Tue May 25 20:52:27 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-06 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-06 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux blg6114.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767932 maxlocks unlimited maxsignal 767932 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638260 129664420 17365320 2231068 49608520 58995908 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:52:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Tessellate lh Tue May 25 20:52:29 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 2 found - 2 modified | TOTAL: 8 pass 2 (xy-): 0 found - 2 modified | TOTAL: 8 pass 1 (yz+): 2 found - 2 modified | TOTAL: 10 pass 2 (yz+): 0 found - 2 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 4 found - 4 modified | TOTAL: 16 pass 2 (xz+): 0 found - 4 modified | TOTAL: 16 pass 1 (xz-): 3 found - 3 modified | TOTAL: 19 pass 2 (xz-): 0 found - 3 modified | TOTAL: 19 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 1 found - 1 modified | TOTAL: 5 pass 2 (--): 0 found - 1 modified | TOTAL: 5 pass 1 (-+): 3 found - 3 modified | TOTAL: 8 pass 2 (-+): 0 found - 3 modified | TOTAL: 8 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 31 (out of 486115: 0.006377) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 712 vertices, 800 faces slice 60: 5005 vertices, 5204 faces slice 70: 13311 vertices, 13627 faces slice 80: 23292 vertices, 23662 faces slice 90: 34930 vertices, 35400 faces slice 100: 48605 vertices, 49097 faces slice 110: 63965 vertices, 64463 faces slice 120: 79001 vertices, 79527 faces slice 130: 95455 vertices, 96063 faces slice 140: 111643 vertices, 112240 faces slice 150: 127553 vertices, 128161 faces slice 160: 142493 vertices, 143042 faces slice 170: 156940 vertices, 157411 faces slice 180: 168636 vertices, 169101 faces slice 190: 179984 vertices, 180436 faces slice 200: 190127 vertices, 190498 faces slice 210: 199324 vertices, 199728 faces slice 220: 208371 vertices, 208722 faces slice 230: 214789 vertices, 215039 faces slice 240: 217236 vertices, 217310 faces slice 250: 217236 vertices, 217310 faces slice 260: 217236 vertices, 217310 faces slice 270: 217236 vertices, 217310 faces slice 280: 217236 vertices, 217310 faces slice 290: 217236 vertices, 217310 faces slice 300: 217236 vertices, 217310 faces slice 310: 217236 vertices, 217310 faces slice 320: 217236 vertices, 217310 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -0.80000 0.00000 0.00000 127.99999; 0.00000 0.00000 0.80000 -127.99999; 0.00000 -0.80000 0.00000 127.99999; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 217228 voxel in cpt #1: X=-76 [v=217228,e=651912,f=434608] located at (-28.024527, -16.821697, 33.460133) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (0.799999, 5.599998, 23.199997) For the whole surface: X=-74 [v=217236,e=651930,f=434620] 2 components have been found keeping component #1 with 217228 vertices done #-------------------------------------------- #@# Smooth1 lh Tue May 25 20:52:36 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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... #-------------------------------------------- #@# Inflation1 lh Tue May 25 20:52:43 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_inflate -no-save-sulc -n 50 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix niterations = 50 Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.3 mm, total surface area = 75379 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 2.1 minutes step 000: RMS=0.145 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.039 (target=0.015) step 065: RMS=0.038 (target=0.015) step 070: RMS=0.037 (target=0.015) step 075: RMS=0.037 (target=0.015) step 080: RMS=0.037 (target=0.015) step 085: RMS=0.036 (target=0.015) step 090: RMS=0.036 (target=0.015) step 095: RMS=0.036 (target=0.015) step 100: RMS=0.036 (target=0.015) step 105: RMS=0.036 (target=0.015) step 110: RMS=0.036 (target=0.015) step 115: RMS=0.036 (target=0.015) step 120: RMS=0.036 (target=0.015) step 125: RMS=0.035 (target=0.015) step 130: RMS=0.035 (target=0.015) step 135: RMS=0.035 (target=0.015) step 140: RMS=0.035 (target=0.015) step 145: RMS=0.035 (target=0.015) step 150: RMS=0.035 (target=0.015) step 155: RMS=0.035 (target=0.015) step 160: RMS=0.035 (target=0.015) step 165: RMS=0.035 (target=0.015) step 170: RMS=0.035 (target=0.015) step 175: RMS=0.035 (target=0.015) step 180: RMS=0.035 (target=0.015) step 185: RMS=0.035 (target=0.015) step 190: RMS=0.035 (target=0.015) step 195: RMS=0.035 (target=0.015) step 200: RMS=0.035 (target=0.015) step 205: RMS=0.035 (target=0.015) step 210: RMS=0.035 (target=0.015) step 215: RMS=0.035 (target=0.015) step 220: RMS=0.035 (target=0.015) step 225: RMS=0.035 (target=0.015) step 230: RMS=0.035 (target=0.015) step 235: RMS=0.035 (target=0.015) step 240: RMS=0.035 (target=0.015) step 245: RMS=0.035 (target=0.015) step 250: RMS=0.035 (target=0.015) step 255: RMS=0.035 (target=0.015) step 260: RMS=0.037 (target=0.015) step 265: RMS=0.037 (target=0.015) step 270: RMS=0.036 (target=0.015) step 275: RMS=0.037 (target=0.015) step 280: RMS=0.037 (target=0.015) step 285: RMS=0.037 (target=0.015) step 290: RMS=0.037 (target=0.015) step 295: RMS=0.037 (target=0.015) step 300: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 625.219620 mris_inflate stimesec 1.947186 mris_inflate ru_maxrss 347872 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 926422 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8 mris_inflate ru_oublock 15288 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 50744 mris_inflate ru_nivcsw 5646 #-------------------------------------------- #@# QSphere lh Tue May 25 20:54:46 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.78 +- 0.42 (0.00-->6.91) (max @ vno 122228 --> 123826) face area 0.02 +- 0.02 (-0.22-->0.76) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.326... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.475, avgs=0 005/300: dt: 0.9000, rms radial error=174.218, avgs=0 010/300: dt: 0.9000, rms radial error=173.665, avgs=0 015/300: dt: 0.9000, rms radial error=172.938, avgs=0 020/300: dt: 0.9000, rms radial error=172.109, avgs=0 025/300: dt: 0.9000, rms radial error=171.220, avgs=0 030/300: dt: 0.9000, rms radial error=170.299, avgs=0 035/300: dt: 0.9000, rms radial error=169.361, avgs=0 040/300: dt: 0.9000, rms radial error=168.416, avgs=0 045/300: dt: 0.9000, rms radial error=167.468, avgs=0 050/300: dt: 0.9000, rms radial error=166.520, avgs=0 055/300: dt: 0.9000, rms radial error=165.575, avgs=0 060/300: dt: 0.9000, rms radial error=164.634, avgs=0 065/300: dt: 0.9000, rms radial error=163.699, avgs=0 070/300: dt: 0.9000, rms radial error=162.769, avgs=0 075/300: dt: 0.9000, rms radial error=161.844, avgs=0 080/300: dt: 0.9000, rms radial error=160.929, avgs=0 085/300: dt: 0.9000, rms radial error=160.019, avgs=0 090/300: dt: 0.9000, rms radial error=159.115, avgs=0 095/300: dt: 0.9000, rms radial error=158.216, avgs=0 100/300: dt: 0.9000, rms radial error=157.322, avgs=0 105/300: dt: 0.9000, rms radial error=156.432, avgs=0 110/300: dt: 0.9000, rms radial error=155.548, avgs=0 115/300: dt: 0.9000, rms radial error=154.669, avgs=0 120/300: dt: 0.9000, rms radial error=153.795, avgs=0 125/300: dt: 0.9000, rms radial error=152.926, avgs=0 130/300: dt: 0.9000, rms radial error=152.062, avgs=0 135/300: dt: 0.9000, rms radial error=151.202, avgs=0 140/300: dt: 0.9000, rms radial error=150.348, avgs=0 145/300: dt: 0.9000, rms radial error=149.498, avgs=0 150/300: dt: 0.9000, rms radial error=148.653, avgs=0 155/300: dt: 0.9000, rms radial error=147.813, avgs=0 160/300: dt: 0.9000, rms radial error=146.977, avgs=0 165/300: dt: 0.9000, rms radial error=146.146, avgs=0 170/300: dt: 0.9000, rms radial error=145.321, avgs=0 175/300: dt: 0.9000, rms radial error=144.499, avgs=0 180/300: dt: 0.9000, rms radial error=143.683, avgs=0 185/300: dt: 0.9000, rms radial error=142.871, avgs=0 190/300: dt: 0.9000, rms radial error=142.063, avgs=0 195/300: dt: 0.9000, rms radial error=141.260, avgs=0 200/300: dt: 0.9000, rms radial error=140.462, avgs=0 205/300: dt: 0.9000, rms radial error=139.668, avgs=0 210/300: dt: 0.9000, rms radial error=138.879, avgs=0 215/300: dt: 0.9000, rms radial error=138.094, avgs=0 220/300: dt: 0.9000, rms radial error=137.314, avgs=0 225/300: dt: 0.9000, rms radial error=136.538, avgs=0 230/300: dt: 0.9000, rms radial error=135.766, avgs=0 235/300: dt: 0.9000, rms radial error=134.999, avgs=0 240/300: dt: 0.9000, rms radial error=134.236, avgs=0 245/300: dt: 0.9000, rms radial error=133.478, avgs=0 250/300: dt: 0.9000, rms radial error=132.724, avgs=0 255/300: dt: 0.9000, rms radial error=131.974, avgs=0 260/300: dt: 0.9000, rms radial error=131.228, avgs=0 265/300: dt: 0.9000, rms radial error=130.486, avgs=0 270/300: dt: 0.9000, rms radial error=129.749, avgs=0 275/300: dt: 0.9000, rms radial error=129.016, avgs=0 280/300: dt: 0.9000, rms radial error=128.287, avgs=0 285/300: dt: 0.9000, rms radial error=127.562, avgs=0 290/300: dt: 0.9000, rms radial error=126.842, avgs=0 295/300: dt: 0.9000, rms radial error=126.125, avgs=0 300/300: dt: 0.9000, rms radial error=125.412, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 26535.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 4777.08 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 516.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00459 epoch 4 (K=640.0), pass 1, starting sse = 30.24 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00486 final distance error %22.26 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 607.583028 mris_sphere stimesec 1.887099 mris_sphere ru_maxrss 347896 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 867665 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 16 mris_sphere ru_oublock 15288 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 80764 mris_sphere ru_nivcsw 4410 FSRUNTIME@ mris_sphere 0.0396 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Tue May 25 20:57:09 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Tue May 25 20:57:10 UTC 2021 mris_fix_topology -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-06 lh reading spherical homeomorphism from 'qsphere.