Tue May 25 20:58:32 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-03 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-03 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 blg5611.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 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 30613464 160381828 1969316 5643140 161647860 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: 2021/05/25-20:58:32-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: blg5611.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: 2021/05/25-20:58:32-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: blg5611.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: 2021/05/25-20:58:32-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: blg5611.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: 2021/05/25-20:58:32-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: blg5611.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: 2021/05/25-20:58:32-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: blg5611.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: 2021/05/25-20:58:32-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: blg5611.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: 2021/05/25-20:58:32-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: blg5611.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: 2021/05/25-20:58:32-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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: 2021/05/25-20:58:33-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: blg5611.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 20:58:34 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 6 found - 6 modified | TOTAL: 6 pass 2 (yz+): 0 found - 6 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 7 (out of 529487: 0.001322) 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: 1503 vertices, 1619 faces slice 60: 6805 vertices, 7068 faces slice 70: 16432 vertices, 16808 faces slice 80: 28785 vertices, 29219 faces slice 90: 42865 vertices, 43337 faces slice 100: 57755 vertices, 58303 faces slice 110: 73520 vertices, 74067 faces slice 120: 88189 vertices, 88727 faces slice 130: 105224 vertices, 105785 faces slice 140: 122779 vertices, 123347 faces slice 150: 140510 vertices, 141077 faces slice 160: 155843 vertices, 156462 faces slice 170: 172134 vertices, 172757 faces slice 180: 186595 vertices, 187113 faces slice 190: 198416 vertices, 198916 faces slice 200: 209085 vertices, 209549 faces slice 210: 219329 vertices, 219801 faces slice 220: 228750 vertices, 229188 faces slice 230: 237553 vertices, 237973 faces slice 240: 244973 vertices, 245325 faces slice 250: 249875 vertices, 250086 faces slice 260: 250218 vertices, 250342 faces slice 270: 250218 vertices, 250342 faces slice 280: 250218 vertices, 250342 faces slice 290: 250218 vertices, 250342 faces slice 300: 250218 vertices, 250342 faces slice 310: 250218 vertices, 250342 faces slice 320: 250218 vertices, 250342 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... 250218 voxel in cpt #1: X=-124 [v=250218,e=751026,f=500684] located at (-28.438385, -13.891278, 31.495743) For the whole surface: X=-124 [v=250218,e=751026,f=500684] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue May 25 20:58:40 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 20:58:47 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 = 46.9 mm, total surface area = 87116 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.6 minutes step 000: RMS=0.146 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.042 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.040 (target=0.015) step 065: RMS=0.040 (target=0.015) step 070: RMS=0.039 (target=0.015) step 075: RMS=0.039 (target=0.015) step 080: RMS=0.038 (target=0.015) step 085: RMS=0.038 (target=0.015) step 090: RMS=0.038 (target=0.015) step 095: RMS=0.038 (target=0.015) step 100: RMS=0.038 (target=0.015) step 105: RMS=0.038 (target=0.015) step 110: RMS=0.038 (target=0.015) step 115: RMS=0.038 (target=0.015) step 120: RMS=0.038 (target=0.015) step 125: RMS=0.038 (target=0.015) step 130: RMS=0.038 (target=0.015) step 135: RMS=0.038 (target=0.015) step 140: RMS=0.037 (target=0.015) step 145: RMS=0.038 (target=0.015) step 150: RMS=0.037 (target=0.015) step 155: RMS=0.037 (target=0.015) step 160: RMS=0.038 (target=0.015) step 165: RMS=0.038 (target=0.015) step 170: RMS=0.038 (target=0.015) step 175: RMS=0.038 (target=0.015) step 180: RMS=0.038 (target=0.015) step 185: RMS=0.038 (target=0.015) step 190: RMS=0.038 (target=0.015) step 195: RMS=0.037 (target=0.015) step 200: RMS=0.037 (target=0.015) step 205: RMS=0.038 (target=0.015) step 210: RMS=0.038 (target=0.015) step 215: RMS=0.038 (target=0.015) step 220: RMS=0.038 (target=0.015) step 225: RMS=0.038 (target=0.015) step 230: RMS=0.038 (target=0.015) step 235: RMS=0.038 (target=0.015) step 240: RMS=0.038 (target=0.015) step 245: RMS=0.038 (target=0.015) step 250: RMS=0.038 (target=0.015) step 255: RMS=0.039 (target=0.015) step 260: RMS=0.040 (target=0.015) step 265: RMS=0.040 (target=0.015) step 270: RMS=0.040 (target=0.015) step 275: RMS=0.040 (target=0.015) step 280: RMS=0.040 (target=0.015) step 285: RMS=0.040 (target=0.015) step 290: RMS=0.040 (target=0.015) step 295: RMS=0.040 (target=0.015) step 300: RMS=0.040 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 459.057009 mris_inflate stimesec 2.022581 mris_inflate ru_maxrss 399088 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 843214 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 17608 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 92398 mris_inflate ru_nivcsw 261 #-------------------------------------------- #@# QSphere lh Tue May 25 21:00:24 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 0.73 +- 0.42 (0.00-->6.20) (max @ vno 96093 --> 97844) face area 0.01 +- 0.02 (-0.15-->0.46) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.286... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.584, avgs=0 005/300: dt: 0.9000, rms radial error=175.323, avgs=0 010/300: dt: 0.9000, rms radial error=174.763, avgs=0 015/300: dt: 0.9000, rms radial error=174.027, avgs=0 020/300: dt: 0.9000, rms radial error=173.189, avgs=0 025/300: dt: 0.9000, rms radial error=172.293, avgs=0 030/300: dt: 0.9000, rms radial error=171.365, avgs=0 035/300: dt: 0.9000, rms radial error=170.422, avgs=0 040/300: dt: 0.9000, rms radial error=169.472, avgs=0 045/300: dt: 0.9000, rms radial error=168.522, avgs=0 050/300: dt: 0.9000, rms radial error=167.575, avgs=0 055/300: dt: 0.9000, rms radial error=166.631, avgs=0 060/300: dt: 0.9000, rms radial error=165.691, avgs=0 065/300: dt: 0.9000, rms radial error=164.756, avgs=0 070/300: dt: 0.9000, rms radial error=163.826, avgs=0 075/300: dt: 0.9000, rms radial error=162.900, avgs=0 080/300: dt: 0.9000, rms radial error=161.979, avgs=0 085/300: dt: 0.9000, rms radial error=161.064, avgs=0 090/300: dt: 0.9000, rms radial error=160.154, avgs=0 095/300: dt: 0.9000, rms radial error=159.248, avgs=0 100/300: dt: 0.9000, rms radial error=158.348, avgs=0 105/300: dt: 0.9000, rms radial error=157.453, avgs=0 110/300: dt: 0.9000, rms radial error=156.563, avgs=0 115/300: dt: 0.9000, rms radial error=155.678, avgs=0 120/300: dt: 0.9000, rms radial error=154.798, avgs=0 125/300: dt: 0.9000, rms radial error=153.923, avgs=0 130/300: dt: 0.9000, rms radial error=153.053, avgs=0 135/300: dt: 0.9000, rms radial error=152.188, avgs=0 140/300: dt: 0.9000, rms radial error=151.328, avgs=0 145/300: dt: 0.9000, rms radial error=150.473, avgs=0 150/300: dt: 0.9000, rms radial error=149.622, avgs=0 155/300: dt: 0.9000, rms radial error=148.776, avgs=0 160/300: dt: 0.9000, rms radial error=147.935, avgs=0 165/300: dt: 0.9000, rms radial error=147.099, avgs=0 170/300: dt: 0.9000, rms radial error=146.267, avgs=0 175/300: dt: 0.9000, rms radial error=145.440, avgs=0 180/300: dt: 0.9000, rms radial error=144.618, avgs=0 185/300: dt: 0.9000, rms radial error=143.800, avgs=0 190/300: dt: 0.9000, rms radial error=142.987, avgs=0 195/300: dt: 0.9000, rms radial error=142.179, avgs=0 200/300: dt: 0.9000, rms radial error=141.375, avgs=0 205/300: dt: 0.9000, rms radial error=140.576, avgs=0 210/300: dt: 0.9000, rms radial error=139.781, avgs=0 215/300: dt: 0.9000, rms radial error=138.991, avgs=0 220/300: dt: 0.9000, rms radial error=138.205, avgs=0 225/300: dt: 0.9000, rms radial error=137.423, avgs=0 230/300: dt: 0.9000, rms radial error=136.646, avgs=0 235/300: dt: 0.9000, rms radial error=135.874, avgs=0 240/300: dt: 0.9000, rms radial error=135.105, avgs=0 245/300: dt: 0.9000, rms radial error=134.341, avgs=0 250/300: dt: 0.9000, rms radial error=133.582, avgs=0 255/300: dt: 0.9000, rms radial error=132.827, avgs=0 260/300: dt: 0.9000, rms radial error=132.075, avgs=0 265/300: dt: 0.9000, rms radial error=131.329, avgs=0 270/300: dt: 0.9000, rms radial error=130.586, avgs=0 275/300: dt: 0.9000, rms radial error=129.848, avgs=0 280/300: dt: 0.9000, rms radial error=129.114, avgs=0 285/300: dt: 0.9000, rms radial error=128.384, avgs=0 290/300: dt: 0.9000, rms radial error=127.658, avgs=0 295/300: dt: 0.9000, rms radial error=126.936, avgs=0 300/300: dt: 0.9000, rms radial error=126.218, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 31448.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 6072.78 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 770.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00222 epoch 4 (K=640.0), pass 1, starting sse = 56.63 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/11 = 0.00368 final distance error %25.81 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 536.981783 mris_sphere stimesec 1.716822 mris_sphere ru_maxrss 399096 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 620368 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 17608 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 97869 mris_sphere ru_nivcsw 353 FSRUNTIME@ mris_sphere 0.0372 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Tue May 25 21:02:38 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Tue May 25 21:02:38 UTC 2021 mris_fix_topology -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-03 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=-124 (nv=250218, nf=500684, ne=751026, g=63) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 9289 ambiguous faces found in tessellation segmenting defects... 