (3.098%) maximum number of reductions reached, breaking from loop positioning took 1.7 minutes done positioning surface Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=1 had to be increased for 62 vertices, nripped=7589 mean border=78.9, 67 (26) missing vertices, mean dist -0.2 [0.5 (%66.2)->0.3 (%33.8))] %69 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3014 min Finding expansion regions mean absolute distance = 0.41 +- 0.83 3513 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=compu, 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=567366.9, rms=4.253 013: dt: 0.5000, sse=378261.8, rms=3.005 (29.348%) rms = 3.0204/3.0047, sse=374956.7/378261.8, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 014: dt: 0.2500, sse=295158.4, rms=2.296 (23.594%) 015: dt: 0.2500, sse=246275.4, rms=1.708 (25.608%) 016: dt: 0.2500, sse=223959.8, rms=1.360 (20.354%) 017: dt: 0.2500, sse=212116.5, rms=1.138 (16.324%) 018: dt: 0.2500, sse=206406.6, rms=0.988 (13.229%) 019: dt: 0.2500, sse=203098.9, rms=0.894 (9.485%) 020: dt: 0.2500, sse=201167.3, rms=0.843 (5.684%) rms = 0.8158/0.8431, sse=200421.4/201167.3, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=200421.4, rms=0.816 (3.237%) rms = 0.7938/0.8158, sse=199962.1/200421.4, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=199962.1, rms=0.794 (2.704%) maximum number of reductions reached, breaking from loop positioning took 1.4 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 = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 34 vertices, nripped=7589 mean border=81.3, 88 (20) missing vertices, mean dist -0.2 [0.4 (%68.7)->0.2 (%31.3))] %76 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1678 min Finding expansion regions mean absolute distance = 0.38 +- 0.68 4199 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=compu, 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=447138.5, rms=3.573 023: dt: 0.5000, sse=332994.2, rms=2.681 (24.959%) rms = 2.7927/2.6814, sse=348359.7/332994.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=256279.0, rms=1.877 (29.986%) 025: dt: 0.2500, sse=217031.7, rms=1.267 (32.525%) 026: dt: 0.2500, sse=201595.4, rms=0.977 (22.884%) 027: dt: 0.2500, sse=196106.2, rms=0.851 (12.870%) 028: dt: 0.2500, sse=193890.2, rms=0.787 (7.506%) rms = 0.7600/0.7872, sse=193321.1/193890.2, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=193321.1, rms=0.760 (3.458%) rms = 0.7366/0.7600, sse=192700.9/193321.1, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=192701.0, rms=0.737 (3.080%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes done positioning surface Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.5043870; border_low = 61.0000000; outside_low = 49.2816160; outside_hi = 111.5043870; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 27 vertices, nripped=7589 mean border=82.5, 115 (16) missing vertices, mean dist -0.1 [0.4 (%58.5)->0.3 (%41.5))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1056 min Finding expansion regions mean absolute distance = 0.34 +- 0.56 3244 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=compu, 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=269866.8, rms=2.127 031: dt: 0.5000, sse=238099.5, rms=1.684 (20.860%) rms = 2.1228/1.6836, sse=273778.4/238099.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=199976.4, rms=1.028 (38.937%) 033: dt: 0.2500, sse=193245.3, rms=0.715 (30.488%) rms = 0.6221/0.7146, sse=193282.9/193245.3, time step reduction 2 of 3 to 0.125 0 1 0 034: dt: 0.2500, sse=193282.9, rms=0.622 (12.949%) rms = 0.5954/0.6221, sse=189954.6/193282.9, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=189954.5, rms=0.595 (4.292%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes done positioning surface Removing intersections #ET# mris_place_surface 5.98 minutes Writing output to ../surf/rh.white #VMPC# mris_place_surfaces VmPeak 2027488 mris_place_surface done @#@FSTIME 2023:05:12:23:32:10 mris_place_surface N 25 e 373.08 S 0.92 U 371.65 P 99% M 1650180 F 0 R 244734 W 0 c 196 w 283 I 0 O 7920 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:38:24 mris_place_surface N 25 1.00 1.01 1.04 #-------------------------------------------- #@# T1PialSurf lh Fri May 12 23:38:24 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 dev dev cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data 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 226142 0.34544 0.13097 0.001012 2.5896 Corner 678426 60.00000 13.97869 0.180504 178.3642 Edge 339213 0.90392 0.21087 0.020884 3.9582 Hinge 339213 8.92414 9.74978 0.000002 179.9294 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=11523, wmmin=5, clip=110 MRIfindBrightNonWM(): 3692 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 60.1702 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label MRISripNotLabel() ripped 5329/113073 vertices (107744 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 56537: xyz = (-10.0341,-1.87502,-16.8828) oxyz = (-10.0341,-1.87502,-16.8828) wxzy = (-10.0341,-1.87502,-16.8828) pxyz = (-10.0341,-1.87502,-16.8828) CBVO Creating mask 113073 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.4956130; border_hi = 49.2816160; border_low = 25.8448410; outside_low = 10.0000000; outside_hi = 43.4224240; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=2 had to be increased for 136 vertices, nripped=5329 mean border=48.5, 95 (95) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.9 (%100.0))] % 9 local maxima, %50 large gradients and %36 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3349 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=compu, 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=26217330.0, rms=34.786 001: dt: 0.5000, sse=19027446.0, rms=29.598 (14.912%) 002: dt: 0.5000, sse=13585964.0, rms=24.965 (15.654%) 003: dt: 0.5000, sse=9743528.0, rms=21.088 (15.531%) 004: dt: 0.5000, sse=7189618.5, rms=18.054 (14.386%) 005: dt: 0.5000, sse=5523900.5, rms=15.762 (12.693%) 006: dt: 0.5000, sse=4344145.5, rms=13.912 (11.741%) 007: dt: 0.5000, sse=3487057.2, rms=12.394 (10.910%) 008: dt: 0.5000, sse=2821125.2, rms=11.071 (10.673%) 009: dt: 0.5000, sse=2315001.8, rms=9.948 (10.147%) 010: dt: 0.5000, sse=1904170.6, rms=8.932 (10.214%) 011: dt: 0.5000, sse=1594591.4, rms=8.081 (9.521%) 012: dt: 0.5000, sse=1342526.2, rms=7.315 (9.480%) 013: dt: 0.5000, sse=1163912.8, rms=6.719 (8.154%) 014: dt: 0.5000, sse=1017967.0, rms=6.188 (7.905%) 015: dt: 0.5000, sse=919785.4, rms=5.802 (6.230%) 016: dt: 0.5000, sse=836701.3, rms=5.454 (6.008%) 017: dt: 0.5000, sse=785880.8, rms=5.228 (4.138%) 018: dt: 0.5000, sse=738466.0, rms=5.008 (4.206%) 019: dt: 0.5000, sse=715889.8, rms=4.898 (2.191%) 020: dt: 0.5000, sse=687381.2, rms=4.757 (2.877%) rms = 4.7144/4.7574, sse=679383.8/687381.2, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=679383.8, rms=4.714 (0.903%) 022: dt: 0.2500, sse=581604.5, rms=4.186 (11.206%) 023: dt: 0.2500, sse=562044.2, rms=4.073 (2.697%) rms = 4.0363/4.0732, sse=555936.8/562044.2, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=555936.8, rms=4.036 (0.907%) 025: dt: 0.1250, sse=547046.4, rms=3.982 (1.353%) rms = 3.9671/3.9817, sse=544726.6/547046.4, time step reduction 3 of 3 to 0.062 0 0 1 026: dt: 0.1250, sse=544726.6, rms=3.967 (0.365%) maximum number of reductions reached, breaking from loop positioning took 3.1 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.4956130; border_hi = 49.2816160; border_low = 25.8448410; outside_low = 10.0000000; outside_hi = 43.4224240; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=1 had to be increased for 7732 vertices, nripped=5329 mean border=48.3, 1527 (21) missing vertices, mean dist 0.2 [0.1 (%59.4)->0.8 (%40.6))] %16 local maxima, %46 large gradients and %32 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1108 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=compu, 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=580362.1, rms=3.839 027: dt: 0.5000, sse=567746.5, rms=3.766 (1.910%) rms = 3.8714/3.7660, sse=583172.3/567746.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=534261.8, rms=3.549 (5.749%) 029: dt: 0.2500, sse=520591.3, rms=3.459 (2.553%) rms = 3.4321/3.4588, sse=516765.3/520591.3, time step reduction 2 of 3 to 0.125 0 0 1 030: dt: 0.2500, sse=516765.3, rms=3.432 (0.772%) rms = 3.3931/3.4321, sse=511486.3/516765.3, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=511486.2, rms=3.393 (1.138%) 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 = 94.4956130; border_hi = 49.2816160; border_low = 25.8448410; outside_low = 10.0000000; outside_hi = 43.4224240; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 7959 vertices, nripped=5329 mean border=47.9, 2023 (12) missing vertices, mean dist 0.1 [0.1 (%54.4)->0.6 (%45.6))] %26 local maxima, %36 large gradients and %32 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0632 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=compu, 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=544569.2, rms=3.601 rms = 3.6777/3.6006, sse=555857.9/544569.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=526502.2, rms=3.481 (3.331%) 033: dt: 0.2500, sse=517079.9, rms=3.418 (1.786%) rms = 3.4047/3.4185, sse=514923.8/517079.9, time step reduction 2 of 3 to 0.125 0 0 1 034: dt: 0.2500, sse=514923.8, rms=3.405 (0.402%) rms = 3.3771/3.4047, sse=511163.2/514923.8, time step reduction 3 of 3 to 0.062 0 0 1 035: dt: 0.1250, sse=511163.2, rms=3.377 (0.810%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.4956130; border_hi = 49.2816160; border_low = 25.8448410; outside_low = 10.0000000; outside_hi = 43.4224240; 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=113073 Gdiag_no=-1 vno start=0, stop=113073 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 6248 vertices, nripped=5329 mean border=47.1, 4381 (9) missing vertices, mean dist 0.1 [0.1 (%50.5)->0.5 (%49.5))] %34 local maxima, %27 large gradients and %30 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0395 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=compu, 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=539360.4, rms=3.571 rms = 3.6274/3.5706, sse=547069.1/539360.