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 $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-76 (nv=217228, nf=434608, ne=651912, g=39) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 6786 ambiguous faces found in tessellation segmenting defects... 47 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 25 into 24 46 defects to be corrected 0 vertices coincident reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5434 (-4.7717) -vertex loglikelihood: -5.9719 (-2.9859) -normal dot loglikelihood: -3.6178 (-3.6178) -quad curv loglikelihood: -6.4930 (-3.2465) Total Loglikelihood : -25.6260 CORRECTING DEFECT 0 (vertices=26, convex hull=49, v0=4386) After retessellation of defect 0 (v0=4386), euler #=-44 (213212,638454,425198) : difference with theory (-43) = 1 CORRECTING DEFECT 1 (vertices=16, convex hull=14, v0=5738) After retessellation of defect 1 (v0=5738), euler #=-43 (213213,638461,425205) : difference with theory (-42) = 1 CORRECTING DEFECT 2 (vertices=24, convex hull=43, v0=25293) After retessellation of defect 2 (v0=25293), euler #=-42 (213219,638494,425233) : difference with theory (-41) = 1 CORRECTING DEFECT 3 (vertices=27, convex hull=42, v0=37553) After retessellation of defect 3 (v0=37553), euler #=-41 (213222,638520,425257) : difference with theory (-40) = 1 CORRECTING DEFECT 4 (vertices=38, convex hull=40, v0=43020) After retessellation of defect 4 (v0=43020), euler #=-40 (213226,638542,425276) : difference with theory (-39) = 1 CORRECTING DEFECT 5 (vertices=327, convex hull=139, v0=48499) After retessellation of defect 5 (v0=48499), euler #=-39 (213249,638672,425384) : difference with theory (-38) = 1 CORRECTING DEFECT 6 (vertices=64, convex hull=26, v0=51223) After retessellation of defect 6 (v0=51223), euler #=-38 (213252,638690,425400) : difference with theory (-37) = 1 CORRECTING DEFECT 7 (vertices=24, convex hull=37, v0=52088) After retessellation of defect 7 (v0=52088), euler #=-37 (213254,638706,425415) : difference with theory (-36) = 1 CORRECTING DEFECT 8 (vertices=27, convex hull=61, v0=52766) After retessellation of defect 8 (v0=52766), euler #=-36 (213262,638755,425457) : difference with theory (-35) = 1 CORRECTING DEFECT 9 (vertices=22, convex hull=28, v0=58173) After retessellation of defect 9 (v0=58173), euler #=-35 (213263,638766,425468) : difference with theory (-34) = 1 CORRECTING DEFECT 10 (vertices=55, convex hull=27, v0=65821) After retessellation of defect 10 (v0=65821), euler #=-34 (213268,638792,425490) : difference with theory (-33) = 1 CORRECTING DEFECT 11 (vertices=606, convex hull=192, v0=75337) After retessellation of defect 11 (v0=75337), euler #=-33 (213280,638922,425609) : difference with theory (-32) = 1 CORRECTING DEFECT 12 (vertices=40, convex hull=72, v0=78959) After retessellation of defect 12 (v0=78959), euler #=-32 (213291,638985,425662) : difference with theory (-31) = 1 CORRECTING DEFECT 13 (vertices=24, convex hull=68, v0=92684) After retessellation of defect 13 (v0=92684), euler #=-31 (213298,639033,425704) : difference with theory (-30) = 1 CORRECTING DEFECT 14 (vertices=70, convex hull=37, v0=95100) After retessellation of defect 14 (v0=95100), euler #=-30 (213303,639056,425723) : difference with theory (-29) = 1 CORRECTING DEFECT 15 (vertices=49, convex hull=27, v0=96400) After retessellation of defect 15 (v0=96400), euler #=-29 (213306,639077,425742) : difference with theory (-28) = 1 CORRECTING DEFECT 16 (vertices=6, convex hull=36, v0=96444) After retessellation of defect 16 (v0=96444), euler #=-28 (213308,639094,425758) : difference with theory (-27) = 1 CORRECTING DEFECT 17 (vertices=946, convex hull=508, v0=106390) After retessellation of defect 17 (v0=106390), euler #=-27 (213358,639512,426127) : difference with theory (-26) = 1 CORRECTING DEFECT 18 (vertices=6, convex hull=17, v0=115520) After retessellation of defect 18 (v0=115520), euler #=-26 (213359,639519,426134) : difference with theory (-25) = 1 CORRECTING DEFECT 19 (vertices=80, convex hull=65, v0=117380) After retessellation of defect 19 (v0=117380), euler #=-25 (213368,639572,426179) : difference with theory (-24) = 1 CORRECTING DEFECT 20 (vertices=75, convex hull=29, v0=118261) After retessellation of defect 20 (v0=118261), euler #=-24 (213371,639592,426197) : difference with theory (-23) = 1 CORRECTING DEFECT 21 (vertices=31, convex hull=24, v0=129554) After retessellation of defect 21 (v0=129554), euler #=-23 (213373,639601,426205) : difference with theory (-22) = 1 CORRECTING DEFECT 22 (vertices=8, convex hull=24, v0=130820) After retessellation of defect 22 (v0=130820), euler #=-22 (213374,639612,426216) : difference with theory (-21) = 1 CORRECTING DEFECT 23 (vertices=53, convex hull=75, v0=134688) After retessellation of defect 23 (v0=134688), euler #=-21 (213389,639688,426278) : difference with theory (-20) = 1 CORRECTING DEFECT 24 (vertices=338, convex hull=287, v0=136153) After retessellation of defect 24 (v0=136153), euler #=-19 (213465,640066,426582) : difference with theory (-19) = 0 CORRECTING DEFECT 25 (vertices=56, convex hull=78, v0=140847) After retessellation of defect 25 (v0=140847), euler #=-18 (213476,640129,426635) : difference with theory (-18) = 0 CORRECTING DEFECT 26 (vertices=32, convex hull=17, v0=142557) After retessellation of defect 26 (v0=142557), euler #=-17 (213476,640135,426642) : difference with theory (-17) = 0 CORRECTING DEFECT 27 (vertices=187, convex hull=59, v0=143367) After retessellation of defect 27 (v0=143367), euler #=-16 (213489,640200,426695) : difference with theory (-16) = 0 CORRECTING DEFECT 28 (vertices=12, convex hull=22, v0=143613) After retessellation of defect 28 (v0=143613), euler #=-15 (213491,640212,426706) : difference with theory (-15) = 0 CORRECTING DEFECT 29 (vertices=61, convex hull=52, v0=144758) After retessellation of defect 29 (v0=144758), euler #=-14 (213500,640272,426758) : difference with theory (-14) = 0 CORRECTING DEFECT 30 (vertices=71, convex hull=70, v0=145103) After retessellation of defect 30 (v0=145103), euler #=-13 (213517,640355,426825) : difference with theory (-13) = 0 CORRECTING DEFECT 31 (vertices=57, convex hull=37, v0=147982) After retessellation of defect 31 (v0=147982), euler #=-12 (213525,640391,426854) : difference with theory (-12) = 0 CORRECTING DEFECT 32 (vertices=19, convex hull=35, v0=149423) After retessellation of defect 32 (v0=149423), euler #=-11 (213527,640405,426867) : difference with theory (-11) = 0 CORRECTING DEFECT 33 (vertices=28, convex hull=28, v0=149556) After retessellation of defect 33 (v0=149556), euler #=-10 (213532,640427,426885) : difference with theory (-10) = 0 CORRECTING DEFECT 34 (vertices=21, convex hull=59, v0=150556) After retessellation of defect 34 (v0=150556), euler #=-9 (213539,640469,426921) : difference with theory (-9) = 0 CORRECTING DEFECT 35 (vertices=128, convex hull=31, v0=151744) After retessellation of defect 35 (v0=151744), euler #=-8 (213543,640489,426938) : difference with theory (-8) = 0 CORRECTING DEFECT 36 (vertices=29, convex hull=27, v0=153733) After retessellation of defect 36 (v0=153733), euler #=-7 (213546,640505,426952) : difference with theory (-7) = 0 CORRECTING DEFECT 37 (vertices=39, convex hull=32, v0=153797) After retessellation of defect 37 (v0=153797), euler #=-6 (213550,640527,426971) : difference with theory (-6) = 0 CORRECTING DEFECT 38 (vertices=6, convex hull=29, v0=153933) After retessellation of defect 38 (v0=153933), euler #=-5 (213552,640541,426984) : difference with theory (-5) = 0 CORRECTING DEFECT 39 (vertices=22, convex hull=27, v0=154774) After retessellation of defect 39 (v0=154774), euler #=-4 (213555,640556,426997) : difference with theory (-4) = 0 CORRECTING DEFECT 40 (vertices=10, convex hull=18, v0=159467) After retessellation of defect 40 (v0=159467), euler #=-3 (213556,640566,427007) : difference with theory (-3) = 0 CORRECTING DEFECT 41 (vertices=32, convex hull=22, v0=166299) After retessellation of defect 41 (v0=166299), euler #=-2 (213560,640584,427022) : difference with theory (-2) = 0 CORRECTING DEFECT 42 (vertices=35, convex hull=27, v0=168021) After retessellation of defect 42 (v0=168021), euler #=-1 (213565,640607,427041) : difference with theory (-1) = 0 CORRECTING DEFECT 43 (vertices=79, convex hull=83, v0=179673) After retessellation of defect 43 (v0=179673), euler #=0 (213575,640678,427103) : difference with theory (0) = 0 CORRECTING DEFECT 44 (vertices=29, convex hull=24, v0=187491) After retessellation of defect 44 (v0=187491), euler #=1 (213577,640690,427114) : difference with theory (1) = 0 CORRECTING DEFECT 45 (vertices=74, convex hull=75, v0=199284) After retessellation of defect 45 (v0=199284), euler #=2 (213589,640761,427174) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.71 +- 0.18 (0.07-->10.50) (max @ vno 51418 --> 70340) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.71 +- 0.18 (0.07-->10.50) (max @ vno 51418 --> 70340) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 176 mutations (37.8%), 289 crossovers (62.2%), 178 vertices were eliminated building final representation... 