73 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 36 into 34 72 defects to be corrected 0 vertices coincident reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4662 (-4.7331) -vertex loglikelihood: -5.8812 (-2.9406) -normal dot loglikelihood: -3.5257 (-3.5257) -quad curv loglikelihood: -6.2601 (-3.1301) Total Loglikelihood : -25.1331 CORRECTING DEFECT 0 (vertices=44, convex hull=32, v0=457) After retessellation of defect 0 (v0=457), euler #=-67 (244746,732562,487749) : difference with theory (-69) = -2 CORRECTING DEFECT 1 (vertices=25, convex hull=59, v0=5594) After retessellation of defect 1 (v0=5594), euler #=-66 (244754,732609,487789) : difference with theory (-68) = -2 CORRECTING DEFECT 2 (vertices=34, convex hull=64, v0=12801) After retessellation of defect 2 (v0=12801), euler #=-65 (244763,732659,487831) : difference with theory (-67) = -2 CORRECTING DEFECT 3 (vertices=24, convex hull=28, v0=16022) After retessellation of defect 3 (v0=16022), euler #=-64 (244764,732669,487841) : difference with theory (-66) = -2 CORRECTING DEFECT 4 (vertices=427, convex hull=78, v0=19415) After retessellation of defect 4 (v0=19415), euler #=-63 (244776,732737,487898) : difference with theory (-65) = -2 CORRECTING DEFECT 5 (vertices=8, convex hull=22, v0=25604) After retessellation of defect 5 (v0=25604), euler #=-62 (244778,732749,487909) : difference with theory (-64) = -2 CORRECTING DEFECT 6 (vertices=9, convex hull=19, v0=32293) After retessellation of defect 6 (v0=32293), euler #=-61 (244779,732756,487916) : difference with theory (-63) = -2 CORRECTING DEFECT 7 (vertices=31, convex hull=54, v0=34053) After retessellation of defect 7 (v0=34053), euler #=-60 (244783,732792,487949) : difference with theory (-62) = -2 CORRECTING DEFECT 8 (vertices=11, convex hull=23, v0=44157) After retessellation of defect 8 (v0=44157), euler #=-59 (244783,732800,487958) : difference with theory (-61) = -2 CORRECTING DEFECT 9 (vertices=37, convex hull=26, v0=75406) After retessellation of defect 9 (v0=75406), euler #=-58 (244784,732814,487972) : difference with theory (-60) = -2 CORRECTING DEFECT 10 (vertices=18, convex hull=44, v0=85579) After retessellation of defect 10 (v0=85579), euler #=-57 (244788,732841,487996) : difference with theory (-59) = -2 CORRECTING DEFECT 11 (vertices=848, convex hull=322, v0=89370) After retessellation of defect 11 (v0=89370), euler #=-56 (244893,733314,488365) : difference with theory (-58) = -2 CORRECTING DEFECT 12 (vertices=25, convex hull=16, v0=98954) After retessellation of defect 12 (v0=98954), euler #=-55 (244894,733323,488374) : difference with theory (-57) = -2 CORRECTING DEFECT 13 (vertices=126, convex hull=51, v0=102812) After retessellation of defect 13 (v0=102812), euler #=-54 (244902,733364,488408) : difference with theory (-56) = -2 CORRECTING DEFECT 14 (vertices=20, convex hull=26, v0=103803) After retessellation of defect 14 (v0=103803), euler #=-53 (244904,733379,488422) : difference with theory (-55) = -2 CORRECTING DEFECT 15 (vertices=12, convex hull=26, v0=110925) After retessellation of defect 15 (v0=110925), euler #=-52 (244905,733390,488433) : difference with theory (-54) = -2 CORRECTING DEFECT 16 (vertices=25, convex hull=41, v0=111006) After retessellation of defect 16 (v0=111006), euler #=-51 (244912,733429,488466) : difference with theory (-53) = -2 CORRECTING DEFECT 17 (vertices=20, convex hull=61, v0=116666) After retessellation of defect 17 (v0=116666), euler #=-50 (244915,733460,488495) : difference with theory (-52) = -2 CORRECTING DEFECT 18 (vertices=32, convex hull=53, v0=119493) After retessellation of defect 18 (v0=119493), euler #=-49 (244923,733502,488530) : difference with theory (-51) = -2 CORRECTING DEFECT 19 (vertices=31, convex hull=17, v0=120158) After retessellation of defect 19 (v0=120158), euler #=-48 (244925,733512,488539) : difference with theory (-50) = -2 CORRECTING DEFECT 20 (vertices=74, convex hull=25, v0=122958) After retessellation of defect 20 (v0=122958), euler #=-47 (244927,733526,488552) : difference with theory (-49) = -2 CORRECTING DEFECT 21 (vertices=1315, convex hull=453, v0=124207) After retessellation of defect 21 (v0=124207), euler #=-47 (244960,733876,488869) : difference with theory (-48) = -1 CORRECTING DEFECT 22 (vertices=76, convex hull=63, v0=127741) After retessellation of defect 22 (v0=127741), euler #=-46 (244973,733950,488931) : difference with theory (-47) = -1 CORRECTING DEFECT 23 (vertices=31, convex hull=47, v0=129642) After retessellation of defect 23 (v0=129642), euler #=-45 (244981,733991,488965) : difference with theory (-46) = -1 CORRECTING DEFECT 24 (vertices=20, convex hull=58, v0=130749) After retessellation of defect 24 (v0=130749), euler #=-44 (244988,734032,489000) : difference with theory (-45) = -1 CORRECTING DEFECT 25 (vertices=29, convex hull=60, v0=133797) After retessellation of defect 25 (v0=133797), euler #=-43 (244994,734069,489032) : difference with theory (-44) = -1 CORRECTING DEFECT 26 (vertices=15, convex hull=19, v0=140535) After retessellation of defect 26 (v0=140535), euler #=-42 (244995,734079,489042) : difference with theory (-43) = -1 CORRECTING DEFECT 27 (vertices=24, convex hull=31, v0=142418) After retessellation of defect 27 (v0=142418), euler #=-41 (244997,734094,489056) : difference with theory (-42) = -1 CORRECTING DEFECT 28 (vertices=19, convex hull=40, v0=143716) After retessellation of defect 28 (v0=143716), euler #=-40 (245002,734121,489079) : difference with theory (-41) = -1 CORRECTING DEFECT 29 (vertices=48, convex hull=84, v0=146626) After retessellation of defect 29 (v0=146626), euler #=-39 (245020,734210,489151) : difference with theory (-40) = -1 CORRECTING DEFECT 30 (vertices=95, convex hull=46, v0=147808) After retessellation of defect 30 (v0=147808), euler #=-38 (245030,734258,489190) : difference with theory (-39) = -1 CORRECTING DEFECT 31 (vertices=12, convex hull=19, v0=150655) After retessellation of defect 31 (v0=150655), euler #=-37 (245032,734267,489198) : difference with theory (-38) = -1 CORRECTING DEFECT 32 (vertices=48, convex hull=61, v0=155243) After retessellation of defect 32 (v0=155243), euler #=-36 (245038,734311,489237) : difference with theory (-37) = -1 CORRECTING DEFECT 33 (vertices=29, convex hull=60, v0=155539) After retessellation of defect 33 (v0=155539), euler #=-35 (245045,734350,489270) : difference with theory (-36) = -1 CORRECTING DEFECT 34 (vertices=85, convex hull=78, v0=155847) After retessellation of defect 34 (v0=155847), euler #=-33 (245055,734415,489327) : difference with theory (-35) = -2 CORRECTING DEFECT 35 (vertices=24, convex hull=33, v0=156592) After retessellation of defect 35 (v0=156592), euler #=-32 (245056,734432,489344) : difference with theory (-34) = -2 CORRECTING DEFECT 36 (vertices=77, convex hull=25, v0=157652) After retessellation of defect 36 (v0=157652), euler #=-31 (245058,734448,489359) : difference with theory (-33) = -2 CORRECTING DEFECT 37 (vertices=19, convex hull=65, v0=157789) After retessellation of defect 37 (v0=157789), euler #=-30 (245063,734487,489394) : difference with theory (-32) = -2 CORRECTING DEFECT 38 (vertices=56, convex hull=93, v0=163322) After retessellation of defect 38 (v0=163322), euler #=-29 (245075,734557,489453) : difference with theory (-31) = -2 CORRECTING DEFECT 39 (vertices=20, convex hull=24, v0=164261) After retessellation of defect 39 (v0=164261), euler #=-28 (245075,734564,489461) : difference with theory (-30) = -2 CORRECTING DEFECT 40 (vertices=45, convex hull=60, v0=164376) After retessellation of defect 40 (v0=164376), euler #=-27 (245085,734616,489504) : difference with theory (-29) = -2 CORRECTING DEFECT 41 (vertices=21, convex hull=55, v0=164721) After retessellation of defect 41 (v0=164721), euler #=-26 (245092,734657,489539) : difference with theory (-28) = -2 CORRECTING DEFECT 42 (vertices=175, convex hull=58, v0=164963) After retessellation of defect 42 (v0=164963), euler #=-25 (245103,734715,489587) : difference with theory (-27) = -2 CORRECTING DEFECT 43 (vertices=19, convex hull=28, v0=166295) After retessellation of defect 43 (v0=166295), euler #=-24 (245106,734734,489604) : difference with theory (-26) = -2 CORRECTING DEFECT 44 (vertices=12, convex hull=23, v0=166818) After retessellation of defect 44 (v0=166818), euler #=-23 (245108,734747,489616) : difference with theory (-25) = -2 CORRECTING DEFECT 45 (vertices=93, convex hull=52, v0=169828) After retessellation of defect 45 (v0=169828), euler #=-22 (245116,734796,489658) : difference with theory (-24) = -2 CORRECTING DEFECT 46 (vertices=46, convex hull=74, v0=170176) After retessellation of defect 46 (v0=170176), euler #=-21 (245125,734854,489708) : difference with theory (-23) = -2 CORRECTING DEFECT 47 (vertices=267, convex hull=120, v0=171358) After retessellation of defect 47 (v0=171358), euler #=-20 (245147,734977,489810) : difference with theory (-22) = -2 CORRECTING DEFECT 48 (vertices=39, convex hull=62, v0=171531) After retessellation of defect 48 (v0=171531), euler #=-19 (245156,735028,489853) : difference with theory (-21) = -2 CORRECTING DEFECT 49 (vertices=41, convex hull=52, v0=171763) After retessellation of defect 49 (v0=171763), euler #=-18 (245164,735071,489889) : difference with theory (-20) = -2 CORRECTING DEFECT 50 (vertices=105, convex hull=87, v0=172998) After retessellation of defect 50 (v0=172998), euler #=-17 (245175,735144,489952) : difference with theory (-19) = -2 CORRECTING DEFECT 51 (vertices=33, convex hull=42, v0=174414) After retessellation of defect 51 (v0=174414), euler #=-16 (245181,735177,489980) : difference with theory (-18) = -2 CORRECTING DEFECT 52 (vertices=106, convex hull=98, v0=174753) After retessellation of defect 52 (v0=174753), euler #=-16 (245190,735254,490048) : difference with theory (-17) = -1 CORRECTING DEFECT 53 (vertices=31, convex hull=51, v0=174984) After retessellation of defect 53 (v0=174984), euler #=-15 (245200,735305,490090) : difference with theory (-16) = -1 CORRECTING DEFECT 54 (vertices=39, convex hull=78, v0=176564) After retessellation of defect 54 (v0=176564), euler #=-14 (245211,735374,490149) : difference with theory (-15) = -1 CORRECTING DEFECT 55 (vertices=63, convex hull=82, v0=176585) After retessellation of defect 55 (v0=176585), euler #=-13 (245227,735450,490210) : difference with theory (-14) = -1 CORRECTING DEFECT 56 (vertices=13, convex hull=17, v0=181374) After retessellation of defect 56 (v0=181374), euler #=-12 (245228,735457,490217) : difference with theory (-13) = -1 CORRECTING DEFECT 57 (vertices=28, convex hull=60, v0=186268) After retessellation of defect 57 (v0=186268), euler #=-11 (245233,735495,490251) : difference with theory (-12) = -1 CORRECTING DEFECT 58 (vertices=49, convex hull=31, v0=187145) After retessellation of defect 58 (v0=187145), euler #=-11 (245238,735523,490274) : difference with theory (-11) = 0 CORRECTING DEFECT 59 (vertices=6, convex hull=13, v0=187358) After retessellation of defect 59 (v0=187358), euler #=-10 (245239,735528,490279) : difference with theory (-10) = 0 CORRECTING DEFECT 60 (vertices=29, convex hull=55, v0=189710) After retessellation of defect 60 (v0=189710), euler #=-9 (245250,735581,490322) : difference with theory (-9) = 0 CORRECTING DEFECT 61 (vertices=10, convex hull=31, v0=190898) After retessellation of defect 61 (v0=190898), euler #=-8 (245252,735597,490337) : difference with theory (-8) = 0 CORRECTING DEFECT 62 (vertices=31, convex hull=27, v0=193692) After retessellation of defect 62 (v0=193692), euler #=-7 (245254,735611,490350) : difference with theory (-7) = 0 CORRECTING DEFECT 63 (vertices=7, convex hull=17, v0=200230) After retessellation of defect 63 (v0=200230), euler #=-6 (245254,735615,490355) : difference with theory (-6) = 0 CORRECTING DEFECT 64 (vertices=47, convex hull=23, v0=200661) After retessellation of defect 64 (v0=200661), euler #=-5 (245255,735625,490365) : difference with theory (-5) = 0 CORRECTING DEFECT 65 (vertices=9, convex hull=19, v0=201366) After retessellation of defect 65 (v0=201366), euler #=-4 (245256,735634,490374) : difference with theory (-4) = 0 CORRECTING DEFECT 66 (vertices=25, convex hull=27, v0=211667) After retessellation of defect 66 (v0=211667), euler #=-3 (245259,735653,490391) : difference with theory (-3) = 0 CORRECTING DEFECT 67 (vertices=46, convex hull=87, v0=214160) After retessellation of defect 67 (v0=214160), euler #=-2 (245272,735732,490458) : difference with theory (-2) = 0 CORRECTING DEFECT 68 (vertices=48, convex hull=58, v0=223269) After retessellation of defect 68 (v0=223269), euler #=-1 (245281,735781,490499) : difference with theory (-1) = 0 CORRECTING DEFECT 69 (vertices=9, convex hull=31, v0=239226) After retessellation of defect 69 (v0=239226), euler #=0 (245281,735789,490508) : difference with theory (0) = 0 CORRECTING DEFECT 70 (vertices=17, convex hull=50, v0=241441) After retessellation of defect 70 (v0=241441), euler #=1 (245287,735825,490539) : difference with theory (1) = 0 CORRECTING DEFECT 71 (vertices=38, convex hull=73, v0=244340) After retessellation of defect 71 (v0=244340), euler #=2 (245295,735879,490586) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.71 +- 0.19 (0.08-->17.68) (max @ vno 95192 --> 105054) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.71 +- 0.19 (0.08-->17.68) (max @ vno 95192 --> 105054) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 265 mutations (36.8%), 456 crossovers (63.2%), 172 vertices were eliminated building final representation... 