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 036: dt: 0.2500, sse=520268.3, rms=3.443 (3.570%) 037: dt: 0.2500, sse=506421.1, rms=3.352 (2.656%) rms = 3.3071/3.3516, sse=499644.9/506421.1, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=499644.9, rms=3.307 (1.328%) rms = 3.2613/3.3071, sse=493458.0/499644.9, time step reduction 3 of 3 to 0.062 0 0 1 039: dt: 0.1250, sse=493458.1, rms=3.261 (1.384%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 14 intersecting terminating search with 0 intersecting #ET# mris_place_surface 5.63 minutes Writing output to ../surf/lh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1372760 mris_place_surface done @#@FSTIME 2023:05:12:23:38:24 mris_place_surface N 28 e 351.83 S 0.68 U 350.61 P 99% M 994880 F 0 R 207666 W 0 c 243 w 299 I 0 O 7968 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:44:16 mris_place_surface N 28 1.00 1.01 1.04 #-------------------------------------------- #@# T1PialSurf rh Fri May 12 23:44:16 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 dev dev cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data 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 224976 0.34795 0.13222 0.001498 2.3000 Corner 674928 60.00000 13.90906 0.336716 177.3749 Edge 337464 0.90752 0.21333 0.023689 4.6840 Hinge 337464 9.06382 9.99598 0.000095 179.8984 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=11523, wmmin=5, clip=110 MRIfindBrightNonWM(): 3692 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 60.1702 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label MRISripNotLabel() ripped 5313/112490 vertices (107177 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 56245: xyz = (51.7963,2.84356,-2.53903) oxyz = (51.7963,2.84356,-2.53903) wxzy = (51.7963,2.84356,-2.53903) pxyz = (51.7963,2.84356,-2.53903) CBVO Creating mask 112490 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.4956130; border_hi = 49.2816160; border_low = 25.8448410; outside_low = 10.0000000; outside_hi = 43.4224240; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=2 had to be increased for 110 vertices, nripped=5313 mean border=48.6, 121 (121) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.9 (%100.0))] % 9 local maxima, %50 large gradients and %37 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.3284 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=compu, 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=25624352.0, rms=34.482 001: dt: 0.5000, sse=18472036.0, rms=29.239 (15.204%) 002: dt: 0.5000, sse=13077119.0, rms=24.554 (16.024%) 003: dt: 0.5000, sse=9293115.0, rms=20.641 (15.935%) 004: dt: 0.5000, sse=6816386.0, rms=17.614 (14.665%) 005: dt: 0.5000, sse=5224821.0, rms=15.356 (12.821%) 006: dt: 0.5000, sse=4108660.2, rms=13.548 (11.773%) 007: dt: 0.5000, sse=3309088.8, rms=12.087 (10.786%) 008: dt: 0.5000, sse=2686358.2, rms=10.811 (10.552%) 009: dt: 0.5000, sse=2215477.8, rms=9.736 (9.949%) 010: dt: 0.5000, sse=1831439.5, rms=8.760 (10.024%) 011: dt: 0.5000, sse=1540461.1, rms=7.940 (9.357%) 012: dt: 0.5000, sse=1301145.8, rms=7.195 (9.380%) 013: dt: 0.5000, sse=1128067.8, rms=6.604 (8.219%) 014: dt: 0.5000, sse=988193.3, rms=6.083 (7.893%) 015: dt: 0.5000, sse=897876.9, rms=5.720 (5.969%) 016: dt: 0.5000, sse=823236.7, rms=5.401 (5.572%) 017: dt: 0.5000, sse=783239.6, rms=5.220 (3.344%) 018: dt: 0.5000, sse=745739.9, rms=5.045 (3.360%) 019: dt: 0.5000, sse=731277.9, rms=4.973 (1.421%) 020: dt: 0.5000, sse=709348.8, rms=4.865 (2.169%) rms = 4.8402/4.8653, sse=705001.9/709348.8, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=705001.9, rms=4.840 (0.517%) 022: dt: 0.2500, sse=611346.4, rms=4.347 (10.188%) 023: dt: 0.2500, sse=593769.4, rms=4.248 (2.269%) rms = 4.2120/4.2484, sse=587560.9/593769.4, time step reduction 2 of 3 to 0.125 0 0 1 024: dt: 0.2500, sse=587560.9, rms=4.212 (0.858%) rms = 4.1655/4.2120, sse=579814.9/587560.9, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=579814.9, rms=4.165 (1.104%) maximum number of reductions reached, breaking from loop positioning took 3.0 minutes done positioning surface Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.4956130; border_hi = 49.2816160; border_low = 25.8448410; outside_low = 10.0000000; outside_hi = 43.4224240; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=1 had to be increased for 7892 vertices, nripped=5313 mean border=48.3, 1366 (26) missing vertices, mean dist 0.2 [0.1 (%56.8)->0.8 (%43.2))] %16 local maxima, %45 large gradients and %33 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1082 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=compu, 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=616941.3, rms=4.052 026: dt: 0.5000, sse=595824.4, rms=3.930 (3.011%) rms = 4.0461/3.9300, sse=613680.1/595824.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=559438.6, rms=3.703 (5.774%) 028: dt: 0.2500, sse=543055.9, rms=3.597 (2.856%) rms = 3.5542/3.5973, sse=536564.3/543055.9, time step reduction 2 of 3 to 0.125 0 0 1 029: dt: 0.2500, sse=536564.3, rms=3.554 (1.199%) rms = 3.5112/3.5542, sse=530570.0/536564.3, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=530570.0, rms=3.511 (1.210%) 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 = 94.4956130; border_hi = 49.2816160; border_low = 25.8448410; outside_low = 10.0000000; outside_hi = 43.4224240; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 8097 vertices, nripped=5313 mean border=47.9, 1894 (25) missing vertices, mean dist 0.1 [0.1 (%53.1)->0.6 (%46.9))] %25 local maxima, %35 large gradients and %33 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0609 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=compu, 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=561717.2, rms=3.701 rms = 3.7482/3.7014, sse=568372.5/561717.3, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=541556.2, rms=3.570 (3.537%) 032: dt: 0.2500, sse=528359.5, rms=3.484 (2.413%) rms = 3.4534/3.4843, sse=523557.1/528359.5, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=523557.1, rms=3.453 (0.888%) rms = 3.4215/3.4534, sse=519139.4/523557.1, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=519139.4, rms=3.421 (0.924%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.4956130; border_hi = 49.2816160; border_low = 25.8448410; outside_low = 10.0000000; outside_hi = 43.4224240; 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=112490 Gdiag_no=-1 vno start=0, stop=112490 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 6431 vertices, nripped=5313 mean border=47.2, 4186 (24) missing vertices, mean dist 0.1 [0.1 (%50.4)->0.5 (%49.6))] %33 local maxima, %27 large gradients and %32 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0384 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=compu, 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=554654.6, rms=3.661 rms = 3.7168/3.6613, sse=562181.5/554654.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=536593.7, rms=3.543 (3.221%) 036: dt: 0.2500, sse=523181.2, rms=3.458 (2.410%) rms = 3.4144/3.4580, sse=516276.8/523181.2, time step reduction 2 of 3 to 0.125 0 0 1 037: dt: 0.2500, sse=516276.8, rms=3.414 (1.262%) rms = 3.3753/3.4144, sse=510869.1/516276.8, time step reduction 3 of 3 to 0.062 0 0 1 038: dt: 0.1250, sse=510869.1, rms=3.375 (1.143%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes done positioning surface Pinning medial wall to white surface Removing intersections removing intersecting faces 000: 31 intersecting 001: 5 intersecting 002: 4 intersecting terminating search with 0 intersecting #ET# mris_place_surface 5.55 minutes Writing output to ../surf/rh.pial.T1 #VMPC# mris_place_surfaces VmPeak 1337704 mris_place_surface done @#@FSTIME 2023:05:12:23:44:16 mris_place_surface N 28 e 346.83 S 0.62 U 345.68 P 99% M 960096 F 0 R 188824 W 0 c 221 w 303 I 0 O 7912 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:50:03 mris_place_surface N 28 1.00 1.01 1.04 #@# white curv lh Fri May 12 23:50:03 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2023:05:12:23:50:03 mris_place_surface N 5 e 3.19 S 0.11 U 2.99 P 97% M 154744 F 0 R 27970 W 0 c 3 w 46 I 0 O 888 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:50:06 mris_place_surface N 5 1.00 1.01 1.04 #@# white area lh Fri May 12 23:50:06 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2023:05:12:23:50:06 mris_place_surface N 3 e 1.47 S 0.10 U 1.30 P 95% M 154744 F 0 R 26423 W 0 c 3 w 27 I 0 O 888 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:50:07 mris_place_surface N 3 1.00 1.01 1.04 #@# pial curv lh Fri May 12 23:50:07 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2023:05:12:23:50:08 mris_place_surface N 5 e 3.13 S 0.11 U 2.95 P 97% M 154744 F 0 R 26948 W 0 c 3 w 38 I 0 O 888 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:50:11 mris_place_surface N 5 1.00 1.01 1.04 #@# pial area lh Fri May 12 23:50:11 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2023:05:12:23:50:11 mris_place_surface N 3 e 1.47 S 0.10 U 1.30 P 95% M 154800 F 0 R 25912 W 0 c 2 w 26 I 0 O 888 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:50:12 mris_place_surface N 3 1.00 1.01 1.04 #@# thickness lh Fri May 12 23:50:12 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 113073 vertices processed 25000 of 113073 vertices processed 50000 of 113073 vertices processed 75000 of 113073 vertices processed 100000 of 113073 vertices processed 0 of 113073 vertices processed 25000 of 113073 vertices processed 50000 of 113073 vertices processed 75000 of 113073 vertices processed 100000 of 113073 vertices processed thickness calculation complete, 797:3851 truncations. 57178 vertices at 0 distance 92523 vertices at 1 distance 44322 vertices at 2 distance 17803 vertices at 3 distance 7958 vertices at 4 distance 3398 vertices at 5 distance 1418 vertices at 6 distance 629 vertices at 7 distance 280 vertices at 8 distance 135 vertices at 9 distance 79 vertices at 10 distance 72 vertices at 11 distance 69 vertices at 12 distance 68 vertices at 13 distance 51 vertices at 14 distance 54 vertices at 15 distance 40 vertices at 16 distance 24 vertices at 17 distance 14 vertices at 18 distance 12 vertices at 19 distance 19 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2023:05:12:23:50:12 mris_place_surface N 6 e 44.82 S 0.12 U 44.62 P 99% M 154880 F 0 R 32819 W 0 c 19 w 36 I 0 O 896 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:50:57 mris_place_surface N 6 1.00 1.01 1.04 #@# area and vertex vol lh Fri May 12 23:50:57 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR lh /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.volume masking with /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Total face volume 215186 Total vertex volume 214947 (mask=0) #@# CR_t2_tra_12_SR lh 214947 vertexvol Done @#@FSTIME 2023:05:12:23:50:57 vertexvol N 4 e 3.09 S 0.19 U 2.47 P 86% M 257988 F 0 R 45520 W 0 c 13 w 235 I 16 O 2664 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:51:00 vertexvol N 4 1.00 1.01 1.04 #@# white curv rh Fri May 12 23:51:00 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2023:05:12:23:51:00 mris_place_surface N 5 e 3.17 S 0.09 U 2.99 P 97% M 153904 F 0 R 26712 W 0 c 4 w 36 I 0 O 880 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:51:04 mris_place_surface N 5 1.00 1.01 1.04 #@# white area rh Fri May 12 23:51:04 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2023:05:12:23:51:04 mris_place_surface N 3 e 1.47 S 0.10 U 1.29 P 94% M 153904 F 0 R 27210 W 0 c 3 w 34 I 0 O 880 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:51:05 mris_place_surface N 3 0.92 1.00 1.03 #@# pial curv rh Fri May 12 23:51:05 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2023:05:12:23:51:05 mris_place_surface N 5 e 3.12 S 0.10 U 2.94 P 97% M 153904 F 0 R 27222 W 0 c 4 w 37 I 0 O 880 L 0.92 1.00 1.03 @#@FSLOADPOST 2023:05:12:23:51:08 mris_place_surface N 5 0.92 1.00 1.03 #@# pial area rh Fri May 12 23:51:08 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2023:05:12:23:51:09 mris_place_surface N 3 e 1.46 S 0.10 U 1.29 P 95% M 153900 F 0 R 26699 W 0 c 2 w 30 I 0 O 880 L 0.92 1.00 1.03 @#@FSLOADPOST 2023:05:12:23:51:10 mris_place_surface N 3 1.01 1.01 1.04 #@# thickness rh Fri May 12 23:51:10 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 112490 vertices processed 25000 of 112490 vertices processed 50000 of 112490 vertices processed 75000 of 112490 vertices processed 100000 of 112490 vertices processed 0 of 112490 vertices processed 25000 of 112490 vertices processed 50000 of 112490 vertices processed 75000 of 112490 vertices processed 100000 of 112490 vertices processed thickness calculation complete, 603:3378 truncations. 