3639 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=213589, nf=427174, ne=640761, g=0) writing corrected surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 25.0 minutes 0 defective edges removing intersecting faces 000: 320 intersecting mris_fix_topology utimesec 1515.338067 mris_fix_topology stimesec 0.711331 mris_fix_topology ru_maxrss 712456 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 367687 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 5336 mris_fix_topology ru_oublock 20136 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 5032 mris_fix_topology ru_nivcsw 505 FSRUNTIME@ mris_fix_topology lh 0.4174 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 213589 - 640761 + 427174 = 2 --> 0 holes F =2V-4: 427174 = 427178-4 (0) 2E=3F: 1281522 = 1281522 (0) total defect index = 0 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 69 intersecting 001: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue May 25 21:22:20 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-06 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... 43072 bright wm thresholded. 19 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.orig... computing class statistics... border white: 444165 voxels (1.36%) border gray 461455 voxels (1.41%) WM (102.0): 102.0 +- 6.9 [70.0 --> 110.0] GM (80.0) : 79.3 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.0 (was 70) setting MAX_BORDER_WHITE to 115.9 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 56.1 (was 40) setting MAX_GRAY to 102.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.66 +- 0.17 (0.02-->4.16) (max @ vno 57290 --> 68926) face area 0.18 +- 0.08 (0.00-->2.69) mean absolute distance = 1.44 +- 1.56 6817 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=76+-5.2 mean inside = 100.1, mean outside = 81.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=95.3, 94 (94) missing vertices, mean dist -0.8 [2.0 (%56.1)->0.5 (%43.9))] %48 local maxima, %37 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg61, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, 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 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 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.70 +- 0.19 (0.03-->4.22) (max @ vno 57290 --> 68926) face area 0.18 +- 0.09 (0.00-->2.54) mean absolute distance = 0.57 +- 0.80 7068 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5143934.0, rms=10.154 001: dt: 0.5000, sse=2477667.2, rms=6.210 (38.837%) 002: dt: 0.5000, sse=1595623.6, rms=4.108 (33.853%) 003: dt: 0.5000, sse=1448218.6, rms=3.573 (13.034%) 004: dt: 0.5000, sse=1408941.2, rms=3.438 (3.770%) 005: dt: 0.5000, sse=1380486.5, rms=3.371 (1.932%) rms = 3.34, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=1379304.4, rms=3.340 (0.939%) 007: dt: 0.2500, sse=1069700.9, rms=1.941 (41.872%) 008: dt: 0.2500, sse=1010147.8, rms=1.533 (21.035%) 009: dt: 0.2500, sse=1013055.4, rms=1.394 (9.050%) 010: dt: 0.2500, sse=989672.1, rms=1.311 (5.981%) rms = 1.28, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=984849.4, rms=1.276 (2.656%) 012: dt: 0.1250, sse=980909.9, rms=1.217 (4.605%) rms = 1.19, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=958783.3, rms=1.189 (2.313%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.3, 164 (42) missing vertices, mean dist -0.2 [1.0 (%37.3)->0.3 (%62.7))] %82 local maxima, %10 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg61, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.69 +- 0.19 (0.05-->4.29) (max @ vno 57290 --> 68926) face area 0.21 +- 0.10 (0.00-->3.28) mean absolute distance = 0.31 +- 0.55 8201 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1781198.6, rms=4.381 014: dt: 0.5000, sse=1426876.6, rms=3.062 (30.119%) rms = 3.16, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=1174129.1, rms=2.052 (32.990%) 016: dt: 0.2500, sse=1119798.0, rms=1.410 (31.252%) 017: dt: 0.2500, sse=1061322.5, rms=1.213 (14.022%) 018: dt: 0.2500, sse=1057813.2, rms=1.126 (7.172%) rms = 1.08, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=1066514.5, rms=1.078 (4.235%) 020: dt: 0.1250, sse=1037120.0, rms=1.021 (5.302%) rms = 1.00, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=1045572.3, rms=0.999 (2.146%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.2, 127 (12) missing vertices, mean dist -0.1 [0.6 (%34.4)->0.2 (%65.6))] %91 local maxima, % 3 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg61, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.69 +- 0.18 (0.03-->3.96) (max @ vno 57290 --> 68926) face area 0.20 +- 0.09 (0.00-->3.39) mean absolute distance = 0.22 +- 0.41 6315 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1202004.0, rms=2.342 rms = 2.37, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=1075946.1, rms=1.672 (28.604%) 023: dt: 0.2500, sse=1035783.0, rms=1.157 (30.834%) 024: dt: 0.2500, sse=1026624.8, rms=1.042 (9.880%) 025: dt: 0.2500, sse=1035930.2, rms=0.991 (4.888%) rms = 0.97, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=1011147.1, rms=0.975 (1.650%) rms = 0.93, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=1012639.9, rms=0.931 (4.524%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=93.8, 165 (11) missing vertices, mean dist -0.0 [0.4 (%29.5)->0.1 (%70.5))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg61, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1085174.2, rms=1.617 rms = 1.68, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=1017293.6, rms=1.133 (29.900%) 029: dt: 0.2500, sse=998400.9, rms=0.801 (29.294%) rms = 0.77, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=996696.4, rms=0.775 (3.307%) rms = 0.75, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=986312.1, rms=0.749 (3.376%) positioning took 0.5 minutes generating cortex label... 13 non-cortical segments detected only using segment with 10814 vertices erasing segment 0 (vno[0] = 14752) erasing segment 1 (vno[0] = 45061) erasing segment 2 (vno[0] = 50972) erasing segment 3 (vno[0] = 67203) erasing segment 5 (vno[0] = 99700) erasing segment 6 (vno[0] = 136465) erasing segment 7 (vno[0] = 137928) erasing segment 8 (vno[0] = 139248) erasing segment 9 (vno[0] = 140687) erasing segment 10 (vno[0] = 143491) erasing segment 11 (vno[0] = 146395) erasing segment 12 (vno[0] = 213531) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.area vertex spacing 0.69 +- 0.19 (0.02-->3.96) (max @ vno 111236 --> 213331) face area 0.20 +- 0.09 (0.00-->3.48) refinement took 5.4 minutes #-------------------------------------------- #@# Smooth2 lh Tue May 25 21:27:45 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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... #-------------------------------------------- #@# Inflation2 lh Tue May 25 21:27:51 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_inflate -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/touch/rusage.mris_inflate.lh.dat -n 50 ../surf/lh.smoothwm ../surf/lh.inflated niterations = 50 Reading ../surf/lh.smoothwm avg radius = 44.3 mm, total surface area = 79192 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.157 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.021 (target=0.015) step 065: RMS=0.020 (target=0.015) step 070: RMS=0.019 (target=0.015) step 075: RMS=0.018 (target=0.015) step 080: RMS=0.017 (target=0.015) step 085: RMS=0.017 (target=0.015) step 090: RMS=0.016 (target=0.015) step 095: RMS=0.016 (target=0.015) step 100: RMS=0.015 (target=0.015) step 105: RMS=0.015 (target=0.015) step 110: RMS=0.015 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 207.077233 mris_inflate stimesec 1.416271 mris_inflate ru_maxrss 341948 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 505111 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 16696 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 76698 mris_inflate ru_nivcsw 283 #-------------------------------------------- #@# Curv .H and .K lh Tue May 25 21:28:30 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf mris_curvature -w lh.white.preaparc total integrated curvature = 35.281*4pi (443.349) --> -34 handles ICI = 240.7, FI = 2490.2, variation=38750.010 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 366 vertices thresholded to be in k1 ~ [-0.14 0.28], k2 ~ [-0.09 0.05] total integrated curvature = 0.692*4pi (8.700) --> 0 handles ICI = 1.4, FI = 6.6, variation=118.669 213 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 242 vertices thresholded to be in [-0.11 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.019 done. #----------------------------------------- #@# Curvature Stats lh Tue May 25 21:29:56 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-06 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-06/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 vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 384 ] Gb_filter = 0 WARN: S lookup min: -0.598167 WARN: S explicit min: 0.000000 vertex = 46 #-------------------------------------------- #@# Sphere lh Tue May 25 21:30:01 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_sphere -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.306... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=blg61, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.26 pass 1: epoch 2 of 3 starting distance error %19.18 unfolding complete - removing small folds... starting distance error %19.13 removing remaining folds... final distance error %19.15 MRISunfold() return, current seed 1234 -01: dt=0.0000, 330 negative triangles 151: dt=0.9900, 330 negative triangles 152: dt=0.9900, 165 negative triangles 153: dt=0.9900, 105 negative triangles 154: dt=0.9900, 83 negative triangles 155: dt=0.9900, 59 negative triangles 156: dt=0.9900, 53 negative triangles 157: dt=0.9900, 50 negative triangles 158: dt=0.9900, 38 negative triangles 159: dt=0.9900, 41 negative triangles 160: dt=0.9900, 38 negative triangles 161: dt=0.9900, 29 negative triangles 162: dt=0.9900, 24 negative triangles 163: dt=0.9900, 23 negative triangles 164: dt=0.9900, 24 negative triangles 165: dt=0.9900, 20 negative triangles 166: dt=0.9900, 17 negative triangles 167: dt=0.9900, 14 negative triangles 168: dt=0.9900, 9 negative triangles 169: dt=0.9900, 9 negative triangles 170: dt=0.9900, 10 negative triangles 171: dt=0.9900, 8 negative triangles 172: dt=0.9900, 7 negative triangles 173: dt=0.9900, 7 negative triangles 174: dt=0.9900, 2 negative triangles 175: dt=0.9900, 4 negative triangles 176: dt=0.9900, 4 negative triangles 177: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.22 hours mris_sphere utimesec 5252.434725 mris_sphere stimesec 7.776878 mris_sphere ru_maxrss 472568 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 4467643 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1032 mris_sphere ru_oublock 15024 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 112415 mris_sphere ru_nivcsw 18658 FSRUNTIME@ mris_sphere 0.2189 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Tue May 25 21:43:09 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts cmdline mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=blg61, 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=blg61, 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 curvature mean = 0.000, std = 5.675 curvature mean = 0.027, std = 0.817 curvature mean = 0.019, std = 0.875 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 481620.3, tmin=1.1849 d=32.00 min @ (0.00, 8.00, -8.00) sse = 375659.8, tmin=2.3758 d=16.00 min @ (0.00, -4.00, 0.00) sse = 331498.7, tmin=3.5815 d=8.00 min @ (2.00, 2.00, 2.00) sse = 320963.3, tmin=4.7699 d=4.00 min @ (0.00, -1.00, -1.00) sse = 317239.5, tmin=5.9641 d=2.00 min @ (0.00, 0.50, 0.00) sse = 316793.8, tmin=7.1198 d=1.00 min @ (-0.25, -0.25, 0.25) sse = 316697.9, tmin=8.2541 d=0.50 min @ (0.25, 0.12, -0.12) sse = 316656.2, tmin=9.4011 tol=1.0e+00, sigma=0.5, host=blg61, 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 MRISrigidBodyAlignGlobal() done 9.40 min curvature mean = -0.009, std = 0.838 curvature mean = 0.005, std = 0.953 curvature mean = -0.016, std = 0.846 curvature mean = 0.002, std = 0.982 curvature mean = -0.021, std = 0.846 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.036, std = 0.353 curvature mean = 0.035, std = 0.245 curvature mean = 0.047, std = 0.305 curvature mean = 0.032, std = 0.302 curvature mean = 0.020, std = 0.485 curvature mean = 0.032, std = 0.327 curvature mean = 0.011, std = 0.625 curvature mean = 0.032, std = 0.337 curvature mean = 0.004, std = 0.728 MRISregister() return, current seed 0 -01: dt=0.0000, 47 negative triangles 119: dt=0.9900, 47 negative triangles 120: dt=0.9405, 54 negative triangles expanding nbhd size to 1 121: dt=0.9900, 53 negative triangles 122: dt=0.9900, 37 negative triangles 123: dt=0.9900, 35 negative triangles 124: dt=0.9900, 31 negative triangles 125: dt=0.9900, 24 negative triangles 126: dt=0.9900, 26 negative triangles 127: dt=0.9900, 19 negative triangles 128: dt=0.9900, 17 negative triangles 129: dt=0.9900, 16 negative triangles 130: dt=0.9900, 12 negative triangles 131: dt=0.9900, 14 negative triangles 132: dt=0.9900, 16 negative triangles 133: dt=0.9900, 13 negative triangles 134: dt=0.9900, 12 negative triangles 135: dt=0.9900, 11 negative triangles 136: dt=0.9900, 8 negative triangles 137: dt=0.9900, 10 negative triangles 138: dt=0.9900, 6 negative triangles 139: dt=0.9900, 6 negative triangles 140: dt=0.9900, 4 negative triangles 141: dt=0.9900, 5 negative triangles 142: dt=0.9900, 3 negative triangles 143: dt=0.9900, 4 negative triangles 144: dt=0.9900, 2 negative triangles 145: dt=0.9900, 4 negative triangles 146: dt=0.9900, 1 negative triangles 147: dt=0.9900, 1 negative triangles 148: dt=0.9900, 1 negative triangles 149: dt=0.9900, 2 negative triangles 150: dt=0.9900, 2 negative triangles 151: dt=0.9900, 2 negative triangles 152: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.58 hours mris_register utimesec 10111.303121 mris_register stimesec 31.234679 mris_register ru_maxrss 391384 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 13874247 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 27100 mris_register ru_oublock 15032 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 99908 mris_register ru_nivcsw 39798 FSRUNTIME@ mris_register 0.5848 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Tue May 25 22:18:15 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 #-------------------------------------------- #@# AvgCurv lh Tue May 25 22:18:18 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue May 25 22:18:20 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-06 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1636 labels changed using aseg relabeling using gibbs priors... 000: 4564 changed, 213589 examined... 001: 1118 changed, 18725 examined... 002: 294 changed, 6088 examined... 003: 108 changed, 1785 examined... 004: 47 changed, 660 examined... 005: 26 changed, 282 examined... 006: 11 changed, 163 examined... 007: 3 changed, 70 examined... 008: 1 changed, 14 examined... 009: 0 changed, 5 examined... 370 labels changed using aseg 000: 145 total segments, 100 labels (555 vertices) changed 001: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2415 vertices marked for relabeling... 2415 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 16 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue May 25 22:18:35 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-06 lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... 43072 bright wm thresholded. 19 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.orig... computing class statistics... border white: 444165 voxels (1.36%) border gray 461455 voxels (1.41%) WM (102.0): 102.0 +- 6.9 [70.0 --> 110.0] GM (80.0) : 79.3 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.0 (was 70) setting MAX_BORDER_WHITE to 115.9 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 56.1 (was 40) setting MAX_GRAY to 102.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.1 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-3.5, GM=76+-5.2 mean inside = 100.1, mean outside = 81.2 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.69 +- 0.19 (0.02-->3.96) (max @ vno 111236 --> 213331) face area 0.20 +- 0.09 (0.00-->3.49) mean absolute distance = 1.29 +- 1.40 6412 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 42 points - only 0.00% unknown deleting segment 3 with 24 points - only 0.00% unknown deleting segment 5 with 97 points - only 0.00% unknown deleting segment 6 with 60 points - only 0.00% unknown deleting segment 7 with 533 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown mean border=95.1, 159 (154) missing vertices, mean dist -0.6 [2.3 (%40.3)->0.5 (%59.7))] %48 local maxima, %37 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg61, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, 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 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 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.70 +- 0.19 (0.03-->4.32) (max @ vno 213327 --> 111236) face area 0.20 +- 0.10 (0.00-->3.77) mean absolute distance = 0.55 +- 0.78 6586 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2251198.0, rms=5.592 001: dt: 0.5000, sse=1430170.9, rms=3.310 (40.806%) 002: dt: 0.5000, sse=1379327.5, rms=3.109 (6.072%) rms = 3.16, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=1152008.9, rms=2.069 (33.444%) 004: dt: 0.2500, sse=1079223.0, rms=1.491 (27.940%) 005: dt: 0.2500, sse=1057431.4, rms=1.333 (10.585%) 006: dt: 0.2500, sse=1044874.9, rms=1.248 (6.427%) 007: dt: 0.2500, sse=1050672.6, rms=1.197 (4.067%) rms = 1.17, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=1038315.2, rms=1.166 (2.547%) rms = 1.13, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=1031261.6, rms=1.131 (3.043%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 39 points - only 0.00% unknown deleting segment 3 with 29 points - only 0.00% unknown deleting segment 4 with 84 points - only 0.00% unknown deleting segment 5 with 64 points - only 0.00% unknown deleting segment 6 with 567 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=94.3, 157 (54) missing vertices, mean dist -0.2 [0.9 (%37.5)->0.3 (%62.5))] %83 local maxima, %10 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg61, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.69 +- 0.19 (0.03-->4.37) (max @ vno 213327 --> 111236) face area 0.21 +- 0.10 (0.00-->4.15) mean absolute distance = 0.31 +- 0.55 8259 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1722184.9, rms=4.195 010: dt: 0.5000, sse=1372976.4, rms=2.972 (29.156%) rms = 3.11, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=1151407.1, rms=1.936 (34.857%) 012: dt: 0.2500, sse=1080795.8, rms=1.300 (32.836%) 013: dt: 0.2500, sse=1059468.4, rms=1.120 (13.873%) 014: dt: 0.2500, sse=1048547.4, rms=1.047 (6.521%) rms = 1.02, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=1051619.6, rms=1.015 (2.998%) 016: dt: 0.1250, sse=1035387.9, rms=0.963 (5.154%) rms = 0.95, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=1033962.6, rms=0.946 (1.794%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 35 points - only 0.00% unknown deleting segment 4 with 31 points - only 0.00% unknown deleting segment 5 with 84 points - only 0.00% unknown deleting segment 6 with 62 points - only 0.00% unknown deleting segment 7 with 417 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 49 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown mean border=94.2, 153 (36) missing vertices, mean dist -0.1 [0.6 (%34.4)->0.2 (%65.6))] %91 local maxima, % 3 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg61, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.69 +- 0.19 (0.02-->4.43) (max @ vno 213327 --> 111236) face area 0.20 +- 0.09 (0.00-->4.16) mean absolute distance = 0.22 +- 0.41 6226 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1178492.6, rms=2.261 rms = 2.33, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=1069598.5, rms=1.587 (29.806%) 019: dt: 0.2500, sse=1019511.6, rms=1.092 (31.183%) 020: dt: 0.2500, sse=1014207.2, rms=0.993 (9.122%) rms = 0.97, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=1011450.9, rms=0.967 (2.549%) 022: dt: 0.1250, sse=1019790.8, rms=0.914 (5.559%) rms = 0.90, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=1000668.4, rms=0.901 (1.333%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 35 points - only 0.00% unknown deleting segment 4 with 30 points - only 0.00% unknown deleting segment 5 with 83 points - only 0.00% unknown deleting segment 6 with 64 points - only 0.00% unknown deleting segment 7 with 406 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 46 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=93.8, 162 (26) missing vertices, mean dist -0.0 [0.4 (%29.6)->0.1 (%70.4))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg61, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1070451.8, rms=1.594 rms = 1.67, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=1013257.6, rms=1.106 (30.611%) 025: dt: 0.2500, sse=998223.2, rms=0.784 (29.143%) rms = 0.76, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=998481.2, rms=0.756 (3.574%) rms = 0.73, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=988418.6, rms=0.728 (3.648%) positioning took 0.5 minutes generating cortex label... 