4923 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=245295, nf=490586, ne=735879, g=0) writing corrected surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 36.9 minutes 0 defective edges removing intersecting faces 000: 338 intersecting mris_fix_topology utimesec 2224.448438 mris_fix_topology stimesec 0.598604 mris_fix_topology ru_maxrss 790712 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 436601 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 23136 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 5190 mris_fix_topology ru_nivcsw 588 FSRUNTIME@ mris_fix_topology lh 0.6152 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 245295 - 735879 + 490586 = 2 --> 0 holes F =2V-4: 490586 = 490590-4 (0) 2E=3F: 1471758 = 1471758 (0) total defect index = 0 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 54 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue May 25 21:39:40 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-03 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-03/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... 48538 bright wm thresholded. 856 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.orig... computing class statistics... border white: 523483 voxels (1.60%) border gray 522637 voxels (1.59%) WM (103.0): 103.0 +- 6.3 [70.0 --> 110.0] GM (83.0) : 82.3 +- 9.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.3 (was 40) setting MAX_GRAY to 102.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.66 +- 0.18 (0.02-->8.41) (max @ vno 95192 --> 105054) face area 0.18 +- 0.08 (0.00-->5.86) mean absolute distance = 1.47 +- 1.54 7848 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+-2.6, GM=78+-7.8 mean inside = 101.4, mean outside = 84.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=96.7, 155 (155) missing vertices, mean dist -0.8 [2.1 (%53.9)->0.6 (%46.1))] %44 local maxima, %41 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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 0.71 +- 0.19 (0.02-->5.11) (max @ vno 91902 --> 244797) face area 0.18 +- 0.09 (0.00-->7.88) mean absolute distance = 0.59 +- 0.77 7273 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5214044.5, rms=9.303 001: dt: 0.5000, sse=2604139.2, rms=5.726 (38.449%) 002: dt: 0.5000, sse=1700780.8, rms=3.719 (35.053%) 003: dt: 0.5000, sse=1518108.8, rms=3.120 (16.096%) 004: dt: 0.5000, sse=1473449.0, rms=2.987 (4.287%) rms = 2.95, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=1468189.5, rms=2.951 (1.179%) 006: dt: 0.2500, sse=1209158.2, rms=1.800 (39.021%) 007: dt: 0.2500, sse=1168204.9, rms=1.515 (15.825%) 008: dt: 0.2500, sse=1171232.9, rms=1.430 (5.634%) 009: dt: 0.2500, sse=1162749.1, rms=1.376 (3.742%) rms = 1.34, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=1151727.9, rms=1.343 (2.375%) rms = 1.31, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=1133664.4, rms=1.311 (2.396%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=95.3, 232 (84) missing vertices, mean dist -0.1 [0.9 (%36.8)->0.3 (%63.2))] %80 local maxima, %13 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg56, 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 0.70 +- 0.18 (0.03-->5.03) (max @ vno 91902 --> 244797) face area 0.21 +- 0.10 (0.00-->9.13) mean absolute distance = 0.32 +- 0.55 9104 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2026260.5, rms=4.227 012: dt: 0.5000, sse=1546770.2, rms=2.727 (35.483%) rms = 2.68, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=1546022.5, rms=2.682 (1.657%) 014: dt: 0.2500, sse=1281111.1, rms=1.437 (46.422%) 015: dt: 0.2500, sse=1246034.0, rms=1.148 (20.127%) 016: dt: 0.2500, sse=1231947.1, rms=1.075 (6.379%) rms = 1.03, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=1222503.0, rms=1.032 (3.951%) rms = 0.99, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=1221070.1, rms=0.991 (3.976%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=95.5, 206 (52) missing vertices, mean dist -0.1 [0.5 (%39.3)->0.2 (%60.7))] %91 local maxima, % 4 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg56, 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 0.70 +- 0.18 (0.02-->4.89) (max @ vno 91902 --> 244797) face area 0.20 +- 0.10 (0.00-->8.94) mean absolute distance = 0.23 +- 0.41 7192 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1403143.8, rms=2.333 019: dt: 0.5000, sse=1406761.0, rms=2.091 (10.359%) rms = 2.45, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=1232371.1, rms=1.360 (34.940%) 021: dt: 0.2500, sse=1217612.2, rms=1.043 (23.339%) 022: dt: 0.2500, sse=1189052.9, rms=0.987 (5.396%) rms = 0.95, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=1219120.9, rms=0.952 (3.534%) rms = 0.92, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=1175203.4, rms=0.917 (3.664%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=95.2, 225 (45) missing vertices, mean dist -0.0 [0.4 (%33.0)->0.1 (%67.0))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg56, 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-03/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1245942.0, rms=1.554 025: dt: 0.5000, sse=1265181.9, rms=1.447 (6.925%) rms = 1.98, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=1181231.4, rms=0.919 (36.497%) 027: dt: 0.2500, sse=1186120.5, rms=0.809 (11.917%) rms = 0.77, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=1162163.0, rms=0.769 (4.937%) rms = 0.74, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=1151897.5, rms=0.738 (4.028%) positioning took 0.7 minutes generating cortex label... 17 non-cortical segments detected only using segment with 10541 vertices erasing segment 0 (vno[0] = 58360) erasing segment 1 (vno[0] = 61320) erasing segment 3 (vno[0] = 162987) erasing segment 4 (vno[0] = 164486) erasing segment 5 (vno[0] = 167488) erasing segment 6 (vno[0] = 170413) erasing segment 7 (vno[0] = 173113) erasing segment 8 (vno[0] = 174498) erasing segment 9 (vno[0] = 174514) erasing segment 10 (vno[0] = 177262) erasing segment 11 (vno[0] = 178755) erasing segment 12 (vno[0] = 178777) erasing segment 13 (vno[0] = 179990) erasing segment 14 (vno[0] = 183355) erasing segment 15 (vno[0] = 245098) erasing segment 16 (vno[0] = 245166) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.area vertex spacing 0.70 +- 0.19 (0.02-->8.41) (max @ vno 95192 --> 105054) face area 0.20 +- 0.10 (0.00-->8.90) refinement took 5.4 minutes #-------------------------------------------- #@# Smooth2 lh Tue May 25 21:45:06 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 21:45:12 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_inflate -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/touch/rusage.mris_inflate.lh.dat -n 50 ../surf/lh.smoothwm ../surf/lh.inflated niterations = 50 Reading ../surf/lh.smoothwm avg radius = 47.1 mm, total surface area = 92011 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=0.113 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) step 065: RMS=0.020 (target=0.015) step 070: RMS=0.019 (target=0.015) step 075: RMS=0.018 (target=0.015) step 080: RMS=0.017 (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 0.7 minutes mris_inflate utimesec 212.971928 mris_inflate stimesec 1.952670 mris_inflate ru_maxrss 391376 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 887075 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 19176 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 88217 mris_inflate ru_nivcsw 88 #-------------------------------------------- #@# Curv .H and .K lh Tue May 25 21:45:53 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf mris_curvature -w lh.white.preaparc total integrated curvature = 30.534*4pi (383.706) --> -30 handles ICI = 272.8, FI = 2883.2, variation=44822.524 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 392 vertices thresholded to be in k1 ~ [-0.14 0.29], k2 ~ [-0.08 0.04] total integrated curvature = 0.689*4pi (8.653) --> 0 handles ICI = 1.4, FI = 7.5, variation=132.135 243 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 = 0.001 283 vertices thresholded to be in [-0.09 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.019 done. #----------------------------------------- #@# Curvature Stats lh Tue May 25 21:47:31 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-03 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-03/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 [ 430 ] Gb_filter = 0 #-------------------------------------------- #@# Sphere lh Tue May 25 21:47:37 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_sphere -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 0.268... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=blg56, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.03 pass 1: epoch 2 of 3 starting distance error %20.99 unfolding complete - removing small folds... starting distance error %20.90 removing remaining folds... final distance error %20.91 MRISunfold() return, current seed 1234 -01: dt=0.0000, 399 negative triangles 135: dt=0.9900, 399 negative triangles 136: dt=0.9900, 212 negative triangles 137: dt=0.9900, 189 negative triangles 138: dt=0.9900, 174 negative triangles 139: dt=0.9900, 158 negative triangles 140: dt=0.9900, 163 negative triangles 141: dt=0.9900, 149 negative triangles 142: dt=0.9900, 158 negative triangles 143: dt=0.9900, 154 negative triangles 144: dt=0.9900, 137 negative triangles 145: dt=0.9900, 123 negative triangles 146: dt=0.9900, 125 negative triangles 147: dt=0.9900, 126 negative triangles 148: dt=0.9900, 110 negative triangles 149: dt=0.9900, 107 negative triangles 150: dt=0.9900, 98 negative triangles 151: dt=0.9900, 95 negative triangles 152: dt=0.9900, 89 negative triangles 153: dt=0.9900, 89 negative triangles 154: dt=0.9900, 86 negative triangles 155: dt=0.9900, 89 negative triangles 156: dt=0.9900, 78 negative triangles 157: dt=0.9900, 77 negative triangles 158: dt=0.9900, 78 negative triangles 159: dt=0.9900, 77 negative triangles 160: dt=0.9900, 77 negative triangles 161: dt=0.9900, 77 negative triangles 162: dt=0.9900, 70 negative triangles 163: dt=0.9900, 74 negative triangles 164: dt=0.9900, 74 negative triangles 165: dt=0.9900, 81 negative triangles 166: dt=0.9900, 77 negative triangles 167: dt=0.9900, 77 negative triangles 168: dt=0.9900, 74 negative triangles 169: dt=0.9900, 72 negative triangles 170: dt=0.9900, 74 negative triangles 171: dt=0.9900, 75 negative triangles 172: dt=0.9405, 70 negative triangles 173: dt=0.9405, 70 negative triangles 174: dt=0.9405, 72 negative triangles 175: dt=0.9405, 73 negative triangles 176: dt=0.9405, 74 negative triangles 177: dt=0.9405, 82 negative triangles 178: dt=0.9405, 68 negative triangles 179: dt=0.9405, 74 negative triangles 180: dt=0.9405, 69 negative triangles 181: dt=0.9405, 71 negative triangles 182: dt=0.9405, 73 negative triangles 183: dt=0.9405, 75 negative triangles 184: dt=0.9405, 66 negative triangles 185: dt=0.9405, 71 negative triangles 186: dt=0.9405, 66 negative triangles 187: dt=0.9405, 68 negative triangles 188: dt=0.9405, 68 negative triangles 189: dt=0.9405, 64 negative triangles 190: dt=0.9405, 62 negative triangles 191: dt=0.9405, 63 negative triangles 192: dt=0.9405, 60 negative triangles 193: dt=0.9405, 66 negative triangles 194: dt=0.9405, 66 negative triangles 195: dt=0.9405, 67 negative triangles 196: dt=0.9405, 65 negative triangles 197: dt=0.9405, 63 negative triangles 198: dt=0.9405, 62 negative triangles 199: dt=0.9405, 65 negative triangles 200: dt=0.9405, 60 negative triangles 201: dt=0.9405, 57 negative triangles 202: dt=0.9405, 58 negative triangles 203: dt=0.9405, 60 negative triangles 204: dt=0.9405, 59 negative triangles 205: dt=0.9405, 59 negative triangles 206: dt=0.9405, 58 negative triangles 207: dt=0.9405, 56 negative triangles 208: dt=0.9405, 54 negative triangles 209: dt=0.9405, 50 negative triangles 210: dt=0.9405, 51 negative triangles 211: dt=0.9405, 52 negative triangles 212: dt=0.9405, 53 negative triangles 213: dt=0.9405, 53 negative triangles 214: dt=0.9405, 52 negative triangles 215: dt=0.9405, 54 negative triangles 216: dt=0.9405, 51 negative triangles 217: dt=0.9405, 56 negative triangles 218: dt=0.9405, 51 negative triangles 219: dt=0.8935, 50 negative triangles 220: dt=0.8935, 49 negative triangles 221: dt=0.8935, 50 negative triangles 222: dt=0.8935, 52 negative triangles 223: dt=0.8935, 50 negative triangles 224: dt=0.8935, 52 negative triangles 225: dt=0.8935, 52 negative triangles 226: dt=0.8935, 48 negative triangles 227: dt=0.8935, 51 negative triangles 228: dt=0.8935, 50 negative triangles 229: dt=0.8935, 51 negative triangles 230: dt=0.8935, 49 negative triangles 231: dt=0.8935, 47 negative triangles 232: dt=0.8935, 53 negative triangles 233: dt=0.8935, 51 negative triangles 234: dt=0.8935, 50 negative triangles 235: dt=0.8935, 51 negative triangles 236: dt=0.8935, 53 negative triangles 237: dt=0.8935, 53 negative triangles 238: dt=0.8935, 52 negative triangles 239: dt=0.8935, 49 negative triangles 240: dt=0.8935, 50 negative triangles 241: dt=0.8488, 49 negative triangles 242: dt=0.8488, 49 negative triangles 243: dt=0.8488, 50 negative triangles 244: dt=0.8488, 46 negative triangles 245: dt=0.8488, 50 negative triangles 246: dt=0.8488, 50 negative triangles 247: dt=0.8488, 48 negative triangles 248: dt=0.8488, 47 negative triangles 249: dt=0.8488, 47 negative triangles 250: dt=0.8488, 48 negative triangles 251: dt=0.8488, 46 negative triangles 252: dt=0.8488, 49 negative triangles 253: dt=0.8488, 49 negative triangles 254: dt=0.8488, 45 negative triangles 255: dt=0.8488, 47 negative triangles 256: dt=0.8488, 50 negative triangles 257: dt=0.8488, 51 negative triangles 258: dt=0.8488, 48 negative triangles 259: dt=0.8488, 49 negative triangles 260: dt=0.8488, 51 negative triangles 261: dt=0.8488, 48 negative triangles 262: dt=0.8488, 46 negative triangles 263: dt=0.8488, 50 negative triangles 264: dt=0.8064, 49 negative triangles 265: dt=0.8064, 47 negative triangles 266: dt=0.8064, 46 negative triangles 267: dt=0.8064, 48 negative triangles 268: dt=0.8064, 45 negative triangles 269: dt=0.8064, 46 negative triangles 270: dt=0.8064, 47 negative triangles 271: dt=0.8064, 44 negative triangles 272: dt=0.8064, 46 negative triangles 273: dt=0.8064, 44 negative triangles 274: dt=0.8064, 47 negative triangles 275: dt=0.8064, 44 negative triangles 276: dt=0.8064, 43 negative triangles 277: dt=0.8064, 46 negative triangles 278: dt=0.8064, 48 negative triangles 279: dt=0.8064, 47 negative triangles 280: dt=0.8064, 46 negative triangles 281: dt=0.8064, 44 negative triangles 282: dt=0.8064, 45 negative triangles 283: dt=0.8064, 42 negative triangles 284: dt=0.8064, 41 negative triangles 285: dt=0.8064, 43 negative triangles 286: dt=0.8064, 44 negative triangles 287: dt=0.8064, 41 negative triangles 288: dt=0.8064, 39 negative triangles 289: dt=0.8064, 43 negative triangles 290: dt=0.8064, 46 negative triangles 291: dt=0.8064, 40 negative triangles 292: dt=0.8064, 40 negative triangles 293: dt=0.8064, 44 negative triangles 294: dt=0.8064, 38 negative triangles 295: dt=0.8064, 38 negative triangles 296: dt=0.8064, 39 negative triangles 297: dt=0.8064, 36 negative triangles 298: dt=0.8064, 35 negative triangles 299: dt=0.8064, 41 negative triangles 300: dt=0.8064, 38 negative triangles 301: dt=0.8064, 37 negative triangles 302: dt=0.8064, 37 negative triangles 303: dt=0.8064, 35 negative triangles 304: dt=0.8064, 33 negative triangles 305: dt=0.8064, 36 negative triangles 306: dt=0.8064, 36 negative triangles 307: dt=0.8064, 37 negative triangles 308: dt=0.8064, 33 negative triangles 309: dt=0.8064, 32 negative triangles 310: dt=0.8064, 33 negative triangles 311: dt=0.8064, 36 negative triangles 312: dt=0.8064, 35 negative triangles 313: dt=0.8064, 31 negative triangles 314: dt=0.8064, 25 negative triangles 315: dt=0.8064, 33 negative triangles 316: dt=0.8064, 30 negative triangles 317: dt=0.8064, 26 negative triangles 318: dt=0.8064, 28 negative triangles 319: dt=0.8064, 27 negative triangles 320: dt=0.8064, 32 negative triangles 321: dt=0.8064, 27 negative triangles 322: dt=0.8064, 25 negative triangles 323: dt=0.8064, 27 negative triangles 324: dt=0.7660, 29 negative triangles 325: dt=0.7660, 32 negative triangles 326: dt=0.7660, 29 negative triangles 327: dt=0.7660, 21 negative triangles 328: dt=0.7660, 22 negative triangles 329: dt=0.7660, 19 negative triangles 330: dt=0.7660, 20 negative triangles 331: dt=0.7660, 16 negative triangles 332: dt=0.7660, 20 negative triangles 333: dt=0.7660, 18 negative triangles 334: dt=0.7660, 17 negative triangles 335: dt=0.7660, 19 negative triangles 336: dt=0.7660, 18 negative triangles 337: dt=0.7660, 14 negative triangles 338: dt=0.7660, 17 negative triangles 339: dt=0.7660, 14 negative triangles 340: dt=0.7660, 15 negative triangles 341: dt=0.7660, 10 negative triangles 342: dt=0.7660, 16 negative triangles 343: dt=0.7660, 10 negative triangles 344: dt=0.7660, 8 negative triangles 345: dt=0.7660, 8 negative triangles 346: dt=0.7660, 7 negative triangles 347: dt=0.7660, 2 negative triangles 348: dt=0.7660, 5 negative triangles 349: dt=0.7660, 7 negative triangles 350: dt=0.7660, 3 negative triangles 351: dt=0.7660, 2 negative triangles 352: dt=0.7660, 1 negative triangles 353: dt=0.7660, 3 negative triangles 354: dt=0.7660, 1 negative triangles 355: dt=0.7660, 2 negative triangles 356: dt=0.7660, 2 negative triangles 357: dt=0.7660, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.22 hours mris_sphere utimesec 5460.655417 mris_sphere stimesec 4.370157 mris_sphere ru_maxrss 530524 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 2458007 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 17256 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 119862 mris_sphere ru_nivcsw 2709 FSRUNTIME@ mris_sphere 0.2218 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Tue May 25 22:00:55 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/scripts cmdline mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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=blg56, 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=blg56, 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 = 5.813 curvature mean = 0.023, std = 0.816 curvature mean = 0.021, std = 0.862 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 611522.7, tmin=1.1604 d=32.00 min @ (8.00, 8.00, -8.00) sse = 373509.3, tmin=2.3371 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 323770.0, tmin=3.5252 d=4.00 min @ (0.00, -1.00, 1.00) sse = 318428.3, tmin=5.9016 d=2.00 min @ (0.00, 0.00, -0.50) sse = 316688.6, tmin=7.2168 d=0.50 min @ (0.00, -0.12, 0.00) sse = 316672.9, tmin=9.8712 tol=1.0e+00, sigma=0.5, host=blg56, 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 9.87 min curvature mean = -0.003, std = 0.827 curvature mean = 0.006, std = 0.948 curvature mean = -0.011, std = 0.830 curvature mean = 0.003, std = 0.979 curvature mean = -0.013, std = 0.830 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.033, std = 0.375 curvature mean = 0.037, std = 0.244 curvature mean = 0.041, std = 0.274 curvature mean = 0.034, std = 0.298 curvature mean = 0.021, std = 0.437 curvature mean = 0.034, std = 0.323 curvature mean = 0.010, std = 0.569 curvature mean = 0.035, std = 0.332 curvature mean = 0.002, std = 0.709 MRISregister() return, current seed 0 -01: dt=0.0000, 118 negative triangles 118: dt=0.9900, 118 negative triangles expanding nbhd size to 1 119: dt=0.9900, 152 negative triangles 120: dt=0.9900, 117 negative triangles 121: dt=0.9900, 114 negative triangles 122: dt=0.9900, 108 negative triangles 123: dt=0.9900, 111 negative triangles 124: dt=0.9900, 101 negative triangles 125: dt=0.9900, 98 negative triangles 126: dt=0.9900, 92 negative triangles 127: dt=0.9900, 88 negative triangles 128: dt=0.9900, 85 negative triangles 129: dt=0.9900, 87 negative triangles 130: dt=0.9900, 88 negative triangles 131: dt=0.9900, 85 negative triangles 132: dt=0.9900, 87 negative triangles 133: dt=0.9900, 85 negative triangles 134: dt=0.9900, 82 negative triangles 135: dt=0.9900, 82 negative triangles 136: dt=0.9900, 84 negative triangles 137: dt=0.9900, 83 negative triangles 138: dt=0.9900, 76 negative triangles 139: dt=0.9900, 74 negative triangles 140: dt=0.9900, 74 negative triangles 141: dt=0.9900, 70 negative triangles 142: dt=0.9900, 69 negative triangles 143: dt=0.9900, 70 negative triangles 144: dt=0.9900, 67 negative triangles 145: dt=0.9900, 64 negative triangles 146: dt=0.9900, 66 negative triangles 147: dt=0.9900, 65 negative triangles 148: dt=0.9900, 62 negative triangles 149: dt=0.9900, 60 negative triangles 150: dt=0.9900, 60 negative triangles 151: dt=0.9900, 58 negative triangles 152: dt=0.9900, 55 negative triangles 153: dt=0.9900, 54 negative triangles 154: dt=0.9900, 56 negative triangles 155: dt=0.9900, 58 negative triangles 156: dt=0.9900, 54 negative triangles 157: dt=0.9900, 51 negative triangles 158: dt=0.9900, 48 negative triangles 159: dt=0.9900, 48 negative triangles 160: dt=0.9900, 46 negative triangles 161: dt=0.9900, 46 negative triangles 162: dt=0.9900, 40 negative triangles 163: dt=0.9900, 42 negative triangles 164: dt=0.9900, 37 negative triangles 165: dt=0.9900, 37 negative triangles 166: dt=0.9900, 37 negative triangles 167: dt=0.9900, 39 negative triangles 168: dt=0.9900, 35 negative triangles 169: dt=0.9900, 36 negative triangles 170: dt=0.9900, 35 negative triangles 171: dt=0.9900, 35 negative triangles 172: dt=0.9900, 35 negative triangles 173: dt=0.9900, 