57179 vertices at 0 distance 90164 vertices at 1 distance 44750 vertices at 2 distance 18551 vertices at 3 distance 8134 vertices at 4 distance 3334 vertices at 5 distance 1379 vertices at 6 distance 618 vertices at 7 distance 290 vertices at 8 distance 143 vertices at 9 distance 84 vertices at 10 distance 77 vertices at 11 distance 60 vertices at 12 distance 45 vertices at 13 distance 30 vertices at 14 distance 39 vertices at 15 distance 23 vertices at 16 distance 21 vertices at 17 distance 22 vertices at 18 distance 17 vertices at 19 distance 20 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2023:05:12:23:51:10 mris_place_surface N 6 e 44.18 S 0.11 U 43.98 P 99% M 153868 F 0 R 31532 W 0 c 17 w 40 I 0 O 888 L 1.01 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:51:54 mris_place_surface N 6 1.00 1.01 1.04 #@# area and vertex vol rh Fri May 12 23:51:54 EDT 2023 cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR rh /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.volume masking with /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Total face volume 212592 Total vertex volume 212345 (mask=0) #@# CR_t2_tra_12_SR rh 212345 vertexvol Done @#@FSTIME 2023:05:12:23:51:54 vertexvol N 4 e 2.99 S 0.17 U 2.46 P 88% M 256632 F 0 R 45624 W 0 c 10 w 194 I 0 O 2640 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:51:57 vertexvol N 4 1.00 1.01 1.04 #----------------------------------------- #@# Curvature Stats lh Fri May 12 23:51:57 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm CR_t2_tra_12_SR 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 [ CR_t2_tra_12_SR/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 [ 242 ] Gb_filter = 0 WARN: S lookup min: -0.078454 WARN: S explicit min: 0.000000 vertex = 797 @#@FSTIME 2023:05:12:23:51:57 mris_curvature_stats N 11 e 4.52 S 0.10 U 3.83 P 87% M 154836 F 0 R 27113 W 0 c 6 w 288 I 0 O 7144 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:52:02 mris_curvature_stats N 11 1.00 1.01 1.04 #----------------------------------------- #@# Curvature Stats rh Fri May 12 23:52:02 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm CR_t2_tra_12_SR 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 [ CR_t2_tra_12_SR/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 [ 249 ] Gb_filter = 0 @#@FSTIME 2023:05:12:23:52:02 mris_curvature_stats N 11 e 4.52 S 0.11 U 3.80 P 86% M 153876 F 0 R 27895 W 0 c 6 w 265 I 0 O 7080 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:52:07 mris_curvature_stats N 11 1.00 1.01 1.04 #-------------------------------------------- #@# Cortical ribbon mask Fri May 12 23:52:07 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR SUBJECTS_DIR is /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data 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 = 235 writing volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/ribbon.mgz mris_volmask took 5.79 minutes writing ribbon files @#@FSTIME 2023:05:12:23:52:07 mris_volmask N 12 e 347.12 S 0.72 U 346.12 P 99% M 876528 F 0 R 138658 W 0 c 169 w 148 I 0 O 784 L 1.00 1.01 1.04 @#@FSLOADPOST 2023:05:12:23:57:54 mris_volmask N 12 1.00 0.97 1.01 #----------------------------------------- #@# Cortical Parc 2 lh Fri May 12 23:57:54 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 CR_t2_tra_12_SR lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev//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 dev dev reading atlas from /usr/local/freesurfer/dev//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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 10 labels changed using aseg relabeling using gibbs priors... 000: 7674 changed, 113073 examined... 001: 1749 changed, 29864 examined... 002: 481 changed, 9289 examined... 003: 211 changed, 2833 examined... 004: 81 changed, 1185 examined... 005: 40 changed, 471 examined... 006: 10 changed, 246 examined... 007: 5 changed, 61 examined... 008: 3 changed, 32 examined... 009: 0 changed, 12 examined... 10 labels changed using aseg 000: 221 total segments, 137 labels (1454 vertices) changed 001: 93 total segments, 9 labels (30 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 33 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 944 vertices marked for relabeling... 944 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 23 seconds. @#@FSTIME 2023:05:12:23:57:54 mris_ca_label N 11 e 22.76 S 1.21 U 19.78 P 92% M 1539100 F 0 R 305251 W 0 c 16 w 97 I 42432 O 1776 L 1.00 0.97 1.01 @#@FSLOADPOST 2023:05:12:23:58:17 mris_ca_label N 11 0.94 0.96 1.01 #----------------------------------------- #@# Cortical Parc 2 rh Fri May 12 23:58:17 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 CR_t2_tra_12_SR rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev//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 dev dev reading atlas from /usr/local/freesurfer/dev//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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 30 labels changed using aseg relabeling using gibbs priors... 000: 7513 changed, 112490 examined... 001: 1682 changed, 29630 examined... 002: 478 changed, 8998 examined... 003: 191 changed, 2708 examined... 004: 93 changed, 1102 examined... 005: 44 changed, 554 examined... 006: 15 changed, 285 examined... 007: 12 changed, 99 examined... 008: 13 changed, 64 examined... 009: 6 changed, 64 examined... 010: 5 changed, 38 examined... 011: 2 changed, 27 examined... 012: 1 changed, 15 examined... 013: 0 changed, 7 examined... 29 labels changed using aseg 000: 196 total segments, 113 labels (1509 vertices) changed 001: 87 total segments, 4 labels (47 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... relabeling unknown label... 783 vertices marked for relabeling... 783 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 23 seconds. @#@FSTIME 2023:05:12:23:58:17 mris_ca_label N 11 e 22.55 S 1.12 U 19.73 P 92% M 1436100 F 0 R 288989 W 0 c 18 w 83 I 42776 O 1776 L 0.94 0.96 1.01 @#@FSLOADPOST 2023:05:12:23:58:40 mris_ca_label N 11 0.96 0.96 1.01 #----------------------------------------- #@# Cortical Parc 3 lh Fri May 12 23:58:40 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 CR_t2_tra_12_SR lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev//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 dev dev reading atlas from /usr/local/freesurfer/dev//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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1028 labels changed using aseg relabeling using gibbs priors... 000: 1653 changed, 113073 examined... 001: 390 changed, 7795 examined... 002: 121 changed, 2247 examined... 003: 61 changed, 729 examined... 004: 34 changed, 343 examined... 005: 23 changed, 195 examined... 006: 14 changed, 129 examined... 007: 8 changed, 83 examined... 008: 5 changed, 51 examined... 009: 1 changed, 29 examined... 010: 1 changed, 8 examined... 011: 0 changed, 7 examined... 212 labels changed using aseg 000: 44 total segments, 11 labels (67 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 8 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 613 vertices marked for relabeling... 613 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 18 seconds. @#@FSTIME 2023:05:12:23:58:40 mris_ca_label N 11 e 17.55 S 0.56 U 15.27 P 90% M 828884 F 0 R 146366 W 0 c 18 w 78 I 42976 O 1776 L 1.12 0.99 1.02 @#@FSLOADPOST 2023:05:12:23:58:57 mris_ca_label N 11 1.01 0.98 1.01 #----------------------------------------- #@# Cortical Parc 3 rh Fri May 12 23:58:57 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 CR_t2_tra_12_SR rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev//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 dev dev reading atlas from /usr/local/freesurfer/dev//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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.smoothwm... GCSA::load_default_data(): ninputs=1 sulc_only=0 which_norm=0 labeling surface... 1037 labels changed using aseg relabeling using gibbs priors... 000: 1744 changed, 112490 examined... 001: 403 changed, 8007 examined... 002: 123 changed, 2288 examined... 003: 47 changed, 725 examined... 004: 24 changed, 275 examined... 005: 13 changed, 140 examined... 006: 10 changed, 76 examined... 007: 8 changed, 57 examined... 008: 5 changed, 40 examined... 009: 5 changed, 31 examined... 010: 3 changed, 29 examined... 011: 4 changed, 22 examined... 012: 3 changed, 23 examined... 013: 5 changed, 22 examined... 014: 4 changed, 31 examined... 015: 5 changed, 17 examined... 016: 3 changed, 21 examined... 017: 1 changed, 18 examined... 018: 1 changed, 7 examined... 019: 2 changed, 8 examined... 020: 1 changed, 12 examined... 021: 0 changed, 7 examined... 269 labels changed using aseg 000: 45 total segments, 12 labels (264 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 367 vertices marked for relabeling... 367 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 18 seconds. @#@FSTIME 2023:05:12:23:58:57 mris_ca_label N 11 e 17.81 S 0.53 U 15.56 P 90% M 831488 F 0 R 147724 W 0 c 23 w 84 I 42952 O 1776 L 1.01 0.98 1.01 @#@FSLOADPOST 2023:05:12:23:59:15 mris_ca_label N 11 1.01 0.98 1.01 #----------------------------------------- #@# WM/GM Contrast lh Fri May 12 23:59:15 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts pctsurfcon --s CR_t2_tra_12_SR --lh-only Log file is /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts/pctsurfcon.log Fri May 12 23:59:15 EDT 2023 setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts /usr/local/freesurfer/dev//bin/pctsurfcon pctsurfcon dev Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev/ mri_vol2surf --mov /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4228/lh.wm.mgh --regheader CR_t2_tra_12_SR --cortex srcvol = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99699 -0.02442 -0.07352 0.00000; 0.06632 -0.22154 0.97289 -0.00002; -0.04004 -0.97485 -0.21925 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Reading surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 = 70382 Masking with /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Writing to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4228/lh.wm.mgh Dim: 113073 1 1 mri_vol2surf done mri_vol2surf --mov /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4228/lh.gm.mgh --projfrac 0.3 --regheader CR_t2_tra_12_SR --cortex srcvol = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99699 -0.02442 -0.07352 0.00000; 0.06632 -0.22154 0.97289 -0.00002; -0.04004 -0.97485 -0.21925 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Reading surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Done reading source surface Reading thickness /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 = 76350 Masking