16 non-cortical segments detected only using segment with 10748 vertices erasing segment 0 (vno[0] = 14752) erasing segment 1 (vno[0] = 45061) erasing segment 2 (vno[0] = 50972) erasing segment 3 (vno[0] = 56827) erasing segment 4 (vno[0] = 68555) erasing segment 6 (vno[0] = 99700) erasing segment 7 (vno[0] = 120345) erasing segment 8 (vno[0] = 123048) erasing segment 9 (vno[0] = 129110) erasing segment 10 (vno[0] = 136492) erasing segment 11 (vno[0] = 140687) erasing segment 12 (vno[0] = 143491) erasing segment 13 (vno[0] = 146395) erasing segment 14 (vno[0] = 153840) erasing segment 15 (vno[0] = 213531) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.area vertex spacing 0.69 +- 0.19 (0.02-->4.56) (max @ vno 111236 --> 213331) face area 0.20 +- 0.09 (0.00-->4.25) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 44 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 31 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 209 points - only 0.00% unknown deleting segment 6 with 86 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 18 points - only 0.00% unknown deleting segment 10 with 52 points - only 0.00% unknown deleting segment 12 with 45 points - only 0.00% unknown deleting segment 16 with 43 points - only 0.00% unknown deleting segment 17 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 18 with 2 points - only 0.00% unknown deleting segment 19 with 82 points - only 0.00% unknown deleting segment 20 with 29 points - only 0.00% unknown deleting segment 21 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 22 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 23 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=73.8, 178 (178) missing vertices, mean dist 0.7 [0.2 (%0.0)->1.1 (%100.0))] %17 local maxima, %43 large gradients and %36 min vals, 38 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg61, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=19126182.0, rms=21.111 001: dt: 0.0500, sse=14662246.0, rms=18.336 (13.147%) 002: dt: 0.0500, sse=12360405.0, rms=16.725 (8.783%) 003: dt: 0.0500, sse=10902969.0, rms=15.620 (6.610%) 004: dt: 0.0500, sse=9865760.0, rms=14.782 (5.360%) 005: dt: 0.0500, sse=9069175.0, rms=14.106 (4.579%) 006: dt: 0.0500, sse=8423725.0, rms=13.532 (4.065%) 007: dt: 0.0500, sse=7880287.0, rms=13.030 (3.713%) 008: dt: 0.0500, sse=7412642.5, rms=12.581 (3.443%) 009: dt: 0.0500, sse=7002282.0, rms=12.174 (3.238%) 010: dt: 0.0500, sse=6636965.0, rms=11.799 (3.077%) positioning took 1.1 minutes mean border=68.2, 94 (61) missing vertices, mean dist 0.8 [0.1 (%0.0)->1.2 (%100.0))] %18 local maxima, %43 large gradients and %35 min vals, 88 gradients ignored tol=1.0e-04, sigma=2.0, host=blg61, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=13727880.0, rms=17.694 011: dt: 0.0500, sse=13148690.0, rms=17.287 (2.299%) 012: dt: 0.0500, sse=12643468.0, rms=16.924 (2.100%) 013: dt: 0.0500, sse=12197955.0, rms=16.597 (1.931%) 014: dt: 0.0500, sse=11800957.0, rms=16.300 (1.788%) 015: dt: 0.0500, sse=11443399.0, rms=16.028 (1.670%) 016: dt: 0.0500, sse=11118521.0, rms=15.777 (1.569%) 017: dt: 0.0500, sse=10820160.0, rms=15.542 (1.487%) 018: dt: 0.0500, sse=10541502.0, rms=15.320 (1.431%) 019: dt: 0.0500, sse=10275106.0, rms=15.104 (1.408%) 020: dt: 0.0500, sse=10017758.0, rms=14.893 (1.399%) positioning took 1.1 minutes mean border=66.2, 116 (42) missing vertices, mean dist 0.8 [0.1 (%0.2)->1.2 (%99.8))] %18 local maxima, %42 large gradients and %35 min vals, 133 gradients ignored tol=1.0e-04, sigma=2.0, host=blg61, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11368791.0, rms=15.975 021: dt: 0.0500, sse=11050944.0, rms=15.727 (1.548%) 022: dt: 0.0500, sse=10752472.0, rms=15.491 (1.500%) 023: dt: 0.0500, sse=10471532.0, rms=15.266 (1.455%) 024: dt: 0.0500, sse=10205538.0, rms=15.049 (1.419%) 025: dt: 0.0500, sse=9952617.0, rms=14.840 (1.389%) 026: dt: 0.0500, sse=9709566.0, rms=14.636 (1.373%) 027: dt: 0.0500, sse=9474753.0, rms=14.437 (1.365%) 028: dt: 0.0500, sse=9246897.0, rms=14.240 (1.362%) 029: dt: 0.0500, sse=9024071.0, rms=14.045 (1.369%) 030: dt: 0.0500, sse=8805163.0, rms=13.851 (1.382%) positioning took 1.1 minutes mean border=65.3, 116 (26) missing vertices, mean dist 0.7 [0.1 (%1.7)->1.1 (%98.3))] %18 local maxima, %43 large gradients and %34 min vals, 111 gradients ignored tol=1.0e-04, sigma=2.0, host=blg61, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=9581819.0, rms=14.523 031: dt: 0.5000, sse=7897381.5, rms=13.009 (10.427%) 032: dt: 0.5000, sse=6529093.5, rms=11.636 (10.553%) 033: dt: 0.5000, sse=5280663.0, rms=10.238 (12.019%) 034: dt: 0.5000, sse=4300848.5, rms=8.981 (12.276%) 035: dt: 0.5000, sse=3525366.5, rms=7.852 (12.572%) 036: dt: 0.5000, sse=3062837.5, rms=7.092 (9.682%) 037: dt: 0.5000, sse=2772731.8, rms=6.573 (7.317%) 038: dt: 0.5000, sse=2642910.0, rms=6.326 (3.756%) 039: dt: 0.5000, sse=2541503.8, rms=6.126 (3.152%) 040: dt: 0.5000, sse=2503271.8, rms=6.048 (1.275%) 041: dt: 0.5000, sse=2456374.0, rms=5.952 (1.587%) rms = 5.93, time step reduction 1 of 3 to 0.250... 042: dt: 0.5000, sse=2447994.2, rms=5.933 (0.321%) 043: dt: 0.2500, sse=2166178.8, rms=5.263 (11.304%) 044: dt: 0.2500, sse=2102721.2, rms=5.111 (2.888%) rms = 5.15, time step reduction 2 of 3 to 0.125... 045: dt: 0.1250, sse=2062111.6, rms=5.006 (2.043%) 046: dt: 0.1250, sse=2011446.5, rms=4.871 (2.700%) rms = 4.85, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=2004846.4, rms=4.852 (0.389%) positioning took 2.6 minutes mean border=62.4, 3417 (6) missing vertices, mean dist 0.2 [0.2 (%19.8)->0.5 (%80.2))] %35 local maxima, %27 large gradients and %32 min vals, 120 gradients ignored tol=1.0e-04, sigma=1.0, host=blg61, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3332876.8, rms=7.047 048: dt: 0.5000, sse=3217586.5, rms=6.828 (3.108%) 049: dt: 0.5000, sse=2842710.0, rms=6.130 (10.227%) rms = 6.11, time step reduction 1 of 3 to 0.250... 050: dt: 0.5000, sse=2840830.0, rms=6.114 (0.260%) 051: dt: 0.2500, sse=2245006.2, rms=4.688 (23.326%) 052: dt: 0.2500, sse=2090234.0, rms=4.248 (9.371%) 053: dt: 0.2500, sse=1995616.2, rms=3.958 (6.826%) 054: dt: 0.2500, sse=1899258.9, rms=3.647 (7.876%) 055: dt: 0.2500, sse=1848573.2, rms=3.468 (4.900%) 056: dt: 0.2500, sse=1801889.1, rms=3.298 (4.888%) rms = 3.28, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1796685.6, rms=3.278 (0.618%) 058: dt: 0.1250, sse=1606560.4, rms=2.414 (26.365%) 059: dt: 0.1250, sse=1581576.9, rms=2.283 (5.408%) rms = 2.25, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1575643.6, rms=2.251 (1.390%) positioning took 2.3 minutes mean border=61.0, 3777 (4) missing vertices, mean dist 0.1 [0.2 (%21.9)->0.2 (%78.1))] %45 local maxima, %17 large gradients and %31 min vals, 131 gradients ignored tol=1.0e-04, sigma=0.5, host=blg61, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1829790.2, rms=3.262 rms = 4.68, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1711004.9, rms=2.757 (15.465%) 062: dt: 0.2500, sse=1686063.2, rms=2.642 (4.191%) rms = 2.79, time step reduction 2 of 3 to 0.125... 063: dt: 0.1250, sse=1668200.1, rms=2.552 (3.381%) 064: dt: 0.1250, sse=1646752.9, rms=2.446 (4.156%) rms = 2.40, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1637175.8, rms=2.399 (1.930%) positioning took 1.1 minutes mean border=60.3, 8067 (4) missing vertices, mean dist 0.0 [0.2 (%28.8)->0.1 (%71.2))] %47 local maxima, %14 large gradients and %30 min vals, 101 gradients ignored tol=1.0e-04, sigma=0.2, host=blg61, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1680167.2, rms=2.594 rms = 3.60, time step reduction 1 of 3 to 0.250... 066: dt: 0.2500, sse=1649239.9, rms=2.435 (6.141%) rms = 2.44, time step reduction 2 of 3 to 0.125... rms = 2.41, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1643548.6, rms=2.405 (1.227%) positioning took 0.6 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.area.pial vertex spacing 0.80 +- 0.35 (0.02-->5.74) (max @ vno 144920 --> 144891) face area 0.25 +- 0.20 (0.00-->4.83) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 213589 vertices processed 25000 of 213589 vertices processed 50000 of 213589 vertices processed 75000 of 213589 vertices processed 100000 of 213589 vertices processed 125000 of 213589 vertices processed 150000 of 213589 vertices processed 175000 of 213589 vertices processed 200000 of 213589 vertices processed 0 of 213589 vertices processed 25000 of 213589 vertices processed 50000 of 213589 vertices processed 75000 of 213589 vertices processed 100000 of 213589 vertices processed 125000 of 213589 vertices processed 150000 of 213589 vertices processed 175000 of 213589 vertices processed 200000 of 213589 vertices processed thickness calculation complete, 161:456 truncations. 