37 negative triangles 174: dt=0.9900, 35 negative triangles 175: dt=0.9900, 34 negative triangles 176: dt=0.9900, 33 negative triangles 177: dt=0.9900, 33 negative triangles 178: dt=0.9900, 35 negative triangles 179: dt=0.9900, 35 negative triangles 180: dt=0.9900, 37 negative triangles 181: dt=0.9900, 36 negative triangles 182: dt=0.9900, 37 negative triangles 183: dt=0.9900, 36 negative triangles 184: dt=0.9900, 36 negative triangles 185: dt=0.9900, 32 negative triangles 186: dt=0.9900, 30 negative triangles 187: dt=0.9900, 30 negative triangles 188: dt=0.9900, 30 negative triangles 189: dt=0.9900, 32 negative triangles 190: dt=0.9900, 31 negative triangles 191: dt=0.9900, 31 negative triangles 192: dt=0.9900, 30 negative triangles 193: dt=0.9900, 30 negative triangles 194: dt=0.9900, 31 negative triangles 195: dt=0.9900, 32 negative triangles 196: dt=0.9405, 32 negative triangles 197: dt=0.9405, 30 negative triangles 198: dt=0.9405, 29 negative triangles 199: dt=0.9405, 29 negative triangles 200: dt=0.9405, 29 negative triangles 201: dt=0.9405, 29 negative triangles 202: dt=0.9405, 30 negative triangles 203: dt=0.9405, 29 negative triangles 204: dt=0.9405, 30 negative triangles 205: dt=0.9405, 29 negative triangles 206: dt=0.9405, 29 negative triangles 207: dt=0.9405, 29 negative triangles 208: dt=0.8935, 30 negative triangles 209: dt=0.8935, 29 negative triangles 210: dt=0.8935, 29 negative triangles 211: dt=0.8935, 29 negative triangles 212: dt=0.8935, 29 negative triangles 213: dt=0.8935, 30 negative triangles 214: dt=0.8935, 29 negative triangles 215: dt=0.8935, 29 negative triangles 216: dt=0.8935, 28 negative triangles 217: dt=0.8935, 28 negative triangles 218: dt=0.8935, 28 negative triangles 219: dt=0.8935, 28 negative triangles 220: dt=0.8935, 29 negative triangles 221: dt=0.8935, 28 negative triangles 222: dt=0.8935, 26 negative triangles 223: dt=0.8935, 26 negative triangles 224: dt=0.8935, 26 negative triangles 225: dt=0.8935, 25 negative triangles 226: dt=0.8935, 25 negative triangles 227: dt=0.8935, 24 negative triangles 228: dt=0.8935, 25 negative triangles 229: dt=0.8935, 24 negative triangles 230: dt=0.8935, 24 negative triangles 231: dt=0.8935, 24 negative triangles 232: dt=0.8935, 24 negative triangles 233: dt=0.8935, 23 negative triangles 234: dt=0.8935, 23 negative triangles 235: dt=0.8935, 23 negative triangles 236: dt=0.8935, 24 negative triangles 237: dt=0.8935, 23 negative triangles 238: dt=0.8935, 24 negative triangles 239: dt=0.8935, 24 negative triangles 240: dt=0.8935, 21 negative triangles 241: dt=0.8935, 21 negative triangles 242: dt=0.8935, 20 negative triangles 243: dt=0.8935, 19 negative triangles 244: dt=0.8935, 21 negative triangles 245: dt=0.8935, 23 negative triangles 246: dt=0.8935, 22 negative triangles 247: dt=0.8935, 22 negative triangles 248: dt=0.8935, 22 negative triangles 249: dt=0.8935, 19 negative triangles 250: dt=0.8935, 18 negative triangles 251: dt=0.8935, 19 negative triangles 252: dt=0.8935, 20 negative triangles 253: dt=0.8935, 20 negative triangles 254: dt=0.8935, 20 negative triangles 255: dt=0.8935, 19 negative triangles 256: dt=0.8935, 18 negative triangles 257: dt=0.8935, 20 negative triangles 258: dt=0.8935, 18 negative triangles 259: dt=0.8935, 18 negative triangles 260: dt=0.8935, 17 negative triangles 261: dt=0.8935, 14 negative triangles 262: dt=0.8935, 15 negative triangles 263: dt=0.8935, 14 negative triangles 264: dt=0.8935, 15 negative triangles 265: dt=0.8935, 17 negative triangles 266: dt=0.8935, 15 negative triangles 267: dt=0.8935, 16 negative triangles 268: dt=0.8935, 15 negative triangles 269: dt=0.8935, 14 negative triangles 270: dt=0.8935, 15 negative triangles 271: dt=0.8488, 16 negative triangles 272: dt=0.8488, 19 negative triangles 273: dt=0.8488, 16 negative triangles 274: dt=0.8488, 18 negative triangles 275: dt=0.8488, 14 negative triangles 276: dt=0.8488, 15 negative triangles 277: dt=0.8488, 14 negative triangles 278: dt=0.8488, 14 negative triangles 279: dt=0.8488, 12 negative triangles 280: dt=0.8488, 12 negative triangles 281: dt=0.8488, 12 negative triangles 282: dt=0.8488, 11 negative triangles 283: dt=0.8488, 13 negative triangles 284: dt=0.8488, 12 negative triangles 285: dt=0.8488, 9 negative triangles 286: dt=0.8488, 11 negative triangles 287: dt=0.8488, 6 negative triangles 288: dt=0.8488, 8 negative triangles 289: dt=0.8488, 4 negative triangles 290: dt=0.8488, 5 negative triangles 291: dt=0.8488, 5 negative triangles 292: dt=0.8488, 4 negative triangles 293: dt=0.8488, 5 negative triangles 294: dt=0.8488, 4 negative triangles 295: dt=0.8488, 3 negative triangles 296: dt=0.8488, 5 negative triangles 297: dt=0.8488, 4 negative triangles 298: dt=0.8488, 3 negative triangles 299: dt=0.8488, 3 negative triangles 300: dt=0.8488, 3 negative triangles 301: dt=0.8488, 2 negative triangles 302: dt=0.8488, 6 negative triangles 303: dt=0.8488, 2 negative triangles 304: dt=0.8488, 2 negative triangles 305: dt=0.8488, 4 negative triangles 306: dt=0.8488, 2 negative triangles 307: dt=0.8488, 2 negative triangles 308: dt=0.8488, 3 negative triangles 309: dt=0.8488, 2 negative triangles 310: dt=0.8488, 1 negative triangles 311: dt=0.8488, 1 negative triangles 312: dt=0.8488, 1 negative triangles 313: dt=0.8488, 2 negative triangles 314: dt=0.8488, 2 negative triangles 315: dt=0.8488, 1 negative triangles 316: dt=0.8488, 1 negative triangles 317: dt=0.8488, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.50 hours mris_register utimesec 7837.018201 mris_register stimesec 5.542665 mris_register ru_maxrss 441112 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 2983216 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5580 mris_register ru_oublock 17256 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 124381 mris_register ru_nivcsw 3788 FSRUNTIME@ mris_register 0.5006 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Tue May 25 22:30:58 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 22:31:00 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 22:31:02 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 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... 2841 labels changed using aseg relabeling using gibbs priors... 000: 4933 changed, 245295 examined... 001: 1259 changed, 20268 examined... 002: 331 changed, 6777 examined... 003: 128 changed, 1980 examined... 004: 62 changed, 755 examined... 005: 31 changed, 373 examined... 006: 16 changed, 190 examined... 007: 8 changed, 91 examined... 008: 6 changed, 46 examined... 009: 0 changed, 32 examined... 388 labels changed using aseg 000: 175 total segments, 134 labels (751 vertices) changed 001: 42 total segments, 4 labels (22 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 3586 vertices marked for relabeling... 3586 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 22:31:18 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-03 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-03/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... 48538 bright wm thresholded. 856 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.orig... computing class statistics... border white: 523483 voxels (1.60%) border gray 522637 voxels (1.59%) WM (103.0): 103.0 +- 6.3 [70.0 --> 110.0] GM (83.0) : 82.3 +- 9.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.3 (was 40) setting MAX_GRAY to 102.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.5 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-2.6, GM=78+-7.8 mean inside = 101.4, mean outside = 84.2 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 0.70 +- 0.19 (0.02-->8.41) (max @ vno 95192 --> 105054) face area 0.20 +- 0.10 (0.00-->8.92) mean absolute distance = 1.33 +- 1.38 7316 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown deleting segment 1 with 17 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 336 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown mean border=96.4, 203 (200) missing vertices, mean dist -0.5 [2.3 (%41.3)->0.5 (%58.7))] %44 local maxima, %41 large gradients and %12 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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 0.71 +- 0.19 (0.02-->5.17) (max @ vno 90220 --> 244797) face area 0.20 +- 0.10 (0.00-->8.66) mean absolute distance = 0.57 +- 0.77 7075 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2504979.2, rms=5.391 001: dt: 0.5000, sse=1565819.1, rms=2.983 (44.676%) 002: dt: 0.5000, sse=1455109.6, rms=2.610 (12.485%) rms = 2.65, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=1280251.0, rms=1.767 (32.321%) 004: dt: 0.2500, sse=1232943.8, rms=1.296 (26.625%) 005: dt: 0.2500, sse=1212416.0, rms=1.194 (7.890%) rms = 1.15, time step reduction 2 of 3 to 0.125... 006: dt: 0.2500, sse=1211357.2, rms=1.151 (3.617%) rms = 1.11, time step reduction 3 of 3 to 0.062... 007: dt: 0.1250, sse=1203478.9, rms=1.115 (3.113%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 307 points - only 0.00% unknown deleting segment 5 with 13 points - only 0.00% unknown deleting segment 6 with 25 points - only 0.00% unknown deleting segment 7 with 13 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown mean border=95.3, 204 (92) missing vertices, mean dist -0.1 [0.9 (%36.6)->0.3 (%63.4))] %80 local maxima, %13 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg56, 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 0.70 +- 0.19 (0.02-->5.24) (max @ vno 90220 --> 244797) face area 0.21 +- 0.10 (0.00-->9.15) mean absolute distance = 0.32 +- 0.54 10629 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1930247.1, rms=3.991 008: dt: 0.5000, sse=1490482.0, rms=2.596 (34.949%) rms = 2.61, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=1316301.6, rms=1.763 (32.088%) 010: dt: 0.2500, sse=1240412.2, rms=1.202 (31.857%) 011: dt: 0.2500, sse=1227403.0, rms=1.056 (12.129%) 012: dt: 0.2500, sse=1226643.0, rms=0.997 (5.548%) rms = 0.97, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=1210573.8, rms=0.974 (2.311%) rms = 0.95, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=1208920.4, rms=0.947 (2.810%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 258 points - only 0.00% unknown deleting segment 4 with 21 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown mean border=95.4, 211 (64) missing vertices, mean dist -0.1 [0.5 (%39.2)->0.2 (%60.8))] %91 local maxima, % 4 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg56, 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 (0.01-->5.21) (max @ vno 91820 --> 244800) face area 0.20 +- 0.10 (0.00-->8.95) mean absolute distance = 0.22 +- 0.41 6949 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1387248.9, rms=2.302 015: dt: 0.5000, sse=1355790.4, rms=2.059 (10.549%) rms = 2.43, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=1216633.8, rms=1.320 (35.922%) 017: dt: 0.2500, sse=1189369.2, rms=0.999 (24.312%) 018: dt: 0.2500, sse=1182224.1, rms=0.940 (5.917%) rms = 0.93, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=1180629.1, rms=0.926 (1.427%) rms = 0.89, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=1174305.2, rms=0.886 (4.370%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 67 points - only 0.00% unknown deleting segment 5 with 43 points - only 0.00% unknown deleting segment 6 with 121 points - only 0.00% unknown deleting segment 8 with 25 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 11 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown mean border=95.2, 231 (47) missing vertices, mean dist -0.0 [0.4 (%33.1)->0.1 (%66.9))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg56, 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-03/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1239775.8, rms=1.508 021: dt: 0.5000, sse=1232896.5, rms=1.423 (5.591%) rms = 1.96, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=1164396.2, rms=0.895 (37.143%) 023: dt: 0.2500, sse=1160216.2, rms=0.782 (12.621%) rms = 0.74, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=1158084.6, rms=0.744 (4.874%) rms = 0.71, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=1149059.4, rms=0.712 (4.213%) positioning took 0.7 minutes generating cortex label... 21 non-cortical segments detected only using segment with 10477 vertices erasing segment 0 (vno[0] = 58360) erasing segment 1 (vno[0] = 61320) erasing segment 3 (vno[0] = 141972) erasing segment 4 (vno[0] = 150648) erasing segment 5 (vno[0] = 162987) erasing segment 6 (vno[0] = 164486) erasing segment 7 (vno[0] = 167488) erasing segment 8 (vno[0] = 167492) erasing segment 9 (vno[0] = 167602) erasing segment 10 (vno[0] = 173113) erasing segment 11 (vno[0] = 174498) erasing segment 12 (vno[0] = 174514) erasing segment 13 (vno[0] = 177262) erasing segment 14 (vno[0] = 178755) erasing segment 15 (vno[0] = 178777) erasing segment 16 (vno[0] = 179990) erasing segment 17 (vno[0] = 183355) erasing segment 18 (vno[0] = 200491) erasing segment 19 (vno[0] = 245098) erasing segment 20 (vno[0] = 245166) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.area vertex spacing 0.70 +- 0.19 (0.02-->8.41) (max @ vno 95192 --> 105054) face area 0.20 +- 0.10 (0.00-->8.91) 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 46 points - only 0.00% unknown deleting segment 1 with 12 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 11 points - only 0.00% unknown deleting segment 4 with 138 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown deleting segment 9 with 78 points - only 0.00% unknown deleting segment 10 with 23 points - only 0.00% unknown deleting segment 11 with 9 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 17 points - only 0.00% unknown deleting segment 18 with 11 points - only 0.00% unknown deleting segment 19 with 42 points - only 0.00% unknown deleting segment 20 with 54 points - only 0.00% unknown deleting segment 21 with 7 points - only 0.00% unknown deleting segment 22 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 23 with 3 points - only 0.00% unknown deleting segment 24 with 44 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=75.1, 214 (214) missing vertices, mean dist 0.7 [2.8 (%0.0)->1.1 (%100.0))] %13 local maxima, %47 large gradients and %36 min vals, 92 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg56, 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=22530182.0, rms=21.299 001: dt: 0.0500, sse=17819024.0, rms=18.811 (11.681%) 002: dt: 0.0500, sse=15320846.0, rms=17.347 (7.783%) 003: dt: 0.0500, sse=13701648.0, rms=16.328 (5.875%) 004: dt: 0.0500, sse=12524974.0, rms=15.545 (4.794%) 005: dt: 0.0500, sse=11605385.0, rms=14.904 (4.120%) 006: dt: 0.0500, sse=10849729.0, rms=14.357 (3.676%) 007: dt: 0.0500, sse=10205683.0, rms=13.872 (3.372%) 008: dt: 0.0500, sse=9642967.0, rms=13.435 (3.153%) 009: dt: 0.0500, sse=9141570.0, rms=13.033 (2.994%) 010: dt: 0.0500, sse=8688214.0, rms=12.658 (2.876%) positioning took 1.1 minutes mean border=69.2, 133 (80) missing vertices, mean dist 0.8 [0.1 (%0.0)->1.3 (%100.0))] %13 local maxima, %47 large gradients and %36 min vals, 156 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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=17646096.0, rms=18.707 011: dt: 0.0500, sse=16979834.0, rms=18.325 (2.041%) 012: dt: 0.0500, sse=16381868.0, rms=17.975 (1.909%) 013: dt: 0.0500, sse=15839241.0, rms=17.652 (1.800%) 014: dt: 0.0500, sse=15343283.0, rms=17.351 (1.706%) 015: dt: 0.0500, sse=14885593.0, rms=17.068 (1.629%) 016: dt: 0.0500, sse=14460414.0, rms=16.801 (1.564%) 017: dt: 0.0500, sse=14060541.0, rms=16.546 (1.518%) 018: dt: 0.0500, sse=13679220.0, rms=16.299 (1.493%) 019: dt: 0.0500, sse=13310025.0, rms=16.056 (1.490%) 020: dt: 0.0500, sse=12949778.0, rms=15.816 (1.497%) positioning took 1.1 minutes mean border=67.7, 131 (52) missing vertices, mean dist 0.8 [0.1 (%0.1)->1.2 (%99.9))] %13 local maxima, %47 large gradients and %36 min vals, 181 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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=14277777.0, rms=16.689 021: dt: 0.0500, sse=13869375.0, rms=16.426 (1.574%) 022: dt: 0.0500, sse=13477186.0, rms=16.170 (1.560%) 023: dt: 0.0500, sse=13100813.0, rms=15.920 (1.546%) 024: dt: 0.0500, sse=12738985.0, rms=15.676 (1.533%) 025: dt: 0.0500, sse=12391014.0, rms=15.437 (1.521%) 026: dt: 0.0500, sse=12053302.0, rms=15.202 (1.523%) 027: dt: 0.0500, sse=11724090.0, rms=14.969 (1.532%) 028: dt: 0.0500, sse=11402537.0, rms=14.738 (1.543%) 029: dt: 0.0500, sse=11087381.0, rms=14.508 (1.561%) 030: dt: 0.0500, sse=10778144.0, rms=14.279 (1.580%) positioning took 1.1 minutes mean border=66.9, 170 (44) missing vertices, mean dist 0.6 [0.1 (%2.0)->1.0 (%98.0))] %13 local maxima, %47 large gradients and %36 min vals, 162 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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=11570537.0, rms=14.855 031: dt: 0.5000, sse=9330542.0, rms=13.148 (11.495%) 032: dt: 0.5000, sse=7515181.0, rms=11.583 (11.904%) 033: dt: 0.5000, sse=5957673.0, rms=10.059 (13.151%) 034: dt: 0.5000, sse=4760442.5, rms=8.701 (13.501%) 035: dt: 0.5000, sse=3872795.5, rms=7.546 (13.272%) 036: dt: 0.5000, sse=3323035.0, rms=6.730 (10.818%) 037: dt: 0.5000, sse=2982198.0, rms=6.173 (8.275%) 038: dt: 0.5000, sse=2814329.2, rms=5.878 (4.773%) 039: dt: 0.5000, sse=2717268.5, rms=5.703 (2.994%) 040: dt: 0.5000, sse=2670850.0, rms=5.615 (1.542%) 041: dt: 0.5000, sse=2634546.8, rms=5.547 (1.196%) rms = 5.52, time step reduction 1 of 3 to 0.250... 042: dt: 0.5000, sse=2618848.5, rms=5.516 (0.562%) 043: dt: 0.2500, sse=2292961.0, rms=4.786 (13.235%) 044: dt: 0.2500, sse=2221885.0, rms=4.624 (3.381%) rms = 4.65, time step reduction 2 of 3 to 0.125... 045: dt: 0.1250, sse=2174220.5, rms=4.507 (2.537%) 046: dt: 0.1250, sse=2114794.2, rms=4.354 (3.388%) rms = 4.33, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=2107068.8, rms=4.333 (0.497%) positioning took 2.7 minutes mean border=64.9, 4669 (24) missing vertices, mean dist 0.2 [0.2 (%23.1)->0.4 (%76.9))] %31 local maxima, %30 large gradients and %33 min vals, 166 gradients ignored tol=1.0e-04, sigma=1.0, host=blg56, 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=3241181.2, rms=6.018 rms = 6.02, time step reduction 1 of 3 to 0.250... 048: dt: 0.2500, sse=2985044.8, rms=5.521 (8.261%) 049: dt: 0.2500, sse=2735011.8, rms=4.971 (9.963%) 050: dt: 0.2500, sse=2603221.2, rms=4.672 (6.013%) 051: dt: 0.2500, sse=2484941.2, rms=4.390 (6.042%) 052: dt: 0.2500, sse=2390967.5, rms=4.156 (5.333%) 053: dt: 0.2500, sse=2289867.0, rms=3.887 (6.467%) 054: dt: 0.2500, sse=2214336.8, rms=3.674 (5.487%) 055: dt: 0.2500, sse=2144575.8, rms=3.466 (5.658%) 056: dt: 0.2500, sse=2104733.8, rms=3.342 (3.572%) 057: dt: 0.2500, sse=2070742.0, rms=3.234 (3.239%) rms = 3.19, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=2058381.8, rms=3.194 (1.218%) 059: dt: 0.1250, sse=1865753.4, rms=2.421 (24.203%) 060: dt: 0.1250, sse=1840946.1, rms=2.311 (4.552%) rms = 2.28, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1834712.5, rms=2.283 (1.223%) positioning took 2.7 minutes mean border=63.8, 5178 (19) missing vertices, mean dist 0.1 [0.2 (%25.5)->0.2 (%74.5))] %43 local maxima, %18 large gradients and %33 min vals, 133 gradients ignored tol=1.0e-04, sigma=0.5, host=blg56, 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=2033814.1, rms=3.017 rms = 4.27, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1929122.9, rms=2.605 (13.675%) 063: dt: 0.2500, sse=1915259.6, rms=2.546 (2.246%) rms = 2.66, time step reduction 2 of 3 to 0.125... 064: dt: 0.1250, sse=1899276.9, rms=2.474 (2.831%) 065: dt: 0.1250, sse=1879897.4, rms=2.388 (3.462%) rms = 2.35, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1871744.4, rms=2.354 (1.458%) positioning took 1.2 minutes mean border=63.1, 9690 (16) missing vertices, mean dist 0.0 [0.2 (%30.8)->0.1 (%69.2))] %45 local maxima, %17 large gradients and %31 min vals, 142 gradients ignored tol=1.0e-04, sigma=0.2, host=blg56, 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-03/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1918190.8, rms=2.547 rms = 3.44, time step reduction 1 of 3 to 0.250... 067: dt: 0.2500, sse=1885055.5, rms=2.396 (5.905%) rms = 2.39, time step reduction 2 of 3 to 0.125... 068: dt: 0.2500, sse=1879582.1, rms=2.393 (0.145%) 069: dt: 0.1250, sse=1859903.1, rms=2.294 (4.127%) rms = 2.25, time step reduction 3 of 3 to 0.062... 070: dt: 0.1250, sse=1849745.9, rms=2.253 (1.807%) positioning took 0.9 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.area.pial vertex spacing 0.80 +- 0.34 (0.04-->6.76) (max @ vno 151031 --> 244951) face area 0.25 +- 0.20 (0.00-->9.84) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 245295 vertices processed 25000 of 245295 vertices processed 50000 of 245295 vertices processed 75000 of 245295 vertices processed 100000 of 245295 vertices processed 125000 of 245295 vertices processed 150000 of 245295 vertices processed 175000 of 245295 vertices processed 200000 of 245295 vertices processed 225000 of 245295 vertices processed 0 of 245295 vertices processed 25000 of 245295 vertices processed 50000 of 245295 vertices processed 75000 of 245295 vertices processed 100000 of 245295 vertices processed 125000 of 245295 vertices processed 150000 of 245295 vertices processed 175000 of 245295 vertices processed 200000 of 245295 vertices processed 225000 of 245295 vertices processed thickness calculation complete, 113:465 truncations. 45675 vertices at 0 distance 147631 vertices at 1 distance 153948 vertices at 2 distance 81932 vertices at 3 distance 30183 vertices at 4 distance 8755 vertices at 5 distance 2527 vertices at 6 distance 844 vertices at 7 distance 321 vertices at 8 distance 168 vertices at 9 distance 86 vertices at 10 distance 53 vertices at 11 distance 36 vertices at 12 distance 36 vertices at 13 distance 30 vertices at 14 distance 24 vertices at 15 distance 18 vertices at 16 distance 18 vertices at 17 distance 12 vertices at 18 distance 17 vertices at 19 distance 10 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.thickness positioning took 17.9 minutes #-------------------------------------------- #@# Surf Volume lh Tue May 25 22:49:14 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label Total face volume 264423 Total vertex volume 261915 (mask=0) #@# sub-03 lh 261915 vertexvol Done #----------------------------------------- #@# Cortical Parc 2 lh Tue May 25 22:49:19 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 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... 37 labels changed using aseg relabeling using gibbs priors... 000: 14487 changed, 245295 examined... 001: 3485 changed, 55849 examined... 002: 1103 changed, 18101 examined... 003: 450 changed, 6100 examined... 004: 228 changed, 2574 examined... 005: 139 changed, 1300 examined... 006: 86 changed, 751 examined... 007: 63 changed, 505 examined... 008: 28 changed, 336 examined... 009: 13 changed, 154 examined... 010: 5 changed, 76 examined... 011: 5 changed, 31 examined... 012: 6 changed, 30 examined... 013: 1 changed, 29 examined... 014: 0 changed, 6 examined... 2 labels changed using aseg 000: 365 total segments, 279 labels (5038 vertices) changed 001: 98 total segments, 12 labels (74 vertices) changed 002: 88 total segments, 2 labels (2 vertices) changed 003: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 85 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 2413 vertices marked for relabeling... 2413 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 22:49:38 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 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... 2027 labels changed using aseg relabeling using gibbs priors... 000: 3090 changed, 245295 examined... 001: 729 changed, 13921 examined... 002: 218 changed, 4003 examined... 003: 81 changed, 1302 examined... 004: 50 changed, 469 examined... 005: 20 changed, 240 examined... 006: 12 changed, 119 examined... 007: 3 changed, 56 examined... 008: 4 changed, 15 examined... 009: 1 changed, 18 examined... 010: 1 changed, 7 examined... 011: 1 changed, 7 examined... 012: 1 changed, 7 examined... 013: 0 changed, 7 examined... 226 labels changed using aseg 000: 74 total segments, 41 labels (430 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2070 vertices marked for relabeling... 2070 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# WM/GM Contrast lh Tue May 25 22:49:54 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts pctsurfcon --s sub-03 --lh-only Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts/pctsurfcon.log Tue May 25 22:49:54 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-03/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux blg5611.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-03/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128872/lh.wm.mgh --regheader sub-03 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/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 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 = 130564 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128872/lh.wm.mgh Dim: 245295 1 1 mri_vol2surf --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128872/lh.gm.mgh --projfrac 0.3 --regheader sub-03 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/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 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white Done reading source surface Reading thickness /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 = 155702 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128872/lh.gm.mgh Dim: 245295 1 1 mri_concat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128872/lh.wm.mgh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128872/lh.gm.mgh --paired-diff-norm --mul 100 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/surf/lh.w-g.pct.mgh mri_segstats --in /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.w-g.pct.mgh --annot sub-03 lh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/surf/lh.w-g.pct.mgh --annot sub-03 lh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/stats/lh.w-g.pct.stats --snr sysname Linux hostname blg5611.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-03/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-03/surf/lh.w-g.pct.mgh Vertex Area is 0.406556 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 20:58:30 UTC 2021 Ended at Tue May 25 22:50:01 UTC 2021 #@#%# recon-all-run-time-hours 1.859 recon-all -s sub-03 finished without error at Tue May 25 22:50:02 UTC 2021 New invocation of recon-all Wed May 26 00:09:15 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-03 -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-03 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 blg5611.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 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 31826296 159010672 1957252 5801464 160453644 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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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: 2021/05/26-00:09:15-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: blg5611.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 00:09:16 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 282888 Total vertex volume 280012 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 2410 1037 2436 2.464 0.347 0.072 0.016 14 1.6 bankssts 1942 766 1931 2.150 0.828 0.088 0.016 19 1.5 caudalanteriorcingulate 7338 3128 9556 2.738 0.485 0.089 0.024 77 7.4 caudalmiddlefrontal 4470 1677 3763 2.030 0.441 0.101 0.029 56 5.6 cuneus 939 383 1977 3.556 0.526 0.097 0.042 12 1.8 entorhinal 7641 3164 10481 2.783 0.649 0.091 0.027 90 9.5 fusiform 13056 5266 14825 2.484 0.439 0.083 0.020 141 10.5 inferiorparietal 9083 3805 12634 2.723 0.656 0.095 0.025 117 9.3 inferiortemporal 3277 1326 3332 2.164 0.915 0.090 0.024 43 3.2 isthmuscingulate 14683 5612 13887 2.171 0.487 0.094 0.025 153 15.4 lateraloccipital 6849 2820 9106 2.732 0.533 0.095 0.030 95 9.6 lateralorbitofrontal 7565 3003 7647 2.222 0.548 0.103 0.033 90 10.8 lingual 4240 1760 5281 2.541 0.512 0.103 0.032 69 6.4 medialorbitofrontal 9478 3863 14345 2.853 0.620 0.093 0.026 121 9.9 middletemporal 1717 674 2188 2.942 0.643 0.055 0.013 6 0.9 parahippocampal 4016 1548 4595 2.622 0.469 0.078 0.022 29 4.1 paracentral 3634 1593 5047 2.659 0.558 0.087 0.020 40 3.1 parsopercularis 1903 767 2695 2.622 0.562 0.098 0.029 26 2.3 parsorbitalis 3074 1263 3983 2.649 0.547 0.079 0.020 31 2.6 parstriangularis 4305 1659 3505 2.272 0.443 0.086 0.027 43 5.1 pericalcarine 10760 4117 9865 2.188 0.484 0.079 0.021 130 9.7 postcentral 3641 1485 4341 2.422 0.737 0.105 0.029 48 4.7 posteriorcingulate 13593 4963 15038 2.748 0.501 0.074 0.025 120 15.6 precentral 10318 4343 11901 2.519 0.437 0.096 0.026 127 11.1 precuneus 2596 1047 4035 2.829 0.772 0.104 0.030 42 3.2 rostralanteriorcingulate 17121 7075 19767 2.404 0.492 0.095 0.024 221 17.6 rostralmiddlefrontal 20814 8668 28213 2.788 0.582 0.093 0.026 231 23.0 superiorfrontal 12779 5319 13501 2.277 0.406 0.085 0.019 136 9.9 superiorparietal 9960 4111 13596 2.790 0.673 0.079 0.021 87 8.7 superiortemporal 10653 4253 12544 2.587 0.466 0.093 0.024 126 10.3 supramarginal 686 289 1149 2.672 0.640 0.153 0.057 24 1.5 frontalpole 1267 520 2597 3.318 0.719 0.106 0.052 19 2.8 temporalpole 1482 516 1502 2.470 0.395 0.086 0.026 14 1.5 transversetemporal 6820 2948 8714 2.820 0.857 0.109 0.051 129 15.0 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-03 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 282888 Total vertex volume 280012 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 2410 923 2436 2.464 0.347 0.077 0.022 21 2.4 bankssts 1942 907 1931 2.150 0.828 0.077 0.019 16 1.6 caudalanteriorcingulate 7338 3684 9556 2.738 0.485 0.077 0.017 58 5.1 caudalmiddlefrontal 4470 1978 3763 2.030 0.441 0.083 0.027 55 4.0 cuneus 939 726 1977 3.556 0.526 0.117 0.024 24 1.2 entorhinal 7641 4068 10481 2.783 0.649 0.089 0.023 74 7.9 fusiform 13056 6326 14825 2.484 0.439 0.084 0.035 306 26.9 inferiorparietal 9083 4923 12634 2.723 0.656 0.086 0.021 106 7.6 inferiortemporal 3277 1613 3332 2.164 0.915 0.090 0.028 59 3.4 isthmuscingulate 14683 6943 13887 2.171 0.487 0.077 0.017 307 10.2 lateraloccipital 6849 3568 9106 2.732 0.533 0.088 0.022 95 6.4 lateralorbitofrontal 7565 3753 7647 2.222 0.548 0.089 0.024 84 7.9 lingual 4240 2237 5281 2.541 0.512 0.094 0.025 67 4.3 medialorbitofrontal 9478 5626 14345 2.853 0.620 0.096 0.020 110 8.5 middletemporal 1717 849 2188 2.942 0.643 0.061 0.012 6 0.9 parahippocampal 4016 1912 4595 2.622 0.469 0.077 0.018 35 2.9 paracentral 3634 2092 5047 2.659 0.558 0.096 0.020 34 3.1 parsopercularis 1903 1154 2695 2.622 0.562 0.093 0.020 16 1.7 parsorbitalis 3074 1626 3983 2.649 0.547 0.109 0.063 349 13.4 parstriangularis 4305 1386 3505 2.272 0.443 0.064 0.021 59 3.6 pericalcarine 10760 4815 9865 2.188 0.484 0.076 0.023 113 10.6 postcentral 3641 1899 4341 2.422 0.737 0.104 0.068 186 5.7 posteriorcingulate 13593 5737 15038 2.748 0.501 0.067 0.022 183 13.3 precentral 10318 4843 11901 2.519 0.437 0.089 0.023 127 10.0 precuneus 2596 1612 4035 2.829 0.772 0.107 0.027 46 2.9 rostralanteriorcingulate 17121 8764 19767 2.404 0.492 0.095 0.022 151 16.8 rostralmiddlefrontal 20814 10661 28213 2.788 0.582 0.087 0.022 288 19.4 superiorfrontal 12779 6210 13501 2.277 0.406 0.083 0.023 199 13.5 superiorparietal 9960 5189 13596 2.790 0.673 0.088 0.022 101 10.0 superiortemporal 10653 5234 12544 2.587 0.466 0.090 0.021 123 10.2 supramarginal 686 510 1149 2.672 0.640 0.136 0.031 8 1.0 frontalpole 1267 928 2597 3.318 0.719 0.110 0.024 14 1.7 temporalpole 1482 728 1502 2.470 0.395 0.083 0.019 9 1.2 transversetemporal 6820 3179 8714 2.820 0.857 0.127 0.083 1099 24.3 insula #----------------------------------------- #@# Parcellation Stats 2 lh Wed May 26 00:11:26 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03 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-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 282888 Total vertex volume 280012 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 2256 963 2510 2.341 0.519 0.089 0.022 21 2.3 G&S_frontomargin 3481 1359 4015 2.400 0.503 0.090 0.021 36 3.1 G&S_occipital_inf 3339 1195 3643 2.531 0.471 0.077 0.022 27 3.6 G&S_paracentral 2305 932 3214 2.815 0.579 0.096 0.027 28 2.7 G&S_subcentral 1540 644 1799 2.228 0.475 0.121 0.035 38 2.2 G&S_transv_frontopol 4406 1845 5924 2.735 0.613 0.092 0.024 47 4.5 G&S_cingul-Ant 2266 969 2674 2.674 0.547 0.078 0.016 14 1.6 G&S_cingul-Mid-Ant 2797 1169 3290 2.581 0.524 0.100 0.029 35 3.5 G&S_cingul-Mid-Post 1503 598 2438 2.927 0.635 0.124 0.043 31 2.8 G_cingul-Post-dorsal 606 243 725 2.411 0.757 0.098 0.027 8 0.6 G_cingul-Post-ventral 4198 1499 3871 2.078 0.502 0.104 0.034 64 5.7 G_cuneus 2170 929 3655 2.960 0.419 0.102 0.024 34 2.5 G_front_inf-Opercular 569 221 926 2.767 0.441 0.105 0.033 10 0.7 G_front_inf-Orbital 2006 798 3239 2.877 0.527 0.099 0.030 33 2.5 G_front_inf-Triangul 10439 4233 15250 2.707 0.534 0.109 0.033 184 14.9 G_front_middle 14453 5887 22944 2.935 0.589 0.105 0.031 213 19.4 G_front_sup 1363 594 1801 2.707 0.824 0.124 0.060 38 3.7 G_Ins_lg&S_cent_ins 1530 660 2829 3.317 0.722 0.128 0.056 41 3.2 G_insular_short 4596 1669 5573 2.482 0.473 0.099 0.027 66 5.4 G_occipital_middle 2601 994 2524 2.162 0.402 0.089 0.025 30 2.6 G_occipital_sup 3018 1227 5265 3.150 0.634 0.108 0.039 52 5.5 G_oc-temp_lat-fusifor 5674 2087 6145 2.294 0.568 0.115 0.042 87 10.3 G_oc-temp_med-Lingual 2188 847 3931 3.411 0.643 0.090 0.038 28 4.0 G_oc-temp_med-Parahip 4560 1837 7491 2.869 0.573 0.109 0.037 90 8.2 G_orbital 4676 1789 6659 2.702 0.511 0.100 0.030 81 5.4 G_pariet_inf-Angular 5808 2258 8139 2.765 0.447 0.100 0.028 84 6.6 G_pariet_inf-Supramar 4607 1881 5931 2.433 0.420 0.100 0.026 75 4.9 G_parietal_sup 4675 1584 4090 2.163 0.409 0.081 0.024 42 4.8 G_postcentral 5529 1620 6664 2.959 0.501 0.073 0.035 66 9.3 G_precentral 4838 2007 7551 2.754 0.481 0.115 0.035 94 7.1 G_precuneus 1437 581 2405 2.801 0.509 0.126 0.055 40 3.8 G_rectus 1149 506 1315 2.375 1.046 0.106 0.061 21 2.7 G_subcallosal 1268 448 1490 2.611 0.389 0.086 0.026 13 1.3 G_temp_sup-G_T_transv 3518 1398 6256 2.977 0.616 0.105 0.035 57 5.2 G_temp_sup-Lateral 1412 563 2508 3.498 0.667 0.073 0.024 9 1.4 G_temp_sup-Plan_polar 1483 616 1719 2.510 0.551 0.058 0.012 7 0.7 G_temp_sup-Plan_tempo 4528 1879 7902 2.949 0.629 0.110 0.034 86 6.3 G_temporal_inf 5525 2191 9791 3.001 0.577 0.106 0.032 94 7.1 G_temporal_middle 487 205 389 2.300 0.323 0.058 0.008 1 0.1 Lat_Fis-ant-Horizont 442 195 455 2.625 0.496 0.059 0.008 1 0.1 Lat_Fis-ant-Vertical 1679 709 1399 2.362 0.349 0.078 0.018 9 1.2 Lat_Fis-post 3806 1384 3240 1.923 0.513 0.098 0.029 46 4.8 Pole_occipital 2991 1289 6201 3.188 0.647 0.107 0.040 48 5.1 Pole_temporal 4940 2124 4040 2.224 0.462 0.082 0.022 35 4.9 S_calcarine 5728 2400 4668 2.225 0.499 0.070 0.019 75 4.7 S_central 1856 780 1664 2.407 0.381 0.066 0.012 7 0.9 S_cingul-Marginalis 915 377 923 2.824 0.475 0.054 0.012 2 0.4 S_circular_insula_ant 2397 1015 2325 2.829 0.564 0.077 0.021 15 2.7 S_circular_insula_inf 2675 1169 2483 2.553 0.534 0.078 0.023 18 2.8 S_circular_insula_sup 1164 491 1323 2.784 0.450 0.079 0.017 9 0.9 S_collat_transv_ant 1191 495 916 2.110 0.404 0.088 0.021 8 1.0 S_collat_transv_post 3806 1704 3596 2.258 0.382 0.071 0.013 21 2.0 S_front_inf 2917 1221 2404 2.186 0.376 0.080 0.017 20 2.0 S_front_middle 6770 2871 6853 2.488 0.370 0.071 0.014 40 3.9 S_front_sup 640 268 460 2.209 0.351 0.082 0.012 3 0.5 S_interm_prim-Jensen 4230 1830 3470 2.162 0.245 0.065 0.011 18 2.0 S_intrapariet&P_trans 2034 861 1488 2.131 0.297 0.085 0.018 13 1.4 S_oc_middle&Lunatus 3096 1299 2620 2.203 0.303 0.080 0.016 19 2.1 S_oc_sup&transversal 1325 537 1046 2.127 0.361 0.073 0.019 8 0.8 S_occipital_ant 1644 698 1371 2.318 0.467 0.067 0.011 6 0.8 S_oc-temp_lat 3333 1440 3033 2.343 0.478 0.066 0.012 13 1.7 S_oc-temp_med&Lingual 849 355 589 1.983 0.300 0.085 0.015 5 0.6 S_orbital_lateral 831 360 748 2.382 0.491 0.083 0.015 4 0.5 S_orbital_med-olfact 2627 1106 3024 2.561 0.507 0.088 0.026 24 2.9 S_orbital-H_Shaped 3909 1636 3495 2.347 0.324 0.082 0.016 28 2.8 S_parieto_occipital 2823 1076 1244 1.382 0.545 0.083 0.017 31 1.7 S_pericallosal 4902 2092 4240 2.201 0.314 0.077 0.015 33 2.8 S_postcentral 2821 1210 2770 2.446 0.388 0.079 0.017 22 1.8 S_precentral-inf-part 2237 985 2445 2.721 0.383 0.063 0.011 7 1.2 S_precentral-sup-part 1329 554 1108 2.295 0.441 0.076 0.014 8 0.9 S_suborbital 2215 936 1922 2.308 0.327 0.089 0.023 20 1.9 S_subparietal 3764 1570 2984 2.303 0.417 0.076 0.014 19 2.3 S_temporal_inf 10695 4522 10505 2.466 0.409 0.070 0.015 64 6.1 S_temporal_sup 734 296 473 1.884 0.389 0.076 0.014 5 0.4 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 3 lh Wed May 26 00:12:33 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03 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-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 282888 Total vertex volume 280012 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 3451 1421 4237 2.528 0.852 0.092 0.021 35 3.3 caudalanteriorcingulate 7818 3338 10016 2.724 0.489 0.088 0.024 80 8.0 caudalmiddlefrontal 5713 2205 5087 2.100 0.457 0.097 0.027 68 6.5 cuneus 958 389 1972 3.516 0.578 0.100 0.044 13 1.9 entorhinal 6849 2839 9207 2.765 0.652 0.088 0.025 74 7.9 fusiform 12993 5255 14872 2.488 0.444 0.085 0.021 148 10.9 inferiorparietal 9009 3758 13218 2.795 0.635 0.096 0.027 127 9.9 inferiortemporal 3281 1326 3368 2.183 0.903 0.092 0.024 44 3.3 isthmuscingulate 14880 5664 14061 2.170 0.486 0.093 0.025 158 15.5 lateraloccipital 7706 3212 10774 2.752 0.635 0.107 0.039 142 13.7 lateralorbitofrontal 7724 3061 7729 2.208 0.542 0.103 0.033 92 11.0 lingual 4055 1706 5325 2.567 0.615 0.105 0.038 71 6.5 medialorbitofrontal 12486 5126 17400 2.746 0.616 0.090 0.024 143 12.3 middletemporal 1774 703 2252 2.930 0.638 0.059 0.016 8 1.2 parahippocampal 4631 1796 5202 2.639 0.464 0.076 0.021 31 4.4 paracentral 3269 1443 4550 2.670 0.534 0.090 0.021 39 2.9 parsopercularis 1819 727 2107 2.536 0.513 0.077 0.023 15 1.9 parsorbitalis 3994 1650 4999 2.584 0.549 0.081 0.020 41 3.4 parstriangularis 4264 1644 3465 2.275 0.439 0.085 0.027 42 5.1 pericalcarine 12492 4843 11538 2.204 0.478 0.080 0.021 145 11.4 postcentral 3973 1630 4634 2.411 0.719 0.105 0.029 53 4.9 posteriorcingulate 13347 4864 14665 2.741 0.505 0.074 0.024 118 15.0 precentral 9993 4205 11803 2.527 0.448 0.097 0.026 124 10.8 precuneus 3517 1431 4704 2.650 0.822 0.099 0.031 49 4.6 rostralanteriorcingulate 12121 5002 14329 2.420 0.501 0.096 0.025 158 12.6 rostralmiddlefrontal 23099 9579 30656 2.695 0.588 0.094 0.026 285 25.2 superiorfrontal 9870 4122 10283 2.267 0.384 0.085 0.019 107 7.6 superiorparietal 12934 5349 18100 2.825 0.693 0.082 0.026 121 14.1 superiortemporal 9675 3859 11236 2.586 0.463 0.092 0.024 109 8.8 supramarginal 1504 521 1498 2.460 0.406 0.088 0.026 15 1.6 transversetemporal 4920 2112 6728 2.971 0.645 0.101 0.037 76 8.5 insula /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed May 26 00:13:39 UTC 2021 mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 1671 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 5800 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 3153 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 11062 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 1145 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 5222 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 2246 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 8229 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 2445 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 8229 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 1647 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 5717 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 7510 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 21099 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 1401 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 5582 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 2354 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 5776 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 5767 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 10408 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 9370 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 17484 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 2094 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 4112 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 344 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1634 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 318 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1517 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 398 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1412 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 854 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2946 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 297 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1801 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 936 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2932 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 1193 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 3512 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 622 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 2171 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 3243 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 10278 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 449 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2361 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 1013 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 2164 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 4364 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 7769 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 4000 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 7334 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 434 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 947 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 585 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-03 --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-03 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-03/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 245295 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 544 mri_label2label: Done mris_label2annot --s sub-03 --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-03/label cmdline mris_label2annot --s sub-03 --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 blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-03 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-03/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 169965 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/lh.BA_exvivo.annot mris_label2annot --s sub-03 --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-03/label cmdline mris_label2annot --s sub-03 --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 blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-03 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-03/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 201197 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 282888 Total vertex volume 280012 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 2023 650 1881 2.178 0.385 0.086 0.027 23 2.4 BA1_exvivo 7128 2864 6586 2.270 0.361 0.079 0.018 54 5.2 BA2_exvivo 1774 749 1161 2.002 0.330 0.088 0.023 10 1.9 BA3a_exvivo 4443 1660 3965 2.130 0.556 0.077 0.023 83 4.5 BA3b_exvivo 3226 1096 3627 2.778 0.452 0.072 0.027 31 4.5 BA4a_exvivo 2601 968 2550 2.695 0.417 0.064 0.028 19 3.0 BA4p_exvivo 17922 7082 25032 2.955 0.519 0.085 0.026 177 20.2 BA6_exvivo 3403 1514 4696 2.678 0.479 0.087 0.019 36 2.8 BA44_exvivo 5043 2087 6585 2.587 0.574 0.089 0.022 61 4.7 BA45_exvivo 7337 2693 6108 2.166 0.487 0.089 0.030 80 9.7 V1_exvivo 14526 5700 13379 2.083 0.499 0.102 0.030 174 18.7 V2_exvivo 4005 1504 4357 2.412 0.407 0.084 0.022 42 3.7 MT_exvivo 921 354 1829 3.584 0.453 0.071 0.020 5 0.8 perirhinal_exvivo 978 406 1304 2.924 0.505 0.068 0.020 6 0.8 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-03 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-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 282888 Total vertex volume 280012 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 1291 387 1191 2.226 0.373 0.086 0.031 15 1.7 BA1_exvivo 2719 1055 2554 2.278 0.338 0.075 0.017 17 2.0 BA2_exvivo 1495 641 950 1.998 0.301 0.089 0.031 12 1.9 BA3a_exvivo 2771 1072 2094 1.893 0.322 0.065 0.015 61 2.0 BA3b_exvivo 3280 1088 3519 2.801 0.458 0.064 0.025 25 4.1 BA4a_exvivo 1982 758 1937 2.663 0.395 0.066 0.023 12 1.9 BA4p_exvivo 9502 3537 13010 2.985 0.541 0.080 0.027 88 11.1 BA6_exvivo 2084 930 3132 2.730 0.440 0.099 0.023 31 2.1 BA44_exvivo 2129 855 3375 2.825 0.565 0.098 0.029 35 2.5 BA45_exvivo 7703 2832 6416 2.147 0.494 0.089 0.030 82 10.2 V1_exvivo 7279 2806 6260 2.007 0.497 0.108 0.034 94 10.8 V2_exvivo 933 360 850 2.223 0.357 0.077 0.018 9 0.7 MT_exvivo 445 176 857 3.470 0.382 0.059 0.012 1 0.3 perirhinal_exvivo 485 194 636 3.084 0.393 0.055 0.017 2 0.3 entorhinal_exvivo Started at Wed May 26 00:09:14 UTC 2021 Ended at Wed May 26 00:18:59 UTC 2021 #@#%# recon-all-run-time-hours 0.162 recon-all -s sub-03 finished without error at Wed May 26 00:18:59 UTC 2021