with /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Writing to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4228/lh.gm.mgh Dim: 113073 1 1 mri_vol2surf done mri_concat /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4228/lh.wm.mgh /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4228/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.w-g.pct.mgh --annot CR_t2_tra_12_SR lh aparc --sum /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/stats/lh.w-g.pct.stats --snr dev cwd cmdline mri_segstats --in /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.w-g.pct.mgh --annot CR_t2_tra_12_SR lh aparc --sum /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.annot Seg base 1000 MRISannot2seg(): nhits = 106083 Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.w-g.pct.mgh Vertex Area is 0.690877 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up @#@FSTIME 2023:05:12:23:59:15 pctsurfcon N 3 e 4.97 S 0.35 U 4.12 P 90% M 172160 F 0 R 76356 W 0 c 32 w 288 I 24 O 2832 L 1.01 0.98 1.01 @#@FSLOADPOST 2023:05:12:23:59:20 pctsurfcon N 3 1.01 0.98 1.01 #----------------------------------------- #@# WM/GM Contrast rh Fri May 12 23:59:20 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts pctsurfcon --s CR_t2_tra_12_SR --rh-only Log file is /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts/pctsurfcon.log Fri May 12 23:59:21 EDT 2023 setenv SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data cd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/scripts /usr/local/freesurfer/dev//bin/pctsurfcon pctsurfcon dev Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev/ mri_vol2surf --mov /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4297/rh.wm.mgh --regheader CR_t2_tra_12_SR --cortex srcvol = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99699 -0.02442 -0.07352 0.00000; 0.06632 -0.22154 0.97289 -0.00002; -0.04004 -0.97485 -0.21925 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Reading surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 = 70435 Masking with /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Writing to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4297/rh.wm.mgh Dim: 112490 1 1 mri_vol2surf done mri_vol2surf --mov /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4297/rh.gm.mgh --projfrac 0.3 --regheader CR_t2_tra_12_SR --cortex srcvol = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99699 -0.02442 -0.07352 0.00000; 0.06632 -0.22154 0.97289 -0.00002; -0.04004 -0.97485 -0.21925 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Reading surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white Done reading source surface Reading thickness /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 = 76008 Masking with /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Writing to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4297/rh.gm.mgh Dim: 112490 1 1 mri_vol2surf done mri_concat /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4297/rh.wm.mgh /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/tmp.pctsurfcon.4297/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.w-g.pct.mgh --annot CR_t2_tra_12_SR rh aparc --sum /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/stats/rh.w-g.pct.stats --snr dev cwd cmdline mri_segstats --in /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.w-g.pct.mgh --annot CR_t2_tra_12_SR rh aparc --sum /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.aparc.annot Seg base 2000 MRISannot2seg(): nhits = 105336 Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.w-g.pct.mgh Vertex Area is 0.695892 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up @#@FSTIME 2023:05:12:23:59:20 pctsurfcon N 3 e 4.91 S 0.34 U 4.08 P 90% M 171528 F 0 R 75416 W 0 c 28 w 284 I 0 O 2832 L 1.01 0.98 1.01 @#@FSLOADPOST 2023:05:12:23:59:25 pctsurfcon N 3 1.01 0.98 1.01 #----------------------------------------- #@# Relabel Hypointensities Fri May 12 23:59:25 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3371 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3831 voxels changed to hypointensity... 6585 hypointense voxels neighboring cortex changed @#@FSTIME 2023:05:12:23:59:25 mri_relabel_hypointensities N 3 e 27.03 S 0.45 U 26.47 P 99% M 461384 F 0 R 58578 W 0 c 22 w 41 I 0 O 624 L 1.01 0.98 1.01 @#@FSLOADPOST 2023:05:12:23:59:52 mri_relabel_hypointensities N 3 1.01 0.98 1.01 #----------------------------------------- #@# APas-to-ASeg Fri May 12 23:59:53 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/ribbon.mgz --threads 1 --lh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label --lh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white --lh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial --rh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label --rh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white --rh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data outvol aseg.mgz 8 avail.processors, using 1 Loading aseg.presurf.hypos.mgz Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/ribbon.mgz Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 948516 mri_surf2volseg done @#@FSTIME 2023:05:12:23:59:53 mri_surf2volseg N 20 e 28.37 S 0.43 U 27.75 P 99% M 794768 F 0 R 87538 W 0 c 27 w 87 I 0 O 640 L 1.01 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:00:21 mri_surf2volseg N 20 1.00 0.99 1.01 mri_brainvol_stats --subject CR_t2_tra_12_SR ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1340690.0 #CBVS2 BrainSegVol 997466.0 #CBVS2 BrainSegVolNotVent 978306.0 #CBVS2 SupraTentVol 897011.0 #CBVS2 SupraTentVolNotVent 877851.0 #CBVS2 lhCtxGM 214604.2 #CBVS2 rhCtxGM 212126.4 #CBVS2 lhCerebralWM 202900.0 #CBVS2 rhCerebralWM 201478.0 #CBVS2 SubCortGMVol 47397.0 #CBVS2 CerebellumVol 100455.0 #CBVS2 CerebellumGMVol 83497.0 #CBVS2 VentChorVol 15600.0 #CBVS2 3rd4th5thCSF 3560.0 #CBVS2 AllCSF 19160.0 #CBVS2 CCVol 2418.0 @#@FSTIME 2023:05:13:00:00:21 mri_brainvol_stats N 2 e 8.97 S 0.22 U 8.29 P 94% M 196084 F 1 R 51519 W 0 c 11 w 64 I 7256 O 16 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:00:30 mri_brainvol_stats N 2 1.08 1.00 1.02 #----------------------------------------- #@# AParc-to-ASeg aparc Sat May 13 00:00:30 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.annot 1000 --lh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label --lh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white --lh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial --rh-annot /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.aparc.annot 2000 --rh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label --rh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white --rh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data outvol aparc+aseg.mgz 8 avail.processors, using 1 Loading aseg.mgz Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 6990 vertices from lh hemi Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.annot Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7154 vertices from rh hemi Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 = 23747 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 931660 mri_surf2volseg done @#@FSTIME 2023:05:13:00:00:30 mri_surf2volseg N 25 e 232.28 S 0.40 U 231.69 P 99% M 778104 F 0 R 90007 W 0 c 75 w 93 I 0 O 752 L 1.08 1.00 1.02 @#@FSLOADPOST 2023:05:13:00:04:22 mri_surf2volseg N 25 1.00 1.00 1.02 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Sat May 13 00:04:22 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label --lh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white --lh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial --rh-annot /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label --rh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white --rh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data outvol aparc.a2009s+aseg.mgz 8 avail.processors, using 1 Loading aseg.mgz Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 6990 vertices from lh hemi Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.a2009s.annot Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7154 vertices from rh hemi Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 = 23747 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 931752 mri_surf2volseg done @#@FSTIME 2023:05:13:00:04:23 mri_surf2volseg N 25 e 232.49 S 0.41 U 231.85 P 99% M 778196 F 0 R 85936 W 0 c 185 w 114 I 0 O 808 L 1.00 1.00 1.02 @#@FSLOADPOST 2023:05:13:00:08:15 mri_surf2volseg N 25 1.00 1.00 1.02 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Sat May 13 00:08:15 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label --lh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white --lh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial --rh-annot /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label --rh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white --rh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data outvol aparc.DKTatlas+aseg.mgz 8 avail.processors, using 1 Loading aseg.mgz Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 6990 vertices from lh hemi Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.DKTatlas.annot Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7154 vertices from rh hemi Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 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/autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.annot 3000 --lh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label --lh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white --lh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial --rh-annot /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.aparc.annot 4000 --rh-cortex-mask /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label --rh-white /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white --rh-pial /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data outvol wmparc.mgz 8 avail.processors, using 1 Loading aparc+aseg.mgz Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 6990 vertices from lh hemi Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.aparc.annot Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 7154 vertices from rh hemi Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 = 3218 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 931660 mri_surf2volseg done @#@FSTIME 2023:05:13:00:12:08 mri_surf2volseg N 25 e 64.26 S 0.44 U 63.58 P 99% M 778068 F 0 R 88475 W 0 c 32 w 119 I 0 O 832 L 1.06 1.03 1.03 @#@FSLOADPOST 2023:05:13:00:13:12 mri_surf2volseg N 25 1.02 1.02 1.03 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 CR_t2_tra_12_SR --surf-wm-vol --ctab /usr/local/freesurfer/dev//WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 dev 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 CR_t2_tra_12_SR --surf-wm-vol --ctab /usr/local/freesurfer/dev//WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1265446 mm^3 (det: 1.539462 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2023:05:13:00:13:12 mri_segstats N 24 e 673.48 S 0.45 U 672.88 P 99% M 238280 F 0 R 76777 W 0 c 652 w 65 I 56 O 32 L 1.02 1.02 1.03 @#@FSLOADPOST 2023:05:13:00:24:26 mri_segstats N 24 1.02 1.06 1.05 #----------------------------------------- #@# Parcellation Stats lh Sat May 13 00:24:26 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/wm.mgz... reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white... reading input pial surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial... reading input white surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 215186 Total vertex volume 214947 (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) = 1265446 mm^3 (det: 1.539462 ) 1348 863 1865 2.433 0.599 0.068 0.011 3 0.5 bankssts 698 479 1151 2.511 0.511 0.123 0.016 7 0.5 caudalanteriorcingulate 3199 2094 5685 2.447 0.783 0.106 0.021 21 2.7 caudalmiddlefrontal 1404 1184 2932 2.335 0.867 0.164 0.044 15 2.9 cuneus 599 390 1547 3.230 0.900 0.093 0.019 3 0.4 entorhinal 3694 2701 10692 2.938 0.906 0.135 0.030 41 4.9 fusiform 6193 4253 9914 2.155 0.705 0.118 0.026 47 7.1 inferiorparietal 4722 3281 12387 2.819 0.939 0.106 0.024 40 4.9 inferiortemporal 1159 781 2127 2.559 0.853 0.119 0.032 10 1.4 isthmuscingulate 6156 4435 13207 2.498 0.775 0.142 0.038 58 10.0 lateraloccipital 2941 2017 7726 3.026 0.982 0.108 0.020 23 2.6 lateralorbitofrontal 2789 2228 5659 2.312 0.732 0.150 0.040 32 4.8 lingual 2014 1489 5751 3.096 0.976 0.107 0.024 19 1.8 medialorbitofrontal 4230 2911 10061 2.716 0.884 0.115 0.027 33 4.8 middletemporal 922 569 1709 2.473 0.917 0.068 0.009 3 0.3 parahippocampal 1863 1181 3003 2.421 0.689 0.101 0.021 11 1.6 paracentral 1702 1167 3487 2.484 0.764 0.111 0.022 12 1.6 parsopercularis 752 517 2923 3.530 1.025 0.122 0.024 8 0.7 parsorbitalis 1256 861 3016 2.866 0.869 0.112 0.025 9 1.3 parstriangularis 1330 990 1928 2.042 0.512 0.127 0.036 12 1.9 pericalcarine 5777 3796 8307 1.946 0.733 0.097 0.020 35 4.8 postcentral 1198 810 1665 2.171 0.647 0.116 0.022 10 1.1 posteriorcingulate 6603 4327 10359 2.222 0.718 0.104 0.022 42 6.0 precentral 4840 3399 7922 2.209 0.790 0.115 0.026 37 5.6 precuneus 845 600 2262 3.013 1.061 0.111 0.026 7 0.9 rostralanteriorcingulate 5960 4369 12784 2.557 0.788 0.126 0.030 53 7.5 rostralmiddlefrontal 10077 6987 24985 2.924 0.839 0.114 0.028 76 11.4 superiorfrontal 8964 5993 12665 1.961 0.676 0.123 0.028 76 10.3 superiorparietal 4361 3110 8961 2.406 0.852 0.090 0.017 25 3.1 superiortemporal 4345 3088 7174 2.111 0.740 0.126 0.029 35 5.5 supramarginal 282 212 1376 3.583 0.907 0.145 0.035 4 0.4 frontalpole 612 473 3269 4.253 0.665 0.123 0.030 6 0.8 temporalpole 471 355 728 2.036 0.503 0.146 0.028 5 0.4 transversetemporal 2777 1929 5719 2.866 0.962 0.119 0.032 27 3.9 insula @#@FSTIME 2023:05:13:00:24:26 mris_anatomical_stats N 14 e 15.72 S 0.26 U 15.09 P 97% M 400692 F 0 R 62145 W 0 c 15 w 156 I 0 O 296 L 1.02 1.06 1.05 @#@FSLOADPOST 2023:05:13:00:24:42 mris_anatomical_stats N 14 1.01 1.06 1.05 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 CR_t2_tra_12_SR lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/wm.mgz... reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial... reading input pial surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial... reading input white surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 215186 Total vertex volume 214947 (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) = 1265446 mm^3 (det: 1.539462 ) 1348 704 1865 2.433 0.599 0.077 0.044 78 0.9 bankssts 698 469 1151 2.511 0.511 0.102 0.020 5 0.6 caudalanteriorcingulate 3199 2481 5685 2.447 0.783 0.112 0.024 39 3.2 caudalmiddlefrontal 1404 1478 2932 2.335 0.867 0.170 0.039 26 2.3 cuneus 599 649 1547 3.230 0.900 0.266 0.071 27 2.0 entorhinal 3694 4232 10692 2.938 0.906 0.182 0.049 75 7.1 fusiform 6193 4968 9914 2.155 0.705 0.120 0.026 65 6.7 inferiorparietal 4722 4875 12387 2.819 0.939 0.152 0.033 80 7.0 inferiortemporal 1159 945 2127 2.559 0.853 0.147 0.038 25 1.9 isthmuscingulate 6156 5897 13207 2.498 0.775 0.155 0.040 160 10.7 lateraloccipital 2941 2816 7726 3.026 0.982 0.160 0.037 43 5.0 lateralorbitofrontal 2789 2844 5659 2.312 0.732 0.173 0.043 66 5.2 lingual 2014 2229 5751 3.096 0.976 0.187 0.045 43 4.2 medialorbitofrontal 4230 4239 10061 2.716 0.884 0.156 0.034 128 6.5 middletemporal 922 819 1709 2.473 0.917 0.145 0.034 11 1.5 parahippocampal 1863 1362 3003 2.421 0.689 0.099 0.020 14 1.6 paracentral 1702 1594 3487 2.484 0.764 0.147 0.033 25 2.5 parsopercularis 752 1035 2923 3.530 1.025 0.232 0.059 24 2.1 parsorbitalis 1256 1131 3016 2.866 0.869 0.125 0.025 14 1.3 parstriangularis 1330 925 1928 2.042 0.512 0.139 0.038 43 2.0 pericalcarine 5777 4757 8307 1.946 0.733 0.114 0.023 46 5.9 postcentral 1198 793 1665 2.171 0.647 0.113 0.027 17 1.3 posteriorcingulate 6603 4932 10359 2.222 0.718 0.107 0.025 83 6.4 precentral 4840 4044 7922 2.209 0.790 0.137 0.038 71 6.7 precuneus 845 836 2262 3.013 1.061 0.146 0.030 7 1.0 rostralanteriorcingulate 5960 5534 12784 2.557 0.788 0.155 0.035 97 9.1 rostralmiddlefrontal 10077 9448 24985 2.924 0.839 0.150 0.036 164 15.2 superiorfrontal 8964 7143 12665 1.961 0.676 0.132 0.031 114 11.4 superiorparietal 4361 4036 8961 2.406 0.852 0.127 0.025 40 4.9 superiortemporal 4345 3762 7174 2.111 0.740 0.136 0.029 59 5.5 supramarginal 282 501 1376 3.583 0.907 0.241 0.034 2 0.5 frontalpole 612 1025 3269 4.253 0.665 0.199 0.040 8 0.9 temporalpole 471 418 728 2.036 0.503 0.147 0.032 7 0.5 transversetemporal 2777 2130 5719 2.866 0.962 0.169 0.047 68 5.9 insula @#@FSTIME 2023:05:13:00:24:42 mris_anatomical_stats N 14 e 15.61 S 0.29 U 14.98 P 97% M 400696 F 0 R 63166 W 0 c 16 w 142 I 0 O 296 L 1.01 1.06 1.05 @#@FSLOADPOST 2023:05:13:00:24:57 mris_anatomical_stats N 14 1.01 1.05 1.05 #----------------------------------------- #@# Parcellation Stats rh Sat May 13 00:24:57 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/wm.mgz... reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white... reading input pial surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial... reading input white surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 212592 Total vertex volume 212345 (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) = 1265446 mm^3 (det: 1.539462 ) 1316 887 1650 2.024 0.519 0.091 0.016 7 1.1 bankssts 869 619 2190 2.778 0.729 0.125 0.025 8 1.0 caudalanteriorcingulate 3000 2095 4593 2.159 0.582 0.109 0.023 20 2.9 caudalmiddlefrontal 1705 1442 3256 2.120 0.515 0.170 0.048 21 3.7 cuneus 495 313 1249 3.116 0.700 0.100 0.018 4 0.3 entorhinal 2980 2105 7700 2.844 0.915 0.127 0.028 29 3.3 fusiform 6943 5133 12107 2.202 0.666 0.138 0.035 66 10.6 inferiorparietal 4146 2873 12261 2.924 1.057 0.106 0.021 32 4.0 inferiortemporal 1005 710 2075 2.585 0.878 0.132 0.032 10 1.2 isthmuscingulate 6527 4680 14368 2.593 0.734 0.138 0.037 61 10.4 lateraloccipital 3077 2118 7797 3.113 0.869 0.120 0.025 25 3.2 lateralorbitofrontal 3043 2348 6778 2.464 0.703 0.148 0.038 34 4.9 lingual 2419 1732 6487 3.162 0.941 0.116 0.027 26 2.9 medialorbitofrontal 4148 2859 9327 2.592 0.923 0.112 0.023 33 4.0 middletemporal 733 438 1663 2.895 1.166 0.087 0.023 6 0.6 parahippocampal 2023 1206 3052 2.345 0.755 0.101 0.020 14 1.7 paracentral 1406 971 2928 2.596 0.782 0.108 0.023 10 1.5 parsopercularis 1016 692 3461 3.322 0.933 0.120 0.029 9 1.1 parsorbitalis 1353 928 2500 2.454 0.750 0.097 0.017 8 0.9 parstriangularis 1624 1252 2103 1.704 0.491 0.152 0.050 30 3.2 pericalcarine 5302 3506 7716 1.947 0.793 0.101 0.021 33 4.8 postcentral 1227 922 2299 2.418 0.736 0.146 0.040 12 2.2 posteriorcingulate 6153 4072 9699 2.208 0.764 0.102 0.022 40 5.5 precentral 5067 3429 7787 2.275 0.848 0.107 0.024 36 4.7 precuneus 589 439 1871 3.158 0.801 0.108 0.021 5 0.5 rostralanteriorcingulate 7841 5547 15521 2.387 0.799 0.124 0.032 70 10.3 rostralmiddlefrontal 8556 5961 21185 2.898 0.919 0.120 0.027 69 9.6 superiorfrontal 7990 5694 11896 1.925 0.580 0.127 0.028 67 10.2 superiorparietal 4792 3502 10213 2.435 0.937 0.114 0.025 36 5.6 superiortemporal 4086 2741 5961 2.047 0.662 0.109 0.021 28 3.5 supramarginal 452 350 1962 3.659 0.644 0.177 0.053 6 1.2 frontalpole 624 458 2893 3.827 0.723 0.121 0.035 6 0.8 temporalpole 399 268 540 1.953 0.533 0.125 0.025 4 0.4 transversetemporal 2430 1640 5256 3.117 0.920 0.105 0.024 18 2.1 insula @#@FSTIME 2023:05:13:00:24:57 mris_anatomical_stats N 14 e 15.18 S 0.27 U 14.56 P 97% M 398656 F 0 R 62047 W 0 c 18 w 148 I 0 O 304 L 1.01 1.05 1.05 @#@FSLOADPOST 2023:05:13:00:25:12 mris_anatomical_stats N 14 1.01 1.05 1.05 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 CR_t2_tra_12_SR rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/wm.mgz... reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial... reading input pial surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial... reading input white surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 212592 Total vertex volume 212345 (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) = 1265446 mm^3 (det: 1.539462 ) 1316 809 1650 2.024 0.519 0.094 0.026 62 1.1 bankssts 869 886 2190 2.778 0.729 0.195 0.053 28 1.9 caudalanteriorcingulate 3000 2295 4593 2.159 0.582 0.121 0.027 49 3.5 caudalmiddlefrontal 1705 1803 3256 2.120 0.515 0.180 0.046 37 3.5 cuneus 495 564 1249 3.116 0.700 0.320 0.082 33 2.2 entorhinal 2980 2951 7700 2.844 0.915 0.160 0.038 66 5.0 fusiform 6943 6123 12107 2.202 0.666 0.155 0.039 135 11.4 inferiorparietal 4146 4713 12261 2.924 1.057 0.170 0.034 96 6.5 inferiortemporal 1005 905 2075 2.585 0.878 0.161 0.047 31 1.8 isthmuscingulate 6527 6257 14368 2.593 0.734 0.156 0.040 158 10.7 lateraloccipital 3077 2741 7797 3.113 0.869 0.159 0.043 73 5.7 lateralorbitofrontal 3043 3183 6778 2.464 0.703 0.170 0.040 98 5.4 lingual 2419 2426 6487 3.162 0.941 0.174 0.044 59 4.7 medialorbitofrontal 4148 4059 9327 2.592 0.923 0.148 0.031 63 6.0 middletemporal 733 635 1663 2.895 1.166 0.124 0.037 7 0.8 parahippocampal 2023 1417 3052 2.345 0.755 0.103 0.025 20 1.9 paracentral 1406 1291 2928 2.596 0.782 0.143 0.031 14 2.2 parsopercularis 1016 1325 3461 3.322 0.933 0.203 0.042 15 2.1 parsorbitalis 1353 1145 2500 2.454 0.750 0.133 0.031 18 1.7 parstriangularis 1624 1296 2103 1.704 0.491 0.160 0.047 56 2.9 pericalcarine 5302 4399 7716 1.947 0.793 0.114 0.024 42 5.2 postcentral 1227 1065 2299 2.418 0.736 0.159 0.043 25 2.3 posteriorcingulate 6153 4651 9699 2.208 0.764 0.119 0.024 15652 5.7 precentral 5067 3615 7787 2.275 0.848 0.123 0.031 79 6.2 precuneus 589 702 1871 3.158 0.801 0.190 0.040 13 0.9 rostralanteriorcingulate 7841 7141 15521 2.387 0.799 0.158 0.035 147 12.3 rostralmiddlefrontal 8556 8108 21185 2.898 0.919 0.148 0.034 121 12.9 superiorfrontal 7990 7020 11896 1.925 0.580 0.145 0.036 1632 11.0 superiorparietal 4792 4563 10213 2.435 0.937 0.143 0.033 59 6.7 superiortemporal 4086 3097 5961 2.047 0.662 0.117 0.027 58 4.5 supramarginal 452 725 1962 3.659 0.644 0.212 0.035 4 0.8 frontalpole 624 1003 2893 3.827 0.723 0.219 0.040 8 1.3 temporalpole 399 320 540 1.953 0.533 0.114 0.029 2 0.4 transversetemporal 2430 1598 5256 3.117 0.920 0.140 0.037 68 3.7 insula @#@FSTIME 2023:05:13:00:25:13 mris_anatomical_stats N 14 e 15.14 S 0.28 U 14.52 P 97% M 398656 F 0 R 60515 W 0 c 17 w 144 I 0 O 296 L 1.01 1.05 1.05 @#@FSLOADPOST 2023:05:13:00:25:28 mris_anatomical_stats N 14 1.01 1.05 1.05 #----------------------------------------- #@# Parcellation Stats 2 lh