35913 vertices at 0 distance 122653 vertices at 1 distance 132669 vertices at 2 distance 73702 vertices at 3 distance 29108 vertices at 4 distance 9516 vertices at 5 distance 2694 vertices at 6 distance 776 vertices at 7 distance 283 vertices at 8 distance 142 vertices at 9 distance 101 vertices at 10 distance 73 vertices at 11 distance 71 vertices at 12 distance 41 vertices at 13 distance 21 vertices at 14 distance 15 vertices at 15 distance 11 vertices at 16 distance 17 vertices at 17 distance 12 vertices at 18 distance 19 vertices at 19 distance 19 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.thickness positioning took 17.3 minutes #-------------------------------------------- #@# Surf Volume lh Tue May 25 22:35:51 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-06 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label Total face volume 233531 Total vertex volume 231416 (mask=0) #@# sub-06 lh 231416 vertexvol Done #----------------------------------------- #@# Cortical Parc 2 lh Tue May 25 22:35:56 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-06 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 118 labels changed using aseg relabeling using gibbs priors... 000: 13336 changed, 213589 examined... 001: 3235 changed, 51466 examined... 002: 976 changed, 16769 examined... 003: 383 changed, 5403 examined... 004: 181 changed, 2245 examined... 005: 68 changed, 1020 examined... 006: 45 changed, 387 examined... 007: 29 changed, 255 examined... 008: 19 changed, 152 examined... 009: 9 changed, 101 examined... 010: 5 changed, 53 examined... 011: 4 changed, 31 examined... 012: 3 changed, 19 examined... 013: 4 changed, 17 examined... 014: 3 changed, 15 examined... 015: 3 changed, 20 examined... 016: 0 changed, 14 examined... 4 labels changed using aseg 000: 387 total segments, 299 labels (3787 vertices) changed 001: 106 total segments, 18 labels (91 vertices) changed 002: 89 total segments, 1 labels (3 vertices) changed 003: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 61 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1484 vertices marked for relabeling... 1484 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. #----------------------------------------- #@# Cortical Parc 3 lh Tue May 25 22:36:16 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-06 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1644 labels changed using aseg relabeling using gibbs priors... 000: 2752 changed, 213589 examined... 001: 659 changed, 12582 examined... 002: 199 changed, 3848 examined... 003: 94 changed, 1171 examined... 004: 41 changed, 519 examined... 005: 28 changed, 230 examined... 006: 18 changed, 155 examined... 007: 13 changed, 98 examined... 008: 13 changed, 75 examined... 009: 13 changed, 69 examined... 010: 7 changed, 67 examined... 011: 5 changed, 44 examined... 012: 5 changed, 28 examined... 013: 7 changed, 33 examined... 014: 7 changed, 41 examined... 015: 5 changed, 38 examined... 016: 5 changed, 23 examined... 017: 10 changed, 27 examined... 018: 8 changed, 39 examined... 019: 5 changed, 40 examined... 020: 4 changed, 24 examined... 021: 5 changed, 22 examined... 022: 3 changed, 22 examined... 023: 5 changed, 20 examined... 024: 8 changed, 24 examined... 025: 4 changed, 30 examined... 026: 5 changed, 25 examined... 027: 6 changed, 29 examined... 028: 6 changed, 26 examined... 029: 5 changed, 27 examined... 030: 6 changed, 22 examined... 031: 4 changed, 20 examined... 032: 0 changed, 20 examined... 422 labels changed using aseg 000: 65 total segments, 32 labels (514 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1018 vertices marked for relabeling... 1018 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# WM/GM Contrast lh Tue May 25 22:36:32 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts pctsurfcon --s sub-06 --lh-only Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts/pctsurfcon.log Tue May 25 22:36:32 UTC 2021 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux blg6114.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/tmp.pctsurfcon.260221/lh.wm.mgh --regheader sub-06 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00001; 0.00000 -1.00000 0.00000 0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 113520 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/tmp.pctsurfcon.260221/lh.wm.mgh Dim: 213589 1 1 mri_vol2surf --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/tmp.pctsurfcon.260221/lh.gm.mgh --projfrac 0.3 --regheader sub-06 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00001; 0.00000 -1.00000 0.00000 0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Done reading source surface Reading thickness /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 134507 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/tmp.pctsurfcon.260221/lh.gm.mgh Dim: 213589 1 1 mri_concat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/tmp.pctsurfcon.260221/lh.wm.mgh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/tmp.pctsurfcon.260221/lh.gm.mgh --paired-diff-norm --mul 100 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.w-g.pct.mgh mri_segstats --in /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.w-g.pct.mgh --annot sub-06 lh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.w-g.pct.mgh --annot sub-06 lh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/stats/lh.w-g.pct.stats --snr sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Constructing seg from annotation Reading annotation /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.w-g.pct.mgh Vertex Area is 0.401406 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 Started at Tue May 25 20:52:22 UTC 2021 Ended at Tue May 25 22:36:48 UTC 2021 #@#%# recon-all-run-time-hours 1.741 recon-all -s sub-06 finished without error at Tue May 25 22:36:49 UTC 2021 New invocation of recon-all Wed May 26 00:11:01 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-06 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon subjid sub-06 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux blg6114.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767932 maxlocks unlimited maxsignal 767932 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638260 139097436 7280880 2233852 50259944 48614064 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:11:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: blg6114.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# Parcellation Stats lh Wed May 26 00:11:03 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-06 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 239272 Total vertex volume 236896 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) 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) = 1492006 mm^3 (det: 1.305695 ) lhCtxGM: 233674.454 460316.000 diff=-226641.5 pctdiff=-96.990 rhCtxGM: 231736.832 454865.000 diff=-223128.2 pctdiff=-96.285 lhCtxWM: 174557.758 398559.500 diff=-224001.7 pctdiff=-128.325 rhCtxWM: 175837.258 403253.500 diff=-227416.2 pctdiff=-129.333 SubCortGMVol 102400.000 SupraTentVol 943733.301 (1856802.000) diff=-913068.699 pctdiff=-96.751 SupraTentVolNotVent 906351.301 (1819420.000) diff=-913068.699 pctdiff=-100.741 BrainSegVol 2130875.000 (2126469.000) diff=4406.000 pctdiff=0.207 BrainSegVolNotVent 2087714.000 (1186381.301) diff=901332.699 pctdiff=43.173 BrainSegVolNotVent 2087714.000 CerebellumVol 268149.000 VentChorVol 37382.000 3rd4th5thCSF 5779.000 CSFVol 1373.000, OptChiasmVol 145.000 MaskVol 2624308.000 2029 872 2341 2.643 0.498 0.081 0.028 47 3.0 bankssts 1642 618 1910 2.507 0.879 0.094 0.029 27 2.1 caudalanteriorcingulate 5333 2181 6155 2.555 0.417 0.084 0.021 55 4.6 caudalmiddlefrontal 3472 1240 3147 2.235 0.431 0.090 0.024 39 3.8 cuneus 1193 505 2229 3.573 0.816 0.087 0.030 11 1.6 entorhinal 7240 3020 9932 2.803 0.594 0.098 0.027 94 8.7 fusiform 8319 3394 9943 2.585 0.428 0.087 0.021 91 7.0 inferiorparietal 8676 3456 11233 2.732 0.668 0.087 0.027 107 9.9 inferiortemporal 1751 712 1548 2.184 1.053 0.098 0.035 25 2.4 isthmuscingulate 12403 4545 11958 2.314 0.555 0.095 0.028 133 14.6 lateraloccipital 7026 2887 9484 2.848 0.634 0.091 0.025 88 7.5 lateralorbitofrontal 6173 2387 5672 2.123 0.506 0.102 0.034 77 8.6 lingual 4316 1776 5092 2.422 0.640 0.091 0.030 57 5.8 medialorbitofrontal 7373 2916 10869 2.784 0.690 0.091 0.026 95 8.2 middletemporal 1626 635 2263 3.014 0.554 0.082 0.026 15 1.9 parahippocampal 3046 1222 3487 2.573 0.382 0.076 0.176 380 2.0 paracentral 4085 1700 5123 2.653 0.516 0.081 0.019 38 3.3 parsopercularis 2036 814 2668 2.587 0.533 0.108 0.033 35 2.9 parsorbitalis 3399 1375 4138 2.590 0.432 0.085 0.020 35 2.8 parstriangularis 3601 1386 2572 2.004 0.421 0.089 0.031 37 4.8 pericalcarine 10348 3875 9597 2.189 0.420 0.076 0.020 87 9.1 postcentral 2741 1087 3004 2.323 0.736 0.096 0.029 39 3.1 posteriorcingulate 12247 4593 13272 2.656 0.453 0.071 0.020 128 10.5 precentral 7938 3321 8682 2.476 0.423 0.096 0.026 97 8.6 precuneus 2125 836 2817 2.917 0.638 0.090 0.030 33 2.8 rostralanteriorcingulate 13686 5670 15754 2.381 0.452 0.098 0.025 183 14.6 rostralmiddlefrontal 19142 7866 24550 2.681 0.555 0.091 0.025 214 20.3 superiorfrontal 12078 4929 12696 2.271 0.433 0.087 0.020 135 9.6 superiorparietal 9574 3887 12209 2.752 0.595 0.084 0.019 100 7.7 superiortemporal 9905 3953 11058 2.518 0.464 0.091 0.027 159 12.0 supramarginal 651 279 1050 2.554 0.565 0.137 0.043 16 1.3 frontalpole 1059 436 2526 3.821 0.618 0.096 0.036 13 1.7 temporalpole 1137 439 1207 2.571 0.328 0.093 0.022 11 0.9 transversetemporal 4793 2082 6616 3.227 0.824 0.099 0.040 59 8.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-06 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 239272 Total vertex volume 236896 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) 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) = 1492006 mm^3 (det: 1.305695 ) lhCtxGM: 233674.454 460316.000 diff=-226641.5 pctdiff=-96.990 rhCtxGM: 231736.832 454865.000 diff=-223128.2 pctdiff=-96.285 lhCtxWM: 174557.758 398559.500 diff=-224001.7 pctdiff=-128.325 rhCtxWM: 175837.258 403253.500 diff=-227416.2 pctdiff=-129.333 SubCortGMVol 102400.000 SupraTentVol 943733.301 (1856802.000) diff=-913068.699 pctdiff=-96.751 SupraTentVolNotVent 906351.301 (1819420.000) diff=-913068.699 pctdiff=-100.741 BrainSegVol 2130875.000 (2126469.000) diff=4406.000 pctdiff=0.207 BrainSegVolNotVent 2087714.000 (1186381.301) diff=901332.699 pctdiff=43.173 BrainSegVolNotVent 2087714.000 CerebellumVol 268149.000 VentChorVol 37382.000 3rd4th5thCSF 5779.000 CSFVol 1373.000, OptChiasmVol 145.000 MaskVol 2624308.000 2029 850 2341 2.643 0.498 0.080 0.026 30 2.4 bankssts 1642 831 1910 2.507 0.879 0.091 0.027 22 1.4 caudalanteriorcingulate 5333 2525 6155 2.555 0.417 0.080 0.018 63 3.9 caudalmiddlefrontal 3472 1572 3147 2.235 0.431 0.080 0.020 22 3.1 cuneus 1193 734 2229 3.573 0.816 0.085 0.019 19 0.9 entorhinal 7240 3811 9932 2.803 0.594 0.094 0.025 698 7.4 fusiform 8319 4108 9943 2.585 0.428 0.090 0.022 272 8.0 inferiorparietal 8676 4386 11233 2.732 0.668 0.083 0.022 100 8.0 inferiortemporal 1751 814 1548 2.184 1.053 0.100 0.043 59 2.3 isthmuscingulate 12403 5602 11958 2.314 0.555 0.077 0.019 118 9.7 lateraloccipital 7026 3586 9484 2.848 0.634 0.092 0.023 87 7.1 lateralorbitofrontal 6173 2931 5672 2.123 0.506 0.093 0.046 88 17.3 lingual 4316 2353 5092 2.422 0.640 0.101 0.026 43 5.0 medialorbitofrontal 7373 4409 10869 2.784 0.690 0.104 0.043 134 17.7 middletemporal 1626 881 2263 3.014 0.554 0.084 0.020 11 1.2 parahippocampal 3046 1444 3487 2.573 0.382 0.074 0.015 26 2.0 paracentral 4085 2059 5123 2.653 0.516 0.083 0.017 27 3.1 parsopercularis 2036 1193 2668 2.587 0.533 0.113 0.035 36 3.3 parsorbitalis 3399 1722 4138 2.590 0.432 0.085 0.018 28 2.7 parstriangularis 3601 1162 2572 2.004 0.421 0.062 0.020 60 2.4 pericalcarine 10348 4787 9597 2.189 0.420 0.075 0.016 54 7.3 postcentral 2741 1354 3004 2.323 0.736 0.097 0.026 36 2.8 posteriorcingulate 12247 5307 13272 2.656 0.453 0.068 0.016 134 8.5 precentral 7938 3564 8682 2.476 0.423 0.091 0.026 124 9.0 precuneus 2125 1080 2817 2.917 0.638 0.099 0.026 23 2.5 rostralanteriorcingulate 13686 7054 15754 2.381 0.452 0.099 0.025 208 15.5 rostralmiddlefrontal 19142 9763 24550 2.681 0.555 0.094 0.025 220 20.0 superiorfrontal 12078 5836 12696 2.271 0.433 0.086 0.020 132 10.1 superiorparietal 9574 4743 12209 2.752 0.595 0.090 0.022 81 9.1 superiortemporal 9905 4628 11058 2.518 0.464 0.087 0.027 124 10.6 supramarginal 651 496 1050 2.554 0.565 0.146 0.029 8 0.9 frontalpole 1059 856 2526 3.821 0.618 0.110 0.021 6 1.0 temporalpole 1137 514 1207 2.571 0.328 0.073 0.015 18 0.6 transversetemporal 4793 1920 6616 3.227 0.824 0.094 0.073 259 18.5 insula #----------------------------------------- #@# Parcellation Stats 2 lh Wed May 26 00:13:11 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-06 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 239272 Total vertex volume 236896 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) 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) = 1492006 mm^3 (det: 1.305695 ) lhCtxGM: 233674.454 460316.000 diff=-226641.5 pctdiff=-96.990 rhCtxGM: 231736.832 454865.000 diff=-223128.2 pctdiff=-96.285 lhCtxWM: 174557.758 398559.500 diff=-224001.7 pctdiff=-128.325 rhCtxWM: 175837.258 403253.500 diff=-227416.2 pctdiff=-129.333 SubCortGMVol 102400.000 SupraTentVol 943733.301 (1856802.000) diff=-913068.699 pctdiff=-96.751 SupraTentVolNotVent 906351.301 (1819420.000) diff=-913068.699 pctdiff=-100.741 BrainSegVol 2130875.000 (2126469.000) diff=4406.000 pctdiff=0.207 BrainSegVolNotVent 2087714.000 (1186381.301) diff=901332.699 pctdiff=43.173 BrainSegVolNotVent 2087714.000 CerebellumVol 268149.000 VentChorVol 37382.000 3rd4th5thCSF 5779.000 CSFVol 1373.000, OptChiasmVol 145.000 MaskVol 2624308.000 2516 1066 2839 2.243 0.502 0.100 0.026 35 2.9 G&S_frontomargin 2878 1030 3443 2.709 0.565 0.099 0.033 36 3.9 G&S_occipital_inf 2508 849 2732 2.562 0.435 0.070 0.211 378 1.8 G&S_paracentral 2802 1093 3112 2.491 0.460 0.091 0.024 28 2.9 G&S_subcentral 1553 657 1948 2.293 0.403 0.120 0.036 31 2.6 G&S_transv_frontopol 3956 1604 5214 2.857 0.577 0.083 0.024 49 4.2 G&S_cingul-Ant 2140 873 2586 2.860 0.470 0.082 0.028 26 2.4 G&S_cingul-Mid-Ant 2537 1050 2872 2.605 0.401 0.087 0.027 28 2.6 G&S_cingul-Mid-Post 701 279 747 2.276 1.129 0.107 0.037 12 1.0 G_cingul-Post-dorsal 483 194 636 2.841 0.383 0.098 0.028 6 0.5 G_cingul-Post-ventral 3681 1247 3397 2.212 0.480 0.098 0.031 51 5.1 G_cuneus 2415 1003 3774 2.823 0.437 0.094 0.023 34 2.5 G_front_inf-Opercular 891 357 1607 3.061 0.445 0.096 0.026 12 1.0 G_front_inf-Orbital 2002 791 2909 2.749 0.378 0.104 0.028 32 2.3 G_front_inf-Triangul 7393 2924 10445 2.616 0.447 0.108 0.031 137 9.8 G_front_middle 12483 5081 18329 2.780 0.561 0.102 0.031 176 17.1 G_front_sup 903 399 1362 3.214 0.550 0.118 0.050 17 1.8 G_Ins_lg&S_cent_ins 914 351 1918 3.801 0.671 0.110 0.053 18 2.1 G_insular_short 3020 1156 4028 2.621 0.392 0.104 0.026 44 3.0 G_occipital_middle 2286 838 2315 2.274 0.465 0.093 0.032 35 2.7 G_occipital_sup 2584 1071 4320 2.988 0.652 0.113 0.033 44 3.7 G_oc-temp_lat-fusifor 4397 1578 4099 2.044 0.527 0.110 0.042 68 7.7 G_oc-temp_med-Lingual 2483 976 4504 3.441 0.678 0.093 0.034 28 3.8 G_oc-temp_med-Parahip 4533 1820 6938 2.748 0.604 0.103 0.033 84 6.0 G_orbital 3788 1462 5821 2.835 0.493 0.104 0.030 70 4.9 G_pariet_inf-Angular 4996 1931 6338 2.599 0.437 0.101 0.036 113 8.4 G_pariet_inf-Supramar 4436 1818 5788 2.396 0.472 0.103 0.024 70 4.6 G_parietal_sup 3838 1271 3440 2.122 0.379 0.080 0.023 42 3.9 G_postcentral 4778 1552 5853 2.833 0.424 0.074 0.029 85 5.7 G_precentral 3696 1523 5301 2.624 0.410 0.115 0.033 73 5.3 G_precuneus 1345 521 1978 2.488 0.517 0.116 0.038 32 2.5 G_rectus 861 413 1285 3.125 1.077 0.110 0.053 14 1.6 G_subcallosal 849 311 1119 2.840 0.443 0.091 0.025 9 0.8 G_temp_sup-G_T_transv 3160 1251 4920 2.820 0.498 0.102 0.032 84 4.9 G_temp_sup-Lateral 1229 507 2298 3.749 0.640 0.075 0.018 8 1.0 G_temp_sup-Plan_polar 1881 770 2318 2.668 0.407 0.091 0.019 25 1.3 G_temp_sup-Plan_tempo 4565 1719 7041 2.933 0.657 0.096 0.034 77 6.4 G_temporal_inf 4230 1586 7065 2.895 0.670 0.106 0.037 77 6.8 G_temporal_middle 655 270 545 2.276 0.439 0.055 0.009 2 0.2 Lat_Fis-ant-Horizont 763 309 664 2.546 0.524 0.073 0.015 4 0.4 Lat_Fis-ant-Vertical 1882 785 1540 2.421 0.370 0.082 0.019 12 1.5 Lat_Fis-post 3912 1314 3230 2.050 0.566 0.097 0.033 45 5.6 Pole_occipital 2753 1109 5850 3.447 0.719 0.108 0.038 41 4.7 Pole_temporal 3622 1550 2822 2.145 0.465 0.083 0.024 24 3.6 S_calcarine 4767 1936 4015 2.346 0.511 0.061 0.014 18 3.1 S_central 1478 630 1324 2.271 0.273 0.077 0.018 11 1.0 S_cingul-Marginalis 789 328 896 3.333 0.503 0.063 0.016 3 0.5 S_circular_insula_ant 2041 906 2225 3.023 0.613 0.070 0.019 9 1.9 S_circular_insula_inf 2655 1169 2743 2.876 0.660 0.075 0.021 12 2.5 S_circular_insula_sup 1903 800 2020 2.577 0.447 0.076 0.020 23 1.7 S_collat_transv_ant 1126 480 871 2.350 0.348 0.093 0.024 7 1.2 S_collat_transv_post 3149 1342 2950 2.334 0.442 0.077 0.016 20 2.0 S_front_inf 2464 1039 2067 2.199 0.393 0.086 0.019 18 1.9 S_front_middle 5576 2330 5559 2.403 0.374 0.078 0.017 39 3.9 S_front_sup 765 323 645 2.179 0.367 0.073 0.013 5 0.4 S_interm_prim-Jensen 4947 2105 4090 2.181 0.288 0.068 0.011 23 2.2 S_intrapariet&P_trans 1617 685 1181 2.054 0.234 0.073 0.014 7 0.9 S_oc_middle&Lunatus 1866 753 1571 2.326 0.363 0.081 0.019 14 1.4 S_oc_sup&transversal 900 382 682 2.209 0.266 0.083 0.018 6 0.7 S_occipital_ant 1453 620 1286 2.434 0.361 0.063 0.012 5 0.7 S_oc-temp_lat 3050 1303 2967 2.483 0.456 0.081 0.017 20 2.1 S_oc-temp_med&Lingual 368 160 312 2.149 0.236 0.079 0.010 2 0.2 S_orbital_lateral 1036 428 786 2.234 0.646 0.072 0.013 5 0.5 S_orbital_med-olfact 2753 1139 3175 2.697 0.544 0.093 0.023 28 2.9 S_orbital-H_Shaped 2816 1149 2404 2.406 0.440 0.086 0.021 23 2.5 S_parieto_occipital 1816 682 883 1.527 0.882 0.089 0.026 23 1.7 S_pericallosal 4687 1946 3808 2.172 0.349 0.075 0.015 31 2.8 S_postcentral 2808 1201 2522 2.361 0.319 0.057 0.008 9 1.0 S_precentral-inf-part 1975 848 1696 2.297 0.279 0.068 0.011 8 0.9 S_precentral-sup-part 1095 466 896 2.155 0.507 0.074 0.015 6 0.7 S_suborbital 1816 748 1507 2.300 0.340 0.076 0.017 10 1.3 S_subparietal 2757 1179 2313 2.328 0.464 0.069 0.013 11 1.6 S_temporal_inf 7862 3343 7760 2.453 0.450 0.071 0.014 46 4.4 S_temporal_sup 585 235 448 2.319 0.283 0.071 0.012 3 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 3 lh Wed May 26 00:14:19 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-06 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 239272 Total vertex volume 236896 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) 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) = 1492006 mm^3 (det: 1.305695 ) lhCtxGM: 233674.454 460316.000 diff=-226641.5 pctdiff=-96.990 rhCtxGM: 231736.832 454865.000 diff=-223128.2 pctdiff=-96.285 lhCtxWM: 174557.758 398559.500 diff=-224001.7 pctdiff=-128.325 rhCtxWM: 175837.258 403253.500 diff=-227416.2 pctdiff=-129.333 SubCortGMVol 102400.000 SupraTentVol 943733.301 (1856802.000) diff=-913068.699 pctdiff=-96.751 SupraTentVolNotVent 906351.301 (1819420.000) diff=-913068.699 pctdiff=-100.741 BrainSegVol 2130875.000 (2126469.000) diff=4406.000 pctdiff=0.207 BrainSegVolNotVent 2087714.000 (1186381.301) diff=901332.699 pctdiff=43.173 BrainSegVolNotVent 2087714.000 CerebellumVol 268149.000 VentChorVol 37382.000 3rd4th5thCSF 5779.000 CSFVol 1373.000, OptChiasmVol 145.000 MaskVol 2624308.000 2703 1080 3078 2.603 0.756 0.087 0.027 35 2.9 caudalanteriorcingulate 5764 2348 6658 2.563 0.420 0.082 0.020 57 4.8 caudalmiddlefrontal 4529 1638 4065 2.247 0.429 0.088 0.024 46 4.7 cuneus 1066 441 2020 3.581 0.793 0.088 0.031 11 1.5 entorhinal 6716 2811 8940 2.763 0.583 0.097 0.027 86 7.9 fusiform 8619 3500 10098 2.579 0.436 0.087 0.020 93 7.1 inferiorparietal 8703 3441 11746 2.809 0.677 0.089 0.028 111 10.0 inferiortemporal 1830 746 1617 2.210 1.025 0.097 0.033 24 2.4 isthmuscingulate 12267 4498 11931 2.315 0.555 0.095 0.028 133 14.2 lateraloccipital 7829 3241 10500 2.745 0.688 0.100 0.030 119 9.9 lateralorbitofrontal 6214 2403 5634 2.110 0.514 0.101 0.034 74 8.7 lingual 3366 1385 4006 2.391 0.669 0.095 0.031 47 4.6 medialorbitofrontal 9560 3864 13090 2.695 0.661 0.087 0.024 108 10.0 middletemporal 1702 671 2394 3.007 0.554 0.082 0.026 15 2.0 parahippocampal 3673 1478 4212 2.587 0.392 0.077 0.149 385 2.4 paracentral 3708 1550 4555 2.626 0.503 0.080 0.018 33 3.0 parsopercularis 1879 782 2820 2.948 0.525 0.084 0.021 18 1.6 parsorbitalis 4074 1671 4880 2.566 0.470 0.087 0.020 42 3.5 parstriangularis 3550 1380 2578 2.006 0.425 0.092 0.033 41 5.0 pericalcarine 11540 4359 10560 2.196 0.416 0.077 0.020 97 10.0 postcentral 3012 1206 3189 2.332 0.706 0.096 0.029 42 3.3 posteriorcingulate 12067 4526 13072 2.661 0.447 0.071 0.021 128 10.5 precentral 7692 3203 8687 2.489 0.427 0.096 0.026 95 8.4 precuneus 3196 1282 4522 2.939 0.661 0.089 0.028 50 3.9 rostralanteriorcingulate 9525 3901 10786 2.392 0.432 0.100 0.027 134 10.5 rostralmiddlefrontal 21028 8640 26653 2.594 0.548 0.094 0.026 250 24.0 superiorfrontal 10058 4123 10626 2.264 0.431 0.086 0.019 115 7.9 superiorparietal 12112 4950 16705 2.873 0.684 0.087 0.023 164 12.5 superiortemporal 9037 3621 10251 2.528 0.460 0.092 0.028 151 11.5 supramarginal 1148 443 1220 2.575 0.330 0.093 0.022 11 1.0 transversetemporal 4051 1738 5804 3.284 0.731 0.092 0.036 45 6.5 insula /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed May 26 00:15:22 UTC 2021 mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 1521 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 5650 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 2436 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 10345 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 671 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4748 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 1685 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 7668 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 1628 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 7412 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 1112 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 5182 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 5431 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 19020 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 1861 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 6042 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 2311 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 5733 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-06 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 4641 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 9282 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-06 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 7281 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 15395 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-06 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 822 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2840 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-06 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 607 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1897 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-06 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 561 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1760 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 301 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1315 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 810 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2902 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1642 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 471 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2467 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 696 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 3015 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 404 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1953 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 2289 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 9324 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 684 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2596 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 1119 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 2270 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 3581 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 6986 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 3213 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 6547 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 117 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 630 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 694 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-06 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 213589 Number of reverse mapping hits = 273 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 723 mri_label2label: Done mris_label2annot --s sub-06 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label cmdline mris_label2annot --s sub-06 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-06 hemi lh SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 147048 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.BA_exvivo.annot mris_label2annot --s sub-06 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /opt/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label cmdline mris_label2annot --s sub-06 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-06 hemi lh SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 174187 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-06 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 239272 Total vertex volume 236896 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1492006 mm^3 (det: 1.305695 ) lhCtxGM: 233674.454 460316.000 diff=-226641.5 pctdiff=-96.990 rhCtxGM: 231736.832 454865.000 diff=-223128.2 pctdiff=-96.285 lhCtxWM: 174557.758 398559.500 diff=-224001.7 pctdiff=-128.325 rhCtxWM: 175837.258 403253.500 diff=-227416.2 pctdiff=-129.333 SubCortGMVol 102400.000 SupraTentVol 943733.301 (1856802.000) diff=-913068.699 pctdiff=-96.751 SupraTentVolNotVent 906351.301 (1819420.000) diff=-913068.699 pctdiff=-100.741 BrainSegVol 2130875.000 (2126469.000) diff=4406.000 pctdiff=0.207 BrainSegVolNotVent 2087714.000 (1186381.301) diff=901332.699 pctdiff=43.173 BrainSegVolNotVent 2087714.000 CerebellumVol 268149.000 VentChorVol 37382.000 3rd4th5thCSF 5779.000 CSFVol 1373.000, OptChiasmVol 145.000 MaskVol 2624308.000 1767 571 1634 2.146 0.387 0.083 0.026 22 2.0 BA1_exvivo 6306 2507 5604 2.212 0.343 0.077 0.017 51 4.3 BA2_exvivo 1468 606 1052 2.152 0.370 0.070 0.015 7 0.9 BA3a_exvivo 3978 1446 3407 2.080 0.441 0.076 0.026 42 4.9 BA3b_exvivo 2557 887 2942 2.846 0.358 0.065 0.017 15 1.9 BA4a_exvivo 2213 788 2265 2.865 0.382 0.070 0.034 58 3.2 BA4p_exvivo 15534 6183 20111 2.694 0.531 0.084 0.023 146 15.5 BA6_exvivo 3970 1682 4791 2.556 0.447 0.072 0.015 30 2.6 BA44_exvivo 5001 2044 6030 2.528 0.471 0.090 0.021 58 4.5 BA45_exvivo 6434 2349 5136 2.077 0.509 0.095 0.033 79 9.1 V1_exvivo 12629 4685 11022 2.113 0.480 0.097 0.030 138 16.1 V2_exvivo 2414 941 2675 2.581 0.427 0.091 0.029 25 2.7 MT_exvivo 1059 442 2049 3.563 0.643 0.080 0.025 8 1.3 perirhinal_exvivo 1211 509 1913 3.216 0.670 0.098 0.035 13 2.0 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-06 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 239272 Total vertex volume 236896 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1492006 mm^3 (det: 1.305695 ) lhCtxGM: 233674.454 460316.000 diff=-226641.5 pctdiff=-96.990 rhCtxGM: 231736.832 454865.000 diff=-223128.2 pctdiff=-96.285 lhCtxWM: 174557.758 398559.500 diff=-224001.7 pctdiff=-128.325 rhCtxWM: 175837.258 403253.500 diff=-227416.2 pctdiff=-129.333 SubCortGMVol 102400.000 SupraTentVol 943733.301 (1856802.000) diff=-913068.699 pctdiff=-96.751 SupraTentVolNotVent 906351.301 (1819420.000) diff=-913068.699 pctdiff=-100.741 BrainSegVol 2130875.000 (2126469.000) diff=4406.000 pctdiff=0.207 BrainSegVolNotVent 2087714.000 (1186381.301) diff=901332.699 pctdiff=43.173 BrainSegVolNotVent 2087714.000 CerebellumVol 268149.000 VentChorVol 37382.000 3rd4th5thCSF 5779.000 CSFVol 1373.000, OptChiasmVol 145.000 MaskVol 2624308.000 1118 335 1006 2.150 0.396 0.085 0.027 16 1.3 BA1_exvivo 2668 1019 2362 2.189 0.282 0.073 0.017 19 2.1 BA2_exvivo 1249 519 849 2.140 0.355 0.070 0.015 5 0.8 BA3a_exvivo 2168 848 1670 1.927 0.327 0.050 0.009 6 0.8 BA3b_exvivo 2654 892 2930 2.849 0.363 0.063 0.020 49 1.8 BA4a_exvivo 1687 631 1729 2.874 0.401 0.074 0.027 17 2.1 BA4p_exvivo 8173 3230 10530 2.672 0.516 0.081 0.019 70 6.7 BA6_exvivo 2416 1027 2773 2.445 0.394 0.071 0.013 19 1.3 BA44_exvivo 2258 906 2938 2.623 0.398 0.098 0.023 29 2.4 BA45_exvivo 6829 2467 5517 2.086 0.506 0.092 0.032 78 9.4 V1_exvivo 6383 2320 5351 2.032 0.480 0.102 0.034 74 9.2 V2_exvivo 555 237 681 2.634 0.327 0.085 0.016 4 0.4 MT_exvivo 536 242 1083 3.498 0.566 0.065 0.014 2 0.3 perirhinal_exvivo 708 301 1188 3.326 0.516 0.105 0.035 8 1.2 entorhinal_exvivo Started at Wed May 26 00:10:57 UTC 2021 Ended at Wed May 26 00:21:00 UTC 2021 #@#%# recon-all-run-time-hours 0.168 recon-all -s sub-06 finished without error at Wed May 26 00:21:00 UTC 2021