Sat May 13 00:25:28 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/wm.mgz... reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white... reading input pial surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial... reading input white surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 215186 Total vertex volume 214947 (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) = 1265446 mm^3 (det: 1.539462 ) 904 665 2522 2.963 0.863 0.118 0.028 8 0.9 G_and_S_frontomargin 1180 813 2894 2.739 0.826 0.123 0.035 10 1.5 G_and_S_occipital_inf 1503 950 2968 2.430 0.768 0.097 0.022 9 1.3 G_and_S_paracentral 1150 817 2771 2.757 0.759 0.121 0.029 11 1.3 G_and_S_subcentral 468 353 1737 3.377 0.800 0.130 0.037 5 0.7 G_and_S_transv_frontopol 1856 1362 4486 3.001 0.829 0.116 0.027 14 2.1 G_and_S_cingul-Ant 1267 872 2089 2.465 0.536 0.111 0.017 9 1.0 G_and_S_cingul-Mid-Ant 1240 827 1926 2.372 0.631 0.106 0.018 8 0.9 G_and_S_cingul-Mid-Post 420 328 972 2.472 0.597 0.149 0.040 4 0.7 G_cingul-Post-dorsal 295 199 773 3.173 0.807 0.118 0.033 3 0.3 G_cingul-Post-ventral 1294 1194 3030 2.370 0.864 0.188 0.056 17 3.4 G_cuneus 930 663 2640 2.829 0.855 0.120 0.026 8 0.9 G_front_inf-Opercular 313 200 1143 3.311 0.988 0.104 0.027 3 0.3 G_front_inf-Orbital 745 526 2447 3.234 0.860 0.127 0.036 7 1.1 G_front_inf-Triangul 3614 2648 9172 2.576 0.872 0.139 0.033 40 5.1 G_front_middle 6134 4247 18308 3.187 0.856 0.120 0.032 54 7.9 G_front_sup 543 428 1246 2.981 1.066 0.150 0.039 8 0.9 G_Ins_lg_and_S_cent_ins 605 428 2097 3.483 0.947 0.135 0.042 8 1.1 G_insular_short 1727 1351 4211 2.496 0.692 0.164 0.045 22 3.1 G_occipital_middle 1361 967 2439 2.283 0.675 0.139 0.036 12 2.1 G_occipital_sup 1644 1229 4967 3.036 0.839 0.136 0.030 20 2.2 G_oc-temp_lat-fusifor 2017 1723 4708 2.293 0.741 0.168 0.048 28 4.2 G_oc-temp_med-Lingual 1272 822 3303 2.998 0.890 0.095 0.021 8 1.0 G_oc-temp_med-Parahip 1799 1278 7142 3.726 0.859 0.118 0.025 18 1.9 G_orbital 2211 1527 4063 2.243 0.724 0.133 0.036 20 3.6 G_pariet_inf-Angular 2037 1544 4441 2.354 0.829 0.140 0.035 20 3.1 G_pariet_inf-Supramar 3705 2402 6134 2.109 0.780 0.120 0.028 34 4.3 G_parietal_sup 2341 1515 3681 1.993 0.681 0.111 0.025 17 2.5 G_postcentral 2432 1584 4741 2.299 0.831 0.109 0.026 18 2.5 G_precentral 2492 1942 5199 2.153 0.737 0.145 0.036 27 4.1 G_precuneus 670 553 2676 3.302 0.760 0.132 0.031 11 0.8 G_rectus 617 407 992 2.405 0.974 0.133 0.044 7 1.3 G_subcallosal 313 248 601 2.107 0.478 0.155 0.031 4 0.3 G_temp_sup-G_T_transv 1400 1181 4813 2.899 0.788 0.143 0.033 17 1.9 G_temp_sup-Lateral 657 463 1709 3.275 0.966 0.056 0.011 1 0.2 G_temp_sup-Plan_polar 704 478 964 1.836 0.630 0.056 0.010 2 0.2 G_temp_sup-Plan_tempo 2210 1620 8374 3.257 1.044 0.123 0.031 27 3.1 G_temporal_inf 2444 1730 7277 2.997 0.898 0.128 0.033 24 3.3 G_temporal_middle 197 130 258 2.466 0.656 0.099 0.011 1 0.1 Lat_Fis-ant-Horizont 176 122 229 2.209 0.652 0.123 0.028 1 0.2 Lat_Fis-ant-Vertical 804 507 848 2.192 0.789 0.094 0.016 3 0.6 Lat_Fis-post 1827 1416 5159 2.667 0.907 0.165 0.044 20 3.8 Pole_occipital 1449 1064 6949 3.841 0.913 0.137 0.031 17 2.0 Pole_temporal 1722 1194 2487 2.378 0.697 0.113 0.027 12 1.9 S_calcarine 2958 1917 2744 1.722 0.448 0.092 0.017 15 2.0 S_central 923 577 1015 1.930 0.747 0.096 0.018 6 0.7 S_cingul-Marginalis 390 254 541 2.550 0.480 0.075 0.010 1 0.2 S_circular_insula_ant 1191 764 1470 2.332 0.936 0.081 0.017 6 0.8 S_circular_insula_inf 1363 865 1763 2.415 0.586 0.086 0.015 5 0.8 S_circular_insula_sup 1035 658 1771 2.593 0.678 0.085 0.011 4 0.5 S_collat_transv_ant 232 169 263 2.062 0.308 0.155 0.037 2 0.4 S_collat_transv_post 1705 1089 2164 2.223 0.569 0.090 0.015 7 1.0 S_front_inf 1107 784 1616 2.549 0.674 0.102 0.024 5 1.0 S_front_middle 3106 2168 4832 2.314 0.622 0.107 0.022 18 3.1 S_front_sup 210 140 170 1.566 0.285 0.130 0.029 2 0.4 S_interm_prim-Jensen 2981 2007 3110 1.773 0.460 0.122 0.027 23 3.3 S_intrapariet_and_P_trans 692 467 800 2.082 0.285 0.113 0.021 4 0.6 S_oc_middle_and_Lunatus 1221 820 1366 1.983 0.444 0.119 0.027 8 1.3 S_oc_sup_and_transversal 906 642 1149 2.274 0.558 0.124 0.032 6 1.3 S_occipital_ant 663 482 1129 2.336 0.459 0.115 0.030 5 0.8 S_oc-temp_lat 1385 941 2050 2.155 0.668 0.101 0.020 9 1.0 S_oc-temp_med_and_Lingual 151 110 183 1.762 0.329 0.085 0.007 1 0.0 S_orbital_lateral 433 329 921 2.493 0.983 0.129 0.025 4 0.5 S_orbital_med-olfact 1258 858 2630 2.658 0.894 0.111 0.020 10 1.2 S_orbital-H_Shaped 1478 964 1998 2.332 0.820 0.096 0.019 8 1.1 S_parieto_occipital 876 540 1112 2.380 0.730 0.106 0.025 7 0.9 S_pericallosal 3192 2051 2999 1.666 0.402 0.102 0.017 18 2.5 S_postcentral 1199 778 1434 2.257 0.626 0.080 0.015 4 0.6 S_precentral-inf-part 1497 977 1941 2.434 0.484 0.099 0.018 8 1.0 S_precentral-sup-part 532 345 1179 3.147 1.008 0.078 0.008 2 0.2 S_suborbital 1129 734 1043 1.760 0.395 0.101 0.018 6 0.8 S_subparietal 2030 1331 2369 2.151 0.343 0.101 0.019 10 1.7 S_temporal_inf 5337 3418 7334 2.235 0.671 0.078 0.013 20 2.7 S_temporal_sup 214 142 268 2.113 0.512 0.086 0.012 1 0.1 S_temporal_transverse @#@FSTIME 2023:05:13:00:25:28 mris_anatomical_stats N 14 e 17.45 S 0.28 U 16.59 P 96% M 400696 F 0 R 61163 W 0 c 19 w 237 I 0 O 632 L 1.01 1.05 1.05 @#@FSLOADPOST 2023:05:13:00:25:45 mris_anatomical_stats N 14 0.94 1.03 1.04 #----------------------------------------- #@# Parcellation Stats 2 rh Sat May 13 00:25:45 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/wm.mgz... reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white... reading input pial surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial... reading input white surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 212592 Total vertex volume 212345 (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) = 1265446 mm^3 (det: 1.539462 ) 930 664 2643 3.049 0.871 0.138 0.040 9 1.7 G_and_S_frontomargin 869 622 2529 2.975 0.854 0.131 0.034 8 1.1 G_and_S_occipital_inf 1245 776 2214 2.408 0.759 0.108 0.024 9 1.2 G_and_S_paracentral 1227 864 2854 2.775 0.797 0.129 0.034 11 1.8 G_and_S_subcentral 923 662 3131 3.358 0.963 0.126 0.035 8 1.3 G_and_S_transv_frontopol 2354 1715 6296 3.185 0.744 0.113 0.026 19 2.5 G_and_S_cingul-Ant 1054 741 2177 2.719 0.581 0.121 0.024 8 1.1 G_and_S_cingul-Mid-Ant 1052 738 1845 2.472 0.763 0.115 0.028 7 1.3 G_and_S_cingul-Mid-Post 353 306 793 2.306 0.510 0.192 0.056 5 0.8 G_cingul-Post-dorsal 267 168 812 3.362 0.765 0.114 0.025 2 0.2 G_cingul-Post-ventral 1704 1546 3579 2.117 0.572 0.194 0.058 25 4.7 G_cuneus 964 719 2839 2.819 0.874 0.126 0.032 10 1.3 G_front_inf-Opercular 329 204 1097 3.317 0.673 0.097 0.020 2 0.3 G_front_inf-Orbital 475 356 1160 2.373 0.759 0.126 0.027 4 0.5 G_front_inf-Triangul 3044 2316 7044 2.303 0.768 0.141 0.035 37 4.6 G_front_middle 5900 4108 16974 3.072 0.949 0.126 0.030 55 7.4 G_front_sup 473 355 1335 3.487 0.942 0.140 0.040 7 0.7 G_Ins_lg_and_S_cent_ins 476 342 1627 3.564 0.851 0.139 0.039 5 0.8 G_insular_short 1907 1417 5155 2.698 0.838 0.148 0.036 22 3.1 G_occipital_middle 1402 1015 2545 2.218 0.521 0.144 0.034 14 2.3 G_occipital_sup 1145 898 3922 3.196 0.709 0.151 0.041 16 2.0 G_oc-temp_lat-fusifor 1902 1539 4730 2.511 0.796 0.155 0.040 23 3.2 G_oc-temp_med-Lingual 1039 631 2957 3.281 0.855 0.103 0.026 10 1.0 G_oc-temp_med-Parahip 2102 1557 8270 3.488 0.905 0.146 0.039 25 3.3 G_orbital 2314 1879 4974 2.154 0.785 0.170 0.049 32 5.2 G_pariet_inf-Angular 1890 1319 3778 2.294 0.721 0.131 0.027 18 2.1 G_pariet_inf-Supramar 3045 2281 5537 1.988 0.644 0.147 0.038 32 5.2 G_parietal_sup 1761 1170 2844 2.007 0.654 0.119 0.025 15 1.9 G_postcentral 2161 1423 4254 2.341 0.875 0.107 0.025 17 2.2 G_precentral 2088 1558 4357 2.373 0.905 0.136 0.034 23 2.8 G_precuneus 633 512 2406 3.189 0.821 0.152 0.036 13 1.1 G_rectus 383 257 552 2.371 0.872 0.130 0.049 5 0.8 G_subcallosal 256 175 395 2.014 0.625 0.153 0.028 3 0.3 G_temp_sup-G_T_transv 1803 1459 5775 2.988 0.886 0.167 0.044 23 3.6 G_temp_sup-Lateral 603 410 1548 3.305 0.894 0.052 0.010 1 0.1 G_temp_sup-Plan_polar 667 469 782 1.631 0.487 0.071 0.012 2 0.4 G_temp_sup-Plan_tempo 2271 1641 9362 3.497 0.987 0.126 0.028 24 2.7 G_temporal_inf 2257 1647 6248 2.695 0.983 0.127 0.029 22 2.9 G_temporal_middle 268 174 316 2.144 0.750 0.075 0.009 1 0.1 Lat_Fis-ant-Horizont 114 84 247 3.093 0.586 0.076 0.020 0 0.0 Lat_Fis-ant-Vertical 1081 689 1305 2.348 0.710 0.093 0.018 5 0.7 Lat_Fis-post 2907 2167 6247 2.468 0.681 0.148 0.044 28 5.4 Pole_occipital 1703 1224 6942 3.474 0.939 0.139 0.035 20 2.4 Pole_temporal 1619 1070 1846 1.954 0.695 0.116 0.038 25 2.2 S_calcarine 2705 1730 2385 1.655 0.434 0.089 0.015 12 1.8 S_central 1019 676 1150 1.814 0.635 0.112 0.025 7 1.1 S_cingul-Marginalis 408 279 817 3.330 0.524 0.074 0.009 1 0.1 S_circular_insula_ant 1160 736 1378 2.324 0.915 0.073 0.011 4 0.6 S_circular_insula_inf 1070 693 1439 2.589 0.661 0.082 0.013 3 0.6 S_circular_insula_sup 931 610 1226 1.970 0.553 0.083 0.010 4 0.4 S_collat_transv_ant 336 225 461 2.427 0.475 0.109 0.021 2 0.3 S_collat_transv_post 1776 1177 2314 2.229 0.529 0.102 0.020 9 1.5 S_front_inf 3106 2133 4751 2.179 0.722 0.114 0.026 22 3.6 S_front_middle 2071 1391 2784 2.162 0.534 0.096 0.019 10 1.4 S_front_sup 201 140 220 1.528 0.266 0.066 0.006 0 0.1 S_interm_prim-Jensen 3165 2094 3550 1.981 0.476 0.101 0.017 18 2.2 S_intrapariet_and_P_trans 808 535 1090 2.482 0.565 0.112 0.028 5 0.7 S_oc_middle_and_Lunatus 1233 849 1783 2.073 0.565 0.120 0.031 11 1.5 S_oc_sup_and_transversal 390 282 560 2.185 0.545 0.131 0.029 3 0.6 S_occipital_ant 756 497 1001 2.300 0.409 0.109 0.021 5 0.7 S_oc-temp_lat 1326 910 2277 2.434 0.909 0.104 0.018 9 1.0 S_oc-temp_med_and_Lingual 375 246 441 2.249 0.455 0.096 0.014 2 0.2 S_orbital_lateral 616 402 936 2.418 0.726 0.109 0.021 4 0.5 S_orbital_med-olfact 1303 852 2501 2.930 0.744 0.109 0.022 8 1.2 S_orbital-H_Shaped 1885 1223 2253 2.216 0.804 0.086 0.016 8 1.2 S_parieto_occipital 1006 622 1246 2.434 0.709 0.110 0.024 9 0.8 S_pericallosal 2737 1760 2529 1.640 0.502 0.098 0.018 15 2.2 S_postcentral 1738 1092 2045 2.262 0.625 0.080 0.015 6 1.0 S_precentral-inf-part 981 666 1222 1.994 0.534 0.104 0.017 6 0.9 S_precentral-sup-part 279 181 651 3.310 1.083 0.064 0.007 1 0.1 S_suborbital 1382 972 1729 1.969 0.563 0.126 0.025 10 1.6 S_subparietal 1343 848 1339 1.962 0.381 0.094 0.013 7 0.7 S_temporal_inf 5994 4055 7716 2.105 0.552 0.095 0.018 29 5.0 S_temporal_sup 276 185 309 1.895 0.559 0.105 0.020 1 0.3 S_temporal_transverse @#@FSTIME 2023:05:13:00:25:45 mris_anatomical_stats N 14 e 17.15 S 0.29 U 16.29 P 96% M 398656 F 0 R 59534 W 0 c 20 w 226 I 0 O 640 L 0.94 1.03 1.04 @#@FSLOADPOST 2023:05:13:00:26:03 mris_anatomical_stats N 14 0.95 1.03 1.04 #----------------------------------------- #@# Parcellation Stats 3 lh Sat May 13 00:26:03 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/wm.mgz... reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white... reading input pial surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.pial... reading input white surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 215186 Total vertex volume 214947 (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) = 1265446 mm^3 (det: 1.539462 ) 1666 1138 3126 2.587 0.629 0.121 0.021 15 1.5 caudalanteriorcingulate 3443 2255 6002 2.426 0.772 0.107 0.021 23 3.1 caudalmiddlefrontal 1956 1562 3756 2.244 0.823 0.149 0.042 20 3.6 cuneus 533 343 1308 3.101 0.858 0.100 0.021 3 0.4 entorhinal 3343 2469 8703 2.793 0.841 0.134 0.030 37 4.4 fusiform 6114 4222 9759 2.130 0.690 0.122 0.027 49 7.3 inferiorparietal 4622 3210 13628 2.990 0.997 0.109 0.025 42 4.9 inferiortemporal 1167 788 2134 2.564 0.859 0.120 0.031 10 1.4 isthmuscingulate 6198 4455 13154 2.498 0.771 0.143 0.038 58 10.1 lateraloccipital 3246 2273 9511 3.134 1.019 0.115 0.023 30 3.3 lateralorbitofrontal 2868 2280 5793 2.308 0.718 0.148 0.039 33 4.8 lingual 1683 1274 4964 3.022 1.049 0.118 0.030 19 2.1 medialorbitofrontal 5856 4002 12907 2.667 0.839 0.107 0.024 40 5.9 middletemporal 949 590 1763 2.466 0.915 0.068 0.009 3 0.3 parahippocampal 2225 1429 3620 2.439 0.656 0.104 0.023 14 2.0 paracentral 1575 1069 3130 2.472 0.754 0.112 0.023 11 1.5 parsopercularis 763 488 2394 3.225 1.026 0.097 0.019 5 0.6 parsorbitalis 1533 1054 3550 2.801 0.844 0.107 0.024 10 1.5 parstriangularis 1312 978 1908 2.044 0.507 0.125 0.035 11 1.8 pericalcarine 6577 4308 9558 1.969 0.760 0.099 0.020 40 5.4 postcentral 1364 917 1894 2.159 0.625 0.114 0.022 10 1.4 posteriorcingulate 6427 4220 10052 2.212 0.706 0.104 0.022 41 5.7 precentral 4973 3539 8419 2.207 0.794 0.120 0.027 40 6.0 precuneus 1186 859 3093 2.960 1.007 0.113 0.026 9 1.4 rostralanteriorcingulate 4269 3065 8924 2.538 0.788 0.122 0.029 36 5.0 rostralmiddlefrontal 10270 7243 26440 2.961 0.856 0.117 0.029 83 12.2 superiorfrontal 7380 4890 9983 1.932 0.648 0.120 0.027 60 8.3 superiorparietal 5752 4091 13223 2.600 0.984 0.092 0.018 34 4.3 superiortemporal 4044 2855 6634 2.113 0.759 0.125 0.029 32 5.1 supramarginal 481 359 738 2.036 0.507 0.144 0.028 5 0.5 transversetemporal 2308 1615 4877 2.896 0.943 0.118 0.030 22 2.9 insula @#@FSTIME 2023:05:13:00:26:03 mris_anatomical_stats N 14 e 15.57 S 0.27 U 14.96 P 97% M 400696 F 0 R 62142 W 0 c 17 w 138 I 0 O 272 L 0.95 1.03 1.04 @#@FSLOADPOST 2023:05:13:00:26:18 mris_anatomical_stats N 14 0.96 1.02 1.04 #----------------------------------------- #@# Parcellation Stats 3 rh Sat May 13 00:26:18 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 CR_t2_tra_12_SR rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/mri/wm.mgz... reading input surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.white... reading input pial surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/rh.pial... reading input white surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 212592 Total vertex volume 212345 (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) = 1265446 mm^3 (det: 1.539462 ) 947 671 2286 2.762 0.709 0.123 0.025 8 1.1 caudalanteriorcingulate 3006 2100 4622 2.160 0.580 0.111 0.024 21 3.0 caudalmiddlefrontal 2160 1742 3792 2.050 0.557 0.157 0.044 24 4.3 cuneus 492 311 1239 3.092 0.713 0.101 0.021 4 0.3 entorhinal 2635 1891 6467 2.774 0.856 0.128 0.027 26 3.0 fusiform 6900 5086 12017 2.197 0.666 0.137 0.034 64 10.5 inferiorparietal 4416 3054 13628 2.989 1.072 0.108 0.023 34 4.3 inferiortemporal 993 696 2028 2.583 0.889 0.132 0.032 10 1.2 isthmuscingulate 6515 4676 14251 2.573 0.738 0.138 0.037 61 10.3 lateraloccipital 3444 2410 9409 3.117 0.890 0.128 0.032 31 4.5 lateralorbitofrontal 3030 2333 6724 2.463 0.696 0.148 0.038 34 4.8 lingual 1707 1234 4998 3.190 1.008 0.117 0.029 19 2.1 medialorbitofrontal 5070 3463 10476 2.525 0.879 0.109 0.022 38 4.7 middletemporal 784 474 1763 2.899 1.151 0.088 0.023 6 0.7 parahippocampal 2111 1256 3205 2.357 0.763 0.102 0.021 15 1.9 paracentral 1542 1067 3159 2.588 0.771 0.107 0.023 11 1.5 parsopercularis 876 583 2697 3.188 0.961 0.104 0.021 6 0.7 parsorbitalis 1349 905 2346 2.429 0.735 0.107 0.018 9 1.1 parstriangularis 1531 1200 2052 1.730 0.465 0.150 0.046 23 2.7 pericalcarine 5861 3887 8355 1.927 0.772 0.105 0.022 38 5.4 postcentral 1249 939 2326 2.399 0.731 0.149 0.040 13 2.2 posteriorcingulate 5942 3930 9514 2.230 0.772 0.103 0.022 39 5.4 precentral 5297 3641 8374 2.251 0.850 0.113 0.026 46 5.7 precuneus 851 593 2206 3.026 0.806 0.106 0.024 7 0.9 rostralanteriorcingulate 5812 4138 11435 2.345 0.798 0.124 0.031 52 7.5 rostralmiddlefrontal 11156 7841 27446 2.870 0.918 0.120 0.027 91 12.6 superiorfrontal 6802 4819 10130 1.938 0.583 0.124 0.027 56 8.3 superiorparietal 6320 4570 14280 2.534 1.000 0.112 0.026 47 7.1 superiortemporal 3905 2631 5779 2.070 0.667 0.110 0.022 27 3.4 supramarginal 392 263 523 1.961 0.524 0.128 0.027 4 0.4 transversetemporal 2241 1528 4816 3.108 0.910 0.107 0.023 17 2.1 insula @#@FSTIME 2023:05:13:00:26:18 mris_anatomical_stats N 14 e 15.32 S 0.26 U 14.71 P 97% M 398656 F 0 R 63067 W 0 c 18 w 153 I 0 O 272 L 0.96 1.02 1.04 @#@FSLOADPOST 2023:05:13:00:26:34 mris_anatomical_stats N 14 0.97 1.02 1.04 #-------------------------------------------- #@# ASeg Stats Sat May 13 00:26:34 EDT 2023 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR 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/dev//ASegStatsLUT.txt --subject CR_t2_tra_12_SR setting seed for random number genererator to 1234 dev 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/dev//ASegStatsLUT.txt --subject CR_t2_tra_12_SR sysname Linux hostname compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1265446 mm^3 (det: 1.539462 ) Computing euler number orig.nofix lheno = -22, rheno = -28 orig.nofix lhholes = 12, rhholes = 15 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2023:05:13:00:26:34 mri_segstats N 32 e 353.39 S 0.30 U 352.91 P 99% M 275596 F 0 R 51502 W 0 c 300 w 88 I 0 O 32 L 0.97 1.02 1.04 @#@FSLOADPOST 2023:05:13:00:32:27 mri_segstats N 32 0.97 0.96 1.01 /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label #-------------------------------------------- #@# BA_exvivo Labels lh Sat May 13 00:32:27 EDT 2023 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA1_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4248 mri_label2label: Done @#@FSTIME 2023:05:13:00:32:27 mri_label2label N 12 e 9.38 S 0.32 U 8.24 P 91% M 502468 F 0 R 74985 W 0 c 8 w 76 I 23392 O 256 L 0.97 0.96 1.01 @#@FSLOADPOST 2023:05:13:00:32:37 mri_label2label N 12 0.97 0.96 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA2_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 317 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8226 mri_label2label: Done @#@FSTIME 2023:05:13:00:32:37 mri_label2label N 12 e 9.52 S 0.30 U 9.08 P 98% M 502668 F 0 R 76076 W 0 c 11 w 49 I 632 O 504 L 0.97 0.96 1.01 @#@FSLOADPOST 2023:05:13:00:32:46 mri_label2label N 12 0.98 0.96 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA3a_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4108 mri_label2label: Done @#@FSTIME 2023:05:13:00:32:47 mri_label2label N 12 e 8.63 S 0.31 U 8.22 P 98% M 502532 F 0 R 75493 W 0 c 13 w 40 I 320 O 216 L 0.98 0.96 1.01 @#@FSLOADPOST 2023:05:13:00:32:55 mri_label2label N 12 0.98 0.96 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA3b_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6047 mri_label2label: Done @#@FSTIME 2023:05:13:00:32:55 mri_label2label N 12 e 9.07 S 0.31 U 8.65 P 98% M 502668 F 0 R 77061 W 0 c 16 w 44 I 472 O 336 L 0.98 0.96 1.01 @#@FSLOADPOST 2023:05:13:00:33:04 mri_label2label N 12 0.98 0.96 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA4a_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5884 mri_label2label: Done @#@FSTIME 2023:05:13:00:33:05 mri_label2label N 12 e 9.03 S 0.31 U 8.61 P 98% M 502528 F 0 R 73992 W 0 c 12 w 45 I 456 O 320 L 0.98 0.96 1.01 @#@FSLOADPOST 2023:05:13:00:33:14 mri_label2label N 12 0.99 0.96 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA4p_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4117 mri_label2label: Done @#@FSTIME 2023:05:13:00:33:14 mri_label2label N 12 e 8.62 S 0.30 U 8.21 P 98% M 502464 F 0 R 73961 W 0 c 15 w 41 I 320 O 224 L 0.99 0.96 1.01 @#@FSLOADPOST 2023:05:13:00:33:22 mri_label2label N 12 0.99 0.96 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA6_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 615 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14204 mri_label2label: Done @#@FSTIME 2023:05:13:00:33:23 mri_label2label N 12 e 10.76 S 0.31 U 10.29 P 98% M 503136 F 0 R 73623 W 0 c 10 w 59 I 1056 O 864 L 0.99 0.96 1.01 @#@FSLOADPOST 2023:05:13:00:33:33 mri_label2label N 12 0.99 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA44_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4195 mri_label2label: Done @#@FSTIME 2023:05:13:00:33:34 mri_label2label N 12 e 8.67 S 0.34 U 8.21 P 98% M 502536 F 0 R 75495 W 0 c 10 w 52 I 328 O 208 L 0.99 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:33:42 mri_label2label N 12 0.99 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA45_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3467 mri_label2label: Done @#@FSTIME 2023:05:13:00:33:42 mri_label2label N 12 e 8.47 S 0.33 U 8.05 P 98% M 502540 F 0 R 74461 W 0 c 15 w 39 I 272 O 192 L 0.99 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:33:51 mri_label2label N 12 0.99 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.V1_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 359 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5000 mri_label2label: Done @#@FSTIME 2023:05:13:00:33:51 mri_label2label N 12 e 8.81 S 0.30 U 8.40 P 98% M 502624 F 0 R 77041 W 0 c 10 w 44 I 376 O 328 L 0.99 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:34:00 mri_label2label N 12 0.99 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.V2_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 683 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 8797 mri_label2label: Done @#@FSTIME 2023:05:13:00:34:00 mri_label2label N 12 e 9.63 S 0.32 U 9.18 P 98% M 502744 F 0 R 77105 W 0 c 10 w 46 I 664 O 584 L 0.99 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:34:10 mri_label2label N 12 0.99 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.MT_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2263 mri_label2label: Done @#@FSTIME 2023:05:13:00:34:10 mri_label2label N 12 e 8.20 S 0.30 U 7.79 P 98% M 502444 F 0 R 76480 W 0 c 13 w 44 I 168 O 176 L 0.99 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:34:18 mri_label2label N 12 1.00 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1329 mri_label2label: Done @#@FSTIME 2023:05:13:00:34:18 mri_label2label N 12 e 7.97 S 0.34 U 7.55 P 99% M 502224 F 0 R 75448 W 0 c 13 w 35 I 120 O 88 L 1.00 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:34:26 mri_label2label N 12 1.00 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1247 mri_label2label: Done @#@FSTIME 2023:05:13:00:34:26 mri_label2label N 12 e 7.98 S 0.30 U 7.60 P 99% M 502312 F 0 R 77993 W 0 c 15 w 34 I 112 O 88 L 1.00 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:34:34 mri_label2label N 12 1.00 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 438 mri_label2label: Done @#@FSTIME 2023:05:13:00:34:34 mri_label2label N 12 e 8.81 S 0.29 U 8.43 P 99% M 502212 F 0 R 74409 W 0 c 16 w 40 I 40 O 32 L 1.00 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:34:43 mri_label2label N 12 1.00 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 756 mri_label2label: Done @#@FSTIME 2023:05:13:00:34:43 mri_label2label N 12 e 7.87 S 0.33 U 7.45 P 98% M 502224 F 0 R 76457 W 0 c 9 w 39 I 72 O 64 L 1.00 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:34:51 mri_label2label N 12 1.00 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1899 mri_label2label: Done @#@FSTIME 2023:05:13:00:34:51 mri_label2label N 12 e 8.12 S 0.31 U 7.72 P 98% M 502424 F 0 R 75966 W 0 c 13 w 36 I 176 O 112 L 1.00 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:34:59 mri_label2label N 12 1.00 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 187 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2288 mri_label2label: Done @#@FSTIME 2023:05:13:00:35:00 mri_label2label N 12 e 8.19 S 0.32 U 7.77 P 98% M 502384 F 0 R 74950 W 0 c 13 w 39 I 200 O 168 L 1.00 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:35:08 mri_label2label N 12 1.00 0.97 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 246 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4123 mri_label2label: Done @#@FSTIME 2023:05:13:00:35:08 mri_label2label N 12 e 8.64 S 0.31 U 8.23 P 98% M 502584 F 0 R 77026 W 0 c 11 w 39 I 360 O 256 L 1.00 0.97 1.01 @#@FSLOADPOST 2023:05:13:00:35:17 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 343 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 3262 mri_label2label: Done @#@FSTIME 2023:05:13:00:35:17 mri_label2label N 12 e 8.43 S 0.32 U 8.01 P 98% M 502492 F 0 R 76494 W 0 c 15 w 46 I 272 O 248 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:35:25 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1434 mri_label2label: Done @#@FSTIME 2023:05:13:00:35:25 mri_label2label N 12 e 7.99 S 0.32 U 7.58 P 98% M 502404 F 0 R 76472 W 0 c 16 w 37 I 128 O 120 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:35:33 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1080 mri_label2label: Done @#@FSTIME 2023:05:13:00:35:34 mri_label2label N 12 e 7.96 S 0.32 U 7.53 P 98% M 502380 F 0 R 74423 W 0 c 12 w 51 I 96 O 80 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:35:42 mri_label2label N 12 1.00 0.98 1.01 mris_label2annot --s CR_t2_tra_12_SR --ctab /usr/local/freesurfer/dev//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/dev//average/colortable_vpnl.txt Number of ctab entries 9 dev cwd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label cmdline mris_label2annot --s CR_t2_tra_12_SR --ctab /usr/local/freesurfer/dev//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 compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 subject CR_t2_tra_12_SR hemi lh SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data ColorTable /usr/local/freesurfer/dev//average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig convert labels to annotation with label2annotationV2() ... 0 reading lh.FG1.mpm.vpnl.label 1 1376057 FG1.mpm.vpnl (57 255 20 255) 1 reading lh.FG2.mpm.vpnl.label 2 16711935 FG2.mpm.vpnl (255 0 255 255) 2 reading lh.FG3.mpm.vpnl.label 3 16711680 FG3.mpm.vpnl (0 0 255 255) 3 reading lh.FG4.mpm.vpnl.label 4 1705837 FG4.mpm.vpnl (109 7 26 255) 4 reading lh.hOc1.mpm.vpnl.label 5 25600 hOc1.mpm.vpnl (0 100 0 255) 5 reading lh.hOc2.mpm.vpnl.label 6 255 hOc2.mpm.vpnl (255 0 0 255) 6 reading lh.hOc3v.mpm.vpnl.label 7 16776960 hOc3v.mpm.vpnl (0 255 255 255) 7 reading lh.hOc4v.mpm.vpnl.label 8 65535 hOc4v.mpm.vpnl (255 255 0 255) Mapping unhit to unknown Found 101539 unhit vertices Writing annot to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.mpm.vpnl.annot @#@FSTIME 2023:05:13:00:35:42 mris_label2annot N 26 e 1.45 S 0.08 U 1.10 P 81% M 134084 F 0 R 22421 W 0 c 3 w 128 I 8 O 1768 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:35:43 mris_label2annot N 26 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1043 mri_label2label: Done @#@FSTIME 2023:05:13:00:35:43 mri_label2label N 12 e 7.93 S 0.30 U 7.55 P 99% M 502372 F 0 R 77489 W 0 c 9 w 35 I 96 O 72 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:35:51 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 132 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2224 mri_label2label: Done @#@FSTIME 2023:05:13:00:35:51 mri_label2label N 12 e 8.19 S 0.31 U 7.79 P 98% M 502452 F 0 R 74437 W 0 c 14 w 40 I 192 O 160 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:35:59 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1517 mri_label2label: Done @#@FSTIME 2023:05:13:00:36:00 mri_label2label N 12 e 8.04 S 0.30 U 7.65 P 98% M 502244 F 0 R 77490 W 0 c 12 w 37 I 136 O 80 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:36:08 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2008 mri_label2label: Done @#@FSTIME 2023:05:13:00:36:08 mri_label2label N 12 e 8.16 S 0.31 U 7.75 P 98% M 502432 F 0 R 73413 W 0 c 13 w 39 I 184 O 112 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:36:16 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2370 mri_label2label: Done @#@FSTIME 2023:05:13:00:36:16 mri_label2label N 12 e 8.21 S 0.31 U 7.80 P 98% M 502264 F 0 R 75466 W 0 c 14 w 39 I 208 O 136 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:36:24 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1570 mri_label2label: Done @#@FSTIME 2023:05:13:00:36:25 mri_label2label N 12 e 8.05 S 0.31 U 7.64 P 98% M 502316 F 0 R 77491 W 0 c 13 w 42 I 144 O 88 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:36:33 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 267 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7302 mri_label2label: Done @#@FSTIME 2023:05:13:00:36:33 mri_label2label N 12 e 9.33 S 0.32 U 8.87 P 98% M 502636 F 0 R 77081 W 0 c 11 w 55 I 616 O 440 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:36:42 mri_label2label N 12 1.00 0.98 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 5 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1917 mri_label2label: Done @#@FSTIME 2023:05:13:00:36:42 mri_label2label N 12 e 8.13 S 0.30 U 7.72 P 98% M 502392 F 0 R 74944 W 0 c 16 w 46 I 168 O 96 L 1.00 0.98 1.01 @#@FSLOADPOST 2023:05:13:00:36:50 mri_label2label N 12 1.00 0.99 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1161 mri_label2label: Done @#@FSTIME 2023:05:13:00:36:51 mri_label2label N 12 e 7.95 S 0.32 U 7.55 P 98% M 502380 F 0 R 76977 W 0 c 14 w 38 I 104 O 72 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:36:59 mri_label2label N 12 1.00 0.99 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3666 mri_label2label: Done @#@FSTIME 2023:05:13:00:36:59 mri_label2label N 12 e 8.49 S 0.32 U 8.07 P 98% M 502560 F 0 R 77022 W 0 c 20 w 42 I 304 O 240 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:37:07 mri_label2label N 12 1.00 0.99 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 347 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 3681 mri_label2label: Done @#@FSTIME 2023:05:13:00:37:07 mri_label2label N 12 e 8.49 S 0.31 U 8.08 P 98% M 502436 F 0 R 74464 W 0 c 15 w 40 I 296 O 264 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:37:16 mri_label2label N 12 1.00 0.99 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 556 mri_label2label: Done @#@FSTIME 2023:05:13:00:37:16 mri_label2label N 12 e 7.84 S 0.31 U 7.44 P 98% M 502340 F 0 R 74407 W 0 c 9 w 39 I 48 O 48 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:37:24 mri_label2label N 12 1.00 0.99 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 485 mri_label2label: Done @#@FSTIME 2023:05:13:00:37:24 mri_label2label N 12 e 7.80 S 0.30 U 7.42 P 99% M 502324 F 0 R 74408 W 0 c 10 w 33 I 48 O 32 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:37:32 mri_label2label N 12 1.00 0.99 1.01 mri_label2label --srcsubject fsaverage --srclabel /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject CR_t2_tra_12_SR --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = CR_t2_tra_12_SR 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/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data FREESURFER_HOME /usr/local/freesurfer/dev/ Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.white Reading target registration /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/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 113073 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 478 mri_label2label: Done @#@FSTIME 2023:05:13:00:37:32 mri_label2label N 12 e 7.79 S 0.31 U 7.39 P 98% M 502340 F 0 R 73898 W 0 c 14 w 44 I 48 O 40 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:37:40 mri_label2label N 12 1.00 0.99 1.01 mris_label2annot --s CR_t2_tra_12_SR --hemi lh --ctab /usr/local/freesurfer/dev//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/dev//average/colortable_BA.txt Number of ctab entries 15 dev cwd /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label cmdline mris_label2annot --s CR_t2_tra_12_SR --hemi lh --ctab /usr/local/freesurfer/dev//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 compute-0-37.nmr.mgh.harvard.edu machine x86_64 user wk962 subject CR_t2_tra_12_SR hemi lh SUBJECTS_DIR /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data ColorTable /usr/local/freesurfer/dev//average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/surf/lh.orig convert labels to annotation with label2annotationV2() ... 0 reading lh.BA1_exvivo.label 1 1530880 BA1_exvivo (0 92 23 255) 1 reading lh.BA2_exvivo.label 2 16749699 BA2_exvivo (131 148 255 255) 2 reading lh.BA3a_exvivo.label 3 16711680 BA3a_exvivo (0 0 255 255) 3 reading lh.BA3b_exvivo.label 4 3368703 BA3b_exvivo (255 102 51 255) 4 reading lh.BA4a_exvivo.label 5 1376196 BA4a_exvivo (196 255 20 255) 5 reading lh.BA4p_exvivo.label 6 13382655 BA4p_exvivo (255 51 204 255) 6 reading lh.BA6_exvivo.label 7 10036737 BA6_exvivo (1 38 153 255) 7 reading lh.BA44_exvivo.label 8 2490521 BA44_exvivo (153 0 38 255) 8 reading lh.BA45_exvivo.label 9 39283 BA45_exvivo (115 153 0 255) 9 reading lh.V1_exvivo.label 10 3993 V1_exvivo (153 15 0 255) 10 reading lh.V2_exvivo.label 11 8508928 V2_exvivo (0 214 129 255) 11 reading lh.MT_exvivo.label 12 10027163 MT_exvivo (155 0 153 255) 12 reading lh.perirhinal_exvivo.label 13 16422433 perirhinal_exvivo (33 150 250 255) 13 reading lh.entorhinal_exvivo.label 14 16392598 entorhinal_exvivo (150 33 250 255) Mapping unhit to unknown Found 78071 unhit vertices Writing annot to /autofs/vast/lzgroup/Projects/Schmahmann/CharlotteJenny/Data/CR_t2_tra_12_SR/label/lh.BA_exvivo.annot @#@FSTIME 2023:05:13:00:37:40 mris_label2annot N 38 e 1.58 S 0.09 U 1.13 P 77% M 137500 F 0 R 22787 W 0 c 2 w 165 I 8 O 1768 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:37:41 mris_label2annot N 38 1.00 0.99 1.01 mris_label2annot --s CR_t2_tra_12_SR --hemi lh --ctab /usr/local/freesurfer/dev//average/colortable_BA_thresh.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 ERROR: cannot find or read /usr/local/freesurfer/dev//average/colortable_BA_thresh.txt @#@FSTIME 2023:05:13:00:37:41 mris_label2annot N 38 e 0.01 S 0.00 U 0.00 P 25% M 1952 F 0 R 587 W 0 c 1 w 7 I 0 O 0 L 1.00 0.99 1.01 @#@FSLOADPOST 2023:05:13:00:37:41 mris_label2annot N 38 1.00 0.99 1.01 Linux compute-0-37.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CR_t2_tra_12_SR exited with ERRORS at Sat May 13 00:37:42 EDT 2023 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting