Sun Jan 13 01:08:11 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-ADS5115 -sd /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer subjid sub-ADS5115 setenv SUBJECTS_DIR /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/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 n018 3.10.0-862.14.4.el7.x86_64 #1 SMP Fri Sep 21 09:07:21 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 104857600 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 515220 maxlocks unlimited maxsignal 515220 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131915620 15657108 109499540 225100 6758972 114343340 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: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:11-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/13-01:08:12-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: pettitta Machine: n018 Platform: Linux PlatformVersion: 3.10.0-862.14.4.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 Sun Jan 13 01:08:13 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 1 found - 1 modified | TOTAL: 8 pass 2 (xy-): 0 found - 1 modified | TOTAL: 8 pass 1 (yz+): 2 found - 2 modified | TOTAL: 10 pass 2 (yz+): 0 found - 2 modified | TOTAL: 10 pass 1 (yz-): 3 found - 3 modified | TOTAL: 13 pass 2 (yz-): 0 found - 3 modified | TOTAL: 13 pass 1 (xz+): 0 found - 0 modified | TOTAL: 13 pass 1 (xz-): 9 found - 9 modified | TOTAL: 22 pass 2 (xz-): 0 found - 9 modified | TOTAL: 22 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 4 found - 4 modified | TOTAL: 5 pass 2 (-+): 0 found - 4 modified | TOTAL: 5 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 = 27 (out of 2846476: 0.000949) 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 70: 494 vertices, 550 faces slice 80: 4718 vertices, 4924 faces slice 90: 13673 vertices, 14109 faces slice 100: 27310 vertices, 27853 faces slice 110: 44322 vertices, 44984 faces slice 120: 66385 vertices, 67233 faces slice 130: 90208 vertices, 91023 faces slice 140: 113258 vertices, 114098 faces slice 150: 138443 vertices, 139379 faces slice 160: 164150 vertices, 165083 faces slice 170: 188678 vertices, 189675 faces slice 180: 215363 vertices, 216341 faces slice 190: 241230 vertices, 242137 faces slice 200: 265826 vertices, 266769 faces slice 210: 293264 vertices, 294269 faces slice 220: 323745 vertices, 324774 faces slice 230: 354819 vertices, 356010 faces slice 240: 385031 vertices, 386160 faces slice 250: 414074 vertices, 415225 faces slice 260: 443429 vertices, 444647 faces slice 270: 469627 vertices, 470802 faces slice 280: 498354 vertices, 499573 faces slice 290: 526007 vertices, 527347 faces slice 300: 554957 vertices, 556130 faces slice 310: 578437 vertices, 579571 faces slice 320: 599711 vertices, 600798 faces slice 330: 621655 vertices, 622745 faces slice 340: 642623 vertices, 643735 faces slice 350: 661958 vertices, 662951 faces slice 360: 679107 vertices, 680076 faces slice 370: 695466 vertices, 696342 faces slice 380: 710791 vertices, 711660 faces slice 390: 724911 vertices, 725735 faces slice 400: 737311 vertices, 738070 faces slice 410: 748211 vertices, 748933 faces slice 420: 756961 vertices, 757625 faces slice 430: 762535 vertices, 762994 faces slice 440: 763422 vertices, 763786 faces slice 450: 763422 vertices, 763786 faces slice 460: 763422 vertices, 763786 faces slice 470: 763422 vertices, 763786 faces slice 480: 763422 vertices, 763786 faces slice 490: 763422 vertices, 763786 faces slice 500: 763422 vertices, 763786 faces slice 510: 763422 vertices, 763786 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -0.44922 0.00000 0.00000 115.00000; 0.00000 0.00000 0.44922 -115.00000; 0.00000 -0.44922 0.00000 115.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 763422 voxel in cpt #1: X=-364 [v=763422,e=2291358,f=1527572] located at (-29.204325, -6.877007, 33.792252) For the whole surface: X=-364 [v=763422,e=2291358,f=1527572] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Jan 13 01:10:21 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 Sun Jan 13 01:11:48 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 = 46.5 mm, total surface area = 92850 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 77.9 minutes step 000: RMS=0.115 (target=0.015) step 005: RMS=0.093 (target=0.015) step 010: RMS=0.077 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.054 (target=0.015) step 035: RMS=0.051 (target=0.015) step 040: RMS=0.049 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.047 (target=0.015) step 055: RMS=0.045 (target=0.015) step 060: RMS=0.044 (target=0.015) step 065: RMS=0.044 (target=0.015) step 070: RMS=0.043 (target=0.015) step 075: RMS=0.042 (target=0.015) step 080: RMS=0.042 (target=0.015) step 085: RMS=0.041 (target=0.015) step 090: RMS=0.041 (target=0.015) step 095: RMS=0.040 (target=0.015) step 100: RMS=0.040 (target=0.015) step 105: RMS=0.040 (target=0.015) step 110: RMS=0.039 (target=0.015) step 115: RMS=0.039 (target=0.015) step 120: RMS=0.039 (target=0.015) step 125: RMS=0.039 (target=0.015) step 130: RMS=0.038 (target=0.015) step 135: RMS=0.038 (target=0.015) step 140: RMS=0.038 (target=0.015) step 145: RMS=0.038 (target=0.015) step 150: RMS=0.038 (target=0.015) step 155: RMS=0.038 (target=0.015) step 160: RMS=0.038 (target=0.015) step 165: RMS=0.037 (target=0.015) step 170: RMS=0.037 (target=0.015) step 175: RMS=0.037 (target=0.015) step 180: RMS=0.037 (target=0.015) step 185: RMS=0.037 (target=0.015) step 190: RMS=0.037 (target=0.015) step 195: RMS=0.037 (target=0.015) step 200: RMS=0.037 (target=0.015) step 205: RMS=0.037 (target=0.015) step 210: RMS=0.037 (target=0.015) step 215: RMS=0.037 (target=0.015) step 220: RMS=0.037 (target=0.015) step 225: RMS=0.037 (target=0.015) step 230: RMS=0.036 (target=0.015) step 235: RMS=0.036 (target=0.015) step 240: RMS=0.036 (target=0.015) step 245: RMS=0.036 (target=0.015) step 250: RMS=0.036 (target=0.015) step 255: RMS=0.037 (target=0.015) step 260: RMS=0.038 (target=0.015) step 265: RMS=0.038 (target=0.015) step 270: RMS=0.038 (target=0.015) step 275: RMS=0.038 (target=0.015) step 280: RMS=0.038 (target=0.015) step 285: RMS=0.038 (target=0.015) step 290: RMS=0.038 (target=0.015) step 295: RMS=0.038 (target=0.015) step 300: RMS=0.038 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 2103.903630 mris_inflate stimesec 3.354185 mris_inflate ru_maxrss 1195448 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 2245322 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 500 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 71967 mris_inflate ru_nivcsw 187519 #-------------------------------------------- #@# QSphere lh Sun Jan 13 02:29:44 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 0.43 +- 0.27 (0.00-->3.79) (max @ vno 549389 --> 549390) face area 0.00 +- 0.01 (-0.05-->0.14) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.274... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.935, avgs=0 005/300: dt: 0.9000, rms radial error=176.672, avgs=0 010/300: dt: 0.9000, rms radial error=176.108, avgs=0 015/300: dt: 0.9000, rms radial error=175.367, avgs=0 020/300: dt: 0.9000, rms radial error=174.527, avgs=0 025/300: dt: 0.9000, rms radial error=173.631, avgs=0 030/300: dt: 0.9000, rms radial error=172.703, avgs=0 035/300: dt: 0.9000, rms radial error=171.758, avgs=0 040/300: dt: 0.9000, rms radial error=170.802, avgs=0 045/300: dt: 0.9000, rms radial error=169.845, avgs=0 050/300: dt: 0.9000, rms radial error=168.888, avgs=0 055/300: dt: 0.9000, rms radial error=167.933, avgs=0 060/300: dt: 0.9000, rms radial error=166.982, avgs=0 065/300: dt: 0.9000, rms radial error=166.036, avgs=0 070/300: dt: 0.9000, rms radial error=165.094, avgs=0 075/300: dt: 0.9000, rms radial error=164.158, avgs=0 080/300: dt: 0.9000, rms radial error=163.227, avgs=0 085/300: dt: 0.9000, rms radial error=162.301, avgs=0 090/300: dt: 0.9000, rms radial error=161.380, avgs=0 095/300: dt: 0.9000, rms radial error=160.465, avgs=0 100/300: dt: 0.9000, rms radial error=159.555, avgs=0 105/300: dt: 0.9000, rms radial error=158.649, avgs=0 110/300: dt: 0.9000, rms radial error=157.749, avgs=0 115/300: dt: 0.9000, rms radial error=156.855, avgs=0 120/300: dt: 0.9000, rms radial error=155.965, avgs=0 125/300: dt: 0.9000, rms radial error=155.080, avgs=0 130/300: dt: 0.9000, rms radial error=154.201, avgs=0 135/300: dt: 0.9000, rms radial error=153.326, avgs=0 140/300: dt: 0.9000, rms radial error=152.457, avgs=0 145/300: dt: 0.9000, rms radial error=151.592, avgs=0 150/300: dt: 0.9000, rms radial error=150.733, avgs=0 155/300: dt: 0.9000, rms radial error=149.878, avgs=0 160/300: dt: 0.9000, rms radial error=149.028, avgs=0 165/300: dt: 0.9000, rms radial error=148.183, avgs=0 170/300: dt: 0.9000, rms radial error=147.343, avgs=0 175/300: dt: 0.9000, rms radial error=146.508, avgs=0 180/300: dt: 0.9000, rms radial error=145.678, avgs=0 185/300: dt: 0.9000, rms radial error=144.853, avgs=0 190/300: dt: 0.9000, rms radial error=144.032, avgs=0 195/300: dt: 0.9000, rms radial error=143.216, avgs=0 200/300: dt: 0.9000, rms radial error=142.404, avgs=0 205/300: dt: 0.9000, rms radial error=141.597, avgs=0 210/300: dt: 0.9000, rms radial error=140.795, avgs=0 215/300: dt: 0.9000, rms radial error=139.997, avgs=0 220/300: dt: 0.9000, rms radial error=139.204, avgs=0 225/300: dt: 0.9000, rms radial error=138.415, avgs=0 230/300: dt: 0.9000, rms radial error=137.631, avgs=0 235/300: dt: 0.9000, rms radial error=136.851, avgs=0 240/300: dt: 0.9000, rms radial error=136.076, avgs=0 245/300: dt: 0.9000, rms radial error=135.305, avgs=0 250/300: dt: 0.9000, rms radial error=134.538, avgs=0 255/300: dt: 0.9000, rms radial error=133.776, avgs=0 260/300: dt: 0.9000, rms radial error=133.018, avgs=0 265/300: dt: 0.9000, rms radial error=132.264, avgs=0 270/300: dt: 0.9000, rms radial error=131.515, avgs=0 275/300: dt: 0.9000, rms radial error=130.769, avgs=0 280/300: dt: 0.9000, rms radial error=130.028, avgs=0 285/300: dt: 0.9000, rms radial error=129.292, avgs=0 290/300: dt: 0.9000, rms radial error=128.559, avgs=0 295/300: dt: 0.9000, rms radial error=127.831, avgs=0 300/300: dt: 0.9000, rms radial error=127.106, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 102523.78 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 2 (K=40.0), pass 1, starting sse = 23397.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 3 (K=160.0), pass 1, starting sse = 4369.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 4 (K=640.0), pass 1, starting sse = 546.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00195 final distance error %31.20 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 1.36 hours mris_sphere utimesec 2199.499184 mris_sphere stimesec 5.060196 mris_sphere ru_maxrss 1195808 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 4760055 mris_sphere ru_majflt 3 mris_sphere ru_nswap 0 mris_sphere ru_inblock 510 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 60169 mris_sphere ru_nivcsw 200065 FSRUNTIME@ mris_sphere 1.3577 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Sun Jan 13 03:51:12 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Sun Jan 13 03:51:13 UTC 2019 mris_fix_topology -rusage /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-ADS5115 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=-364 (nv=763422, nf=1527572, ne=2291358, g=183) 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 8 iterations marking ambiguous vertices... 80696 ambiguous faces found in tessellation segmenting defects... 182 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 23 into 3 -merging segment 75 into 50 -merging segment 58 into 55 -merging segment 53 into 56 -merging segment 95 into 92 -merging segment 103 into 92 -merging segment 86 into 94 -merging segment 132 into 111 -merging segment 139 into 130 -merging segment 158 into 155 172 defects to be corrected 0 vertices coincident reading input surface /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7775 (-4.3887) -vertex loglikelihood: -5.2645 (-2.6322) -normal dot loglikelihood: -3.4002 (-3.4002) -quad curv loglikelihood: -6.8321 (-3.4161) Total Loglikelihood : -24.2743 CORRECTING DEFECT 0 (vertices=75, convex hull=83, v0=2716) After retessellation of defect 0 (v0=2716), euler #=-153 (718670,2147274,1428451) : difference with theory (-169) = -16 CORRECTING DEFECT 1 (vertices=1861, convex hull=368, v0=4551) After retessellation of defect 1 (v0=4551), euler #=-152 (718679,2147482,1428651) : difference with theory (-168) = -16 CORRECTING DEFECT 2 (vertices=36, convex hull=24, v0=6840) After retessellation of defect 2 (v0=6840), euler #=-151 (718679,2147489,1428659) : difference with theory (-167) = -16 CORRECTING DEFECT 3 (vertices=11447, convex hull=1934, v0=8129) XL defect detected... After retessellation of defect 3 (v0=8129), euler #=-155 (718983,2149474,1430336) : difference with theory (-166) = -11 CORRECTING DEFECT 4 (vertices=45, convex hull=34, v0=16246) After retessellation of defect 4 (v0=16246), euler #=-154 (718984,2149488,1430350) : difference with theory (-165) = -11 CORRECTING DEFECT 5 (vertices=142, convex hull=76, v0=20107) After retessellation of defect 5 (v0=20107), euler #=-153 (718989,2149535,1430393) : difference with theory (-164) = -11 CORRECTING DEFECT 6 (vertices=41, convex hull=62, v0=21268) After retessellation of defect 6 (v0=21268), euler #=-152 (718994,2149575,1430429) : difference with theory (-163) = -11 CORRECTING DEFECT 7 (vertices=41, convex hull=45, v0=28579) After retessellation of defect 7 (v0=28579), euler #=-151 (718998,2149607,1430458) : difference with theory (-162) = -11 CORRECTING DEFECT 8 (vertices=95, convex hull=64, v0=29164) After retessellation of defect 8 (v0=29164), euler #=-150 (719003,2149652,1430499) : difference with theory (-161) = -11 CORRECTING DEFECT 9 (vertices=370, convex hull=139, v0=32803) After retessellation of defect 9 (v0=32803), euler #=-149 (719016,2149759,1430594) : difference with theory (-160) = -11 CORRECTING DEFECT 10 (vertices=515, convex hull=307, v0=42232) After retessellation of defect 10 (v0=42232), euler #=-148 (719062,2150040,1430830) : difference with theory (-159) = -11 CORRECTING DEFECT 11 (vertices=5, convex hull=32, v0=47996) After retessellation of defect 11 (v0=47996), euler #=-147 (719062,2150048,1430839) : difference with theory (-158) = -11 CORRECTING DEFECT 12 (vertices=18, convex hull=27, v0=48063) After retessellation of defect 12 (v0=48063), euler #=-146 (719062,2150059,1430851) : difference with theory (-157) = -11 CORRECTING DEFECT 13 (vertices=31, convex hull=46, v0=50789) After retessellation of defect 13 (v0=50789), euler #=-145 (719065,2150089,1430879) : difference with theory (-156) = -11 CORRECTING DEFECT 14 (vertices=50, convex hull=25, v0=52691) After retessellation of defect 14 (v0=52691), euler #=-144 (719066,2150099,1430889) : difference with theory (-155) = -11 CORRECTING DEFECT 15 (vertices=157, convex hull=138, v0=54192) After retessellation of defect 15 (v0=54192), euler #=-143 (719075,2150194,1430976) : difference with theory (-154) = -11 CORRECTING DEFECT 16 (vertices=87, convex hull=86, v0=55575) After retessellation of defect 16 (v0=55575), euler #=-142 (719081,2150250,1431027) : difference with theory (-153) = -11 CORRECTING DEFECT 17 (vertices=53, convex hull=57, v0=65081) After retessellation of defect 17 (v0=65081), euler #=-141 (719081,2150272,1431050) : difference with theory (-152) = -11 CORRECTING DEFECT 18 (vertices=162, convex hull=78, v0=68708) After retessellation of defect 18 (v0=68708), euler #=-141 (719086,2150331,1431104) : difference with theory (-151) = -10 CORRECTING DEFECT 19 (vertices=1059, convex hull=362, v0=75748) After retessellation of defect 19 (v0=75748), euler #=-140 (719134,2150646,1431372) : difference with theory (-150) = -10 CORRECTING DEFECT 20 (vertices=43, convex hull=63, v0=82360) After retessellation of defect 20 (v0=82360), euler #=-139 (719136,2150677,1431402) : difference with theory (-149) = -10 CORRECTING DEFECT 21 (vertices=10, convex hull=17, v0=83281) After retessellation of defect 21 (v0=83281), euler #=-138 (719137,2150685,1431410) : difference with theory (-148) = -10 CORRECTING DEFECT 22 (vertices=28, convex hull=67, v0=85696) After retessellation of defect 22 (v0=85696), euler #=-137 (719139,2150714,1431438) : difference with theory (-147) = -10 CORRECTING DEFECT 23 (vertices=16, convex hull=38, v0=97946) After retessellation of defect 23 (v0=97946), euler #=-136 (719140,2150732,1431456) : difference with theory (-146) = -10 CORRECTING DEFECT 24 (vertices=15, convex hull=22, v0=101403) After retessellation of defect 24 (v0=101403), euler #=-135 (719142,2150744,1431467) : difference with theory (-145) = -10 CORRECTING DEFECT 25 (vertices=24, convex hull=48, v0=103469) After retessellation of defect 25 (v0=103469), euler #=-134 (719145,2150775,1431496) : difference with theory (-144) = -10 CORRECTING DEFECT 26 (vertices=115, convex hull=84, v0=105840) After retessellation of defect 26 (v0=105840), euler #=-133 (719152,2150829,1431544) : difference with theory (-143) = -10 CORRECTING DEFECT 27 (vertices=85, convex hull=63, v0=122887) After retessellation of defect 27 (v0=122887), euler #=-132 (719158,2150871,1431581) : difference with theory (-142) = -10 CORRECTING DEFECT 28 (vertices=39, convex hull=28, v0=125764) After retessellation of defect 28 (v0=125764), euler #=-131 (719158,2150881,1431592) : difference with theory (-141) = -10 CORRECTING DEFECT 29 (vertices=221, convex hull=83, v0=127488) After retessellation of defect 29 (v0=127488), euler #=-130 (719164,2150941,1431647) : difference with theory (-140) = -10 CORRECTING DEFECT 30 (vertices=224, convex hull=150, v0=128072) After retessellation of defect 30 (v0=128072), euler #=-129 (719175,2151048,1431744) : difference with theory (-139) = -10 CORRECTING DEFECT 31 (vertices=49, convex hull=67, v0=132507) After retessellation of defect 31 (v0=132507), euler #=-128 (719177,2151079,1431774) : difference with theory (-138) = -10 CORRECTING DEFECT 32 (vertices=118, convex hull=58, v0=143356) After retessellation of defect 32 (v0=143356), euler #=-127 (719179,2151105,1431799) : difference with theory (-137) = -10 CORRECTING DEFECT 33 (vertices=27, convex hull=37, v0=145139) After retessellation of defect 33 (v0=145139), euler #=-126 (719180,2151120,1431814) : difference with theory (-136) = -10 CORRECTING DEFECT 34 (vertices=119, convex hull=58, v0=145460) After retessellation of defect 34 (v0=145460), euler #=-125 (719182,2151149,1431842) : difference with theory (-135) = -10 CORRECTING DEFECT 35 (vertices=5, convex hull=24, v0=148116) After retessellation of defect 35 (v0=148116), euler #=-124 (719183,2151157,1431850) : difference with theory (-134) = -10 CORRECTING DEFECT 36 (vertices=25, convex hull=70, v0=156313) After retessellation of defect 36 (v0=156313), euler #=-123 (719186,2151194,1431885) : difference with theory (-133) = -10 CORRECTING DEFECT 37 (vertices=14, convex hull=24, v0=158192) After retessellation of defect 37 (v0=158192), euler #=-122 (719187,2151204,1431895) : difference with theory (-132) = -10 CORRECTING DEFECT 38 (vertices=388, convex hull=139, v0=158235) After retessellation of defect 38 (v0=158235), euler #=-121 (719203,2151318,1431994) : difference with theory (-131) = -10 CORRECTING DEFECT 39 (vertices=56, convex hull=37, v0=161271) After retessellation of defect 39 (v0=161271), euler #=-120 (719204,2151335,1432011) : difference with theory (-130) = -10 CORRECTING DEFECT 40 (vertices=180, convex hull=106, v0=166230) After retessellation of defect 40 (v0=166230), euler #=-119 (719212,2151405,1432074) : difference with theory (-129) = -10 CORRECTING DEFECT 41 (vertices=38, convex hull=35, v0=166871) After retessellation of defect 41 (v0=166871), euler #=-118 (719213,2151420,1432089) : difference with theory (-128) = -10 CORRECTING DEFECT 42 (vertices=34, convex hull=60, v0=168718) After retessellation of defect 42 (v0=168718), euler #=-117 (719216,2151453,1432120) : difference with theory (-127) = -10 CORRECTING DEFECT 43 (vertices=414, convex hull=103, v0=171634) After retessellation of defect 43 (v0=171634), euler #=-116 (719221,2151516,1432179) : difference with theory (-126) = -10 CORRECTING DEFECT 44 (vertices=882, convex hull=280, v0=178521) After retessellation of defect 44 (v0=178521), euler #=-115 (719272,2151813,1432426) : difference with theory (-125) = -10 CORRECTING DEFECT 45 (vertices=63, convex hull=77, v0=185473) After retessellation of defect 45 (v0=185473), euler #=-114 (719278,2151861,1432469) : difference with theory (-124) = -10 CORRECTING DEFECT 46 (vertices=39, convex hull=61, v0=202010) After retessellation of defect 46 (v0=202010), euler #=-113 (719284,2151904,1432507) : difference with theory (-123) = -10 CORRECTING DEFECT 47 (vertices=328, convex hull=58, v0=206877) After retessellation of defect 47 (v0=206877), euler #=-112 (719286,2151936,1432538) : difference with theory (-122) = -10 CORRECTING DEFECT 48 (vertices=58, convex hull=85, v0=246084) After retessellation of defect 48 (v0=246084), euler #=-111 (719296,2152005,1432598) : difference with theory (-121) = -10 CORRECTING DEFECT 49 (vertices=2707, convex hull=909, v0=278924) L defect detected... After retessellation of defect 49 (v0=278924), euler #=-112 (719325,2152597,1433160) : difference with theory (-120) = -8 CORRECTING DEFECT 50 (vertices=200, convex hull=160, v0=282883) After retessellation of defect 50 (v0=282883), euler #=-111 (719340,2152721,1433270) : difference with theory (-119) = -8 CORRECTING DEFECT 51 (vertices=9, convex hull=25, v0=284312) After retessellation of defect 51 (v0=284312), euler #=-110 (719342,2152733,1433281) : difference with theory (-118) = -8 CORRECTING DEFECT 52 (vertices=164, convex hull=63, v0=296911) After retessellation of defect 52 (v0=296911), euler #=-109 (719346,2152770,1433315) : difference with theory (-117) = -8 CORRECTING DEFECT 53 (vertices=154, convex hull=160, v0=299691) After retessellation of defect 53 (v0=299691), euler #=-107 (719358,2152887,1433422) : difference with theory (-116) = -9 CORRECTING DEFECT 54 (vertices=1522, convex hull=613, v0=301473) normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces normal vector of length zero at vertex 743173 with 3 faces After retessellation of defect 54 (v0=301473), euler #=-106 (719408,2153368,1433854) : difference with theory (-115) = -9 CORRECTING DEFECT 55 (vertices=143, convex hull=133, v0=303337) After retessellation of defect 55 (v0=303337), euler #=-105 (719420,2153481,1433956) : difference with theory (-114) = -9 CORRECTING DEFECT 56 (vertices=162, convex hull=163, v0=318163) After retessellation of defect 56 (v0=318163), euler #=-104 (719434,2153603,1434065) : difference with theory (-113) = -9 CORRECTING DEFECT 57 (vertices=62, convex hull=68, v0=318525) After retessellation of defect 57 (v0=318525), euler #=-103 (719440,2153654,1434111) : difference with theory (-112) = -9 CORRECTING DEFECT 58 (vertices=188, convex hull=134, v0=320922) After retessellation of defect 58 (v0=320922), euler #=-102 (719450,2153746,1434194) : difference with theory (-111) = -9 CORRECTING DEFECT 59 (vertices=111, convex hull=106, v0=320942) After retessellation of defect 59 (v0=320942), euler #=-102 (719458,2153826,1434266) : difference with theory (-110) = -8 CORRECTING DEFECT 60 (vertices=31, convex hull=25, v0=333659) After retessellation of defect 60 (v0=333659), euler #=-101 (719460,2153841,1434280) : difference with theory (-109) = -8 CORRECTING DEFECT 61 (vertices=79, convex hull=66, v0=335680) After retessellation of defect 61 (v0=335680), euler #=-100 (719466,2153885,1434319) : difference with theory (-108) = -8 CORRECTING DEFECT 62 (vertices=77, convex hull=67, v0=342310) After retessellation of defect 62 (v0=342310), euler #=-99 (719468,2153924,1434357) : difference with theory (-107) = -8 CORRECTING DEFECT 63 (vertices=227, convex hull=119, v0=342526) After retessellation of defect 63 (v0=342526), euler #=-98 (719479,2154012,1434435) : difference with theory (-106) = -8 CORRECTING DEFECT 64 (vertices=110, convex hull=36, v0=345939) After retessellation of defect 64 (v0=345939), euler #=-97 (719480,2154025,1434448) : difference with theory (-105) = -8 CORRECTING DEFECT 65 (vertices=45, convex hull=28, v0=348982) After retessellation of defect 65 (v0=348982), euler #=-96 (719482,2154039,1434461) : difference with theory (-104) = -8 CORRECTING DEFECT 66 (vertices=46, convex hull=47, v0=353539) After retessellation of defect 66 (v0=353539), euler #=-95 (719486,2154067,1434486) : difference with theory (-103) = -8 CORRECTING DEFECT 67 (vertices=13, convex hull=28, v0=353643) After retessellation of defect 67 (v0=353643), euler #=-94 (719488,2154083,1434501) : difference with theory (-102) = -8 CORRECTING DEFECT 68 (vertices=21, convex hull=42, v0=357866) After retessellation of defect 68 (v0=357866), euler #=-93 (719489,2154099,1434517) : difference with theory (-101) = -8 CORRECTING DEFECT 69 (vertices=46, convex hull=85, v0=359530) After retessellation of defect 69 (v0=359530), euler #=-92 (719494,2154150,1434564) : difference with theory (-100) = -8 CORRECTING DEFECT 70 (vertices=84, convex hull=36, v0=365490) After retessellation of defect 70 (v0=365490), euler #=-91 (719498,2154174,1434585) : difference with theory (-99) = -8 CORRECTING DEFECT 71 (vertices=26, convex hull=28, v0=368370) After retessellation of defect 71 (v0=368370), euler #=-90 (719500,2154190,1434600) : difference with theory (-98) = -8 CORRECTING DEFECT 72 (vertices=9, convex hull=32, v0=372229) After retessellation of defect 72 (v0=372229), euler #=-89 (719502,2154207,1434616) : difference with theory (-97) = -8 CORRECTING DEFECT 73 (vertices=334, convex hull=310, v0=372521) After retessellation of defect 73 (v0=372521), euler #=-89 (719532,2154472,1434851) : difference with theory (-96) = -7 CORRECTING DEFECT 74 (vertices=125, convex hull=122, v0=373296) After retessellation of defect 74 (v0=373296), euler #=-88 (719540,2154552,1434924) : difference with theory (-95) = -7 CORRECTING DEFECT 75 (vertices=355, convex hull=106, v0=374729) After retessellation of defect 75 (v0=374729), euler #=-89 (719561,2154680,1435030) : difference with theory (-94) = -5 CORRECTING DEFECT 76 (vertices=59, convex hull=73, v0=379758) After retessellation of defect 76 (v0=379758), euler #=-88 (719568,2154731,1435075) : difference with theory (-93) = -5 CORRECTING DEFECT 77 (vertices=64, convex hull=67, v0=388020) After retessellation of defect 77 (v0=388020), euler #=-87 (719574,2154774,1435113) : difference with theory (-92) = -5 CORRECTING DEFECT 78 (vertices=1293, convex hull=338, v0=402306) After retessellation of defect 78 (v0=402306), euler #=-86 (719583,2154967,1435298) : difference with theory (-91) = -5 CORRECTING DEFECT 79 (vertices=84, convex hull=64, v0=407221) After retessellation of defect 79 (v0=407221), euler #=-85 (719587,2155004,1435332) : difference with theory (-90) = -5 CORRECTING DEFECT 80 (vertices=19, convex hull=52, v0=410043) After retessellation of defect 80 (v0=410043), euler #=-84 (719588,2155026,1435354) : difference with theory (-89) = -5 CORRECTING DEFECT 81 (vertices=640, convex hull=313, v0=413583) After retessellation of defect 81 (v0=413583), euler #=-83 (719620,2155289,1435586) : difference with theory (-88) = -5 CORRECTING DEFECT 82 (vertices=52, convex hull=64, v0=417838) After retessellation of defect 82 (v0=417838), euler #=-82 (719625,2155334,1435627) : difference with theory (-87) = -5 CORRECTING DEFECT 83 (vertices=5, convex hull=33, v0=418726) After retessellation of defect 83 (v0=418726), euler #=-81 (719625,2155343,1435637) : difference with theory (-86) = -5 CORRECTING DEFECT 84 (vertices=5, convex hull=31, v0=418733) After retessellation of defect 84 (v0=418733), euler #=-80 (719625,2155352,1435647) : difference with theory (-85) = -5 CORRECTING DEFECT 85 (vertices=17, convex hull=34, v0=421399) After retessellation of defect 85 (v0=421399), euler #=-79 (719628,2155375,1435668) : difference with theory (-84) = -5 CORRECTING DEFECT 86 (vertices=34, convex hull=34, v0=421492) After retessellation of defect 86 (v0=421492), euler #=-78 (719630,2155392,1435684) : difference with theory (-83) = -5 CORRECTING DEFECT 87 (vertices=185, convex hull=181, v0=424435) After retessellation of defect 87 (v0=424435), euler #=-75 (719645,2155523,1435803) : difference with theory (-82) = -7 CORRECTING DEFECT 88 (vertices=72, convex hull=90, v0=425986) After retessellation of defect 88 (v0=425986), euler #=-74 (719652,2155583,1435857) : difference with theory (-81) = -7 CORRECTING DEFECT 89 (vertices=236, convex hull=211, v0=429235) After retessellation of defect 89 (v0=429235), euler #=-72 (719665,2155729,1435992) : difference with theory (-80) = -8 CORRECTING DEFECT 90 (vertices=50, convex hull=77, v0=435385) After retessellation of defect 90 (v0=435385), euler #=-71 (719671,2155781,1436039) : difference with theory (-79) = -8 CORRECTING DEFECT 91 (vertices=43, convex hull=53, v0=437977) After retessellation of defect 91 (v0=437977), euler #=-70 (719675,2155816,1436071) : difference with theory (-78) = -8 CORRECTING DEFECT 92 (vertices=15, convex hull=38, v0=446706) After retessellation of defect 92 (v0=446706), euler #=-69 (719676,2155833,1436088) : difference with theory (-77) = -8 CORRECTING DEFECT 93 (vertices=30, convex hull=57, v0=451918) After retessellation of defect 93 (v0=451918), euler #=-68 (719681,2155871,1436122) : difference with theory (-76) = -8 CORRECTING DEFECT 94 (vertices=6, convex hull=25, v0=452622) After retessellation of defect 94 (v0=452622), euler #=-67 (719683,2155884,1436134) : difference with theory (-75) = -8 CORRECTING DEFECT 95 (vertices=18, convex hull=23, v0=453453) After retessellation of defect 95 (v0=453453), euler #=-66 (719685,2155898,1436147) : difference with theory (-74) = -8 CORRECTING DEFECT 96 (vertices=632, convex hull=153, v0=453469) After retessellation of defect 96 (v0=453469), euler #=-65 (719704,2156031,1436262) : difference with theory (-73) = -8 CORRECTING DEFECT 97 (vertices=36, convex hull=77, v0=458053) After retessellation of defect 97 (v0=458053), euler #=-64 (719706,2156068,1436298) : difference with theory (-72) = -8 CORRECTING DEFECT 98 (vertices=31, convex hull=65, v0=460947) After retessellation of defect 98 (v0=460947), euler #=-63 (719712,2156112,1436337) : difference with theory (-71) = -8 CORRECTING DEFECT 99 (vertices=24, convex hull=23, v0=461915) After retessellation of defect 99 (v0=461915), euler #=-62 (719712,2156116,1436342) : difference with theory (-70) = -8 CORRECTING DEFECT 100 (vertices=155, convex hull=104, v0=461984) After retessellation of defect 100 (v0=461984), euler #=-61 (719724,2156204,1436419) : difference with theory (-69) = -8 CORRECTING DEFECT 101 (vertices=8, convex hull=19, v0=463657) After retessellation of defect 101 (v0=463657), euler #=-60 (719724,2156210,1436426) : difference with theory (-68) = -8 CORRECTING DEFECT 102 (vertices=20, convex hull=22, v0=465405) After retessellation of defect 102 (v0=465405), euler #=-59 (719724,2156216,1436433) : difference with theory (-67) = -8 CORRECTING DEFECT 103 (vertices=321, convex hull=101, v0=468168) After retessellation of defect 103 (v0=468168), euler #=-59 (719737,2156303,1436507) : difference with theory (-66) = -7 CORRECTING DEFECT 104 (vertices=361, convex hull=324, v0=468791) After retessellation of defect 104 (v0=468791), euler #=-57 (719745,2156491,1436689) : difference with theory (-65) = -8 CORRECTING DEFECT 105 (vertices=69, convex hull=82, v0=470705) After retessellation of defect 105 (v0=470705), euler #=-56 (719752,2156545,1436737) : difference with theory (-64) = -8 CORRECTING DEFECT 106 (vertices=28, convex hull=25, v0=471808) After retessellation of defect 106 (v0=471808), euler #=-55 (719755,2156566,1436756) : difference with theory (-63) = -8 CORRECTING DEFECT 107 (vertices=491, convex hull=220, v0=474706) After retessellation of defect 107 (v0=474706), euler #=-55 (719790,2156783,1436938) : difference with theory (-62) = -7 CORRECTING DEFECT 108 (vertices=63, convex hull=42, v0=477036) After retessellation of defect 108 (v0=477036), euler #=-54 (719792,2156807,1436961) : difference with theory (-61) = -7 CORRECTING DEFECT 109 (vertices=9, convex hull=46, v0=480235) After retessellation of defect 109 (v0=480235), euler #=-53 (719793,2156829,1436983) : difference with theory (-60) = -7 CORRECTING DEFECT 110 (vertices=58, convex hull=27, v0=480376) After retessellation of defect 110 (v0=480376), euler #=-52 (719795,2156847,1437000) : difference with theory (-59) = -7 CORRECTING DEFECT 111 (vertices=65, convex hull=53, v0=480622) After retessellation of defect 111 (v0=480622), euler #=-51 (719801,2156885,1437033) : difference with theory (-58) = -7 CORRECTING DEFECT 112 (vertices=42, convex hull=61, v0=488662) After retessellation of defect 112 (v0=488662), euler #=-50 (719805,2156923,1437068) : difference with theory (-57) = -7 CORRECTING DEFECT 113 (vertices=57, convex hull=84, v0=490819) After retessellation of defect 113 (v0=490819), euler #=-49 (719811,2156979,1437119) : difference with theory (-56) = -7 CORRECTING DEFECT 114 (vertices=170, convex hull=87, v0=492243) After retessellation of defect 114 (v0=492243), euler #=-48 (719817,2157031,1437166) : difference with theory (-55) = -7 CORRECTING DEFECT 115 (vertices=374, convex hull=150, v0=493667) After retessellation of defect 115 (v0=493667), euler #=-49 (719838,2157174,1437287) : difference with theory (-54) = -5 CORRECTING DEFECT 116 (vertices=48, convex hull=36, v0=493996) After retessellation of defect 116 (v0=493996), euler #=-48 (719840,2157193,1437305) : difference with theory (-53) = -5 CORRECTING DEFECT 117 (vertices=246, convex hull=119, v0=494547) After retessellation of defect 117 (v0=494547), euler #=-47 (719854,2157284,1437383) : difference with theory (-52) = -5 CORRECTING DEFECT 118 (vertices=15, convex hull=20, v0=494805) After retessellation of defect 118 (v0=494805), euler #=-46 (719856,2157295,1437393) : difference with theory (-51) = -5 CORRECTING DEFECT 119 (vertices=64, convex hull=35, v0=496380) After retessellation of defect 119 (v0=496380), euler #=-45 (719857,2157320,1437418) : difference with theory (-50) = -5 CORRECTING DEFECT 120 (vertices=120, convex hull=72, v0=497771) After retessellation of defect 120 (v0=497771), euler #=-44 (719865,2157369,1437460) : difference with theory (-49) = -5 CORRECTING DEFECT 121 (vertices=26, convex hull=59, v0=497905) After retessellation of defect 121 (v0=497905), euler #=-43 (719866,2157395,1437486) : difference with theory (-48) = -5 CORRECTING DEFECT 122 (vertices=7, convex hull=33, v0=499950) After retessellation of defect 122 (v0=499950), euler #=-42 (719867,2157407,1437498) : difference with theory (-47) = -5 CORRECTING DEFECT 123 (vertices=2619, convex hull=1106, v0=500055) XL defect detected... After retessellation of defect 123 (v0=500055), euler #=-45 (720042,2158568,1438481) : difference with theory (-46) = -1 CORRECTING DEFECT 124 (vertices=5, convex hull=26, v0=502569) After retessellation of defect 124 (v0=502569), euler #=-44 (720042,2158575,1438489) : difference with theory (-45) = -1 CORRECTING DEFECT 125 (vertices=16, convex hull=22, v0=506133) After retessellation of defect 125 (v0=506133), euler #=-43 (720043,2158583,1438497) : difference with theory (-44) = -1 CORRECTING DEFECT 126 (vertices=285, convex hull=191, v0=507922) After retessellation of defect 126 (v0=507922), euler #=-42 (720061,2158739,1438636) : difference with theory (-43) = -1 CORRECTING DEFECT 127 (vertices=237, convex hull=79, v0=511139) After retessellation of defect 127 (v0=511139), euler #=-41 (720069,2158797,1438687) : difference with theory (-42) = -1 CORRECTING DEFECT 128 (vertices=30, convex hull=24, v0=513195) After retessellation of defect 128 (v0=513195), euler #=-40 (720069,2158806,1438697) : difference with theory (-41) = -1 CORRECTING DEFECT 129 (vertices=90, convex hull=99, v0=518095) After retessellation of defect 129 (v0=518095), euler #=-39 (720078,2158877,1438760) : difference with theory (-40) = -1 CORRECTING DEFECT 130 (vertices=5, convex hull=20, v0=521928) After retessellation of defect 130 (v0=521928), euler #=-38 (720079,2158885,1438768) : difference with theory (-39) = -1 CORRECTING DEFECT 131 (vertices=6, convex hull=21, v0=524544) After retessellation of defect 131 (v0=524544), euler #=-37 (720081,2158898,1438780) : difference with theory (-38) = -1 CORRECTING DEFECT 132 (vertices=23, convex hull=37, v0=530858) After retessellation of defect 132 (v0=530858), euler #=-36 (720082,2158914,1438796) : difference with theory (-37) = -1 CORRECTING DEFECT 133 (vertices=26, convex hull=51, v0=531503) After retessellation of defect 133 (v0=531503), euler #=-35 (720086,2158943,1438822) : difference with theory (-36) = -1 CORRECTING DEFECT 134 (vertices=68, convex hull=108, v0=536715) After retessellation of defect 134 (v0=536715), euler #=-34 (720094,2159008,1438880) : difference with theory (-35) = -1 CORRECTING DEFECT 135 (vertices=6, convex hull=25, v0=539946) After retessellation of defect 135 (v0=539946), euler #=-33 (720094,2159015,1438888) : difference with theory (-34) = -1 CORRECTING DEFECT 136 (vertices=100, convex hull=62, v0=543647) After retessellation of defect 136 (v0=543647), euler #=-32 (720098,2159049,1438919) : difference with theory (-33) = -1 CORRECTING DEFECT 137 (vertices=7, convex hull=17, v0=543978) After retessellation of defect 137 (v0=543978), euler #=-31 (720099,2159059,1438929) : difference with theory (-32) = -1 CORRECTING DEFECT 138 (vertices=54, convex hull=27, v0=545932) After retessellation of defect 138 (v0=545932), euler #=-30 (720101,2159072,1438941) : difference with theory (-31) = -1 CORRECTING DEFECT 139 (vertices=5, convex hull=30, v0=546674) After retessellation of defect 139 (v0=546674), euler #=-29 (720101,2159078,1438948) : difference with theory (-30) = -1 CORRECTING DEFECT 140 (vertices=420, convex hull=153, v0=548649) After retessellation of defect 140 (v0=548649), euler #=-29 (720125,2159231,1439077) : difference with theory (-29) = 0 CORRECTING DEFECT 141 (vertices=91, convex hull=72, v0=549118) After retessellation of defect 141 (v0=549118), euler #=-28 (720133,2159285,1439124) : difference with theory (-28) = 0 CORRECTING DEFECT 142 (vertices=6, convex hull=23, v0=553919) After retessellation of defect 142 (v0=553919), euler #=-27 (720134,2159294,1439133) : difference with theory (-27) = 0 CORRECTING DEFECT 143 (vertices=95, convex hull=40, v0=554163) After retessellation of defect 143 (v0=554163), euler #=-26 (720137,2159316,1439153) : difference with theory (-26) = 0 CORRECTING DEFECT 144 (vertices=26, convex hull=28, v0=567731) After retessellation of defect 144 (v0=567731), euler #=-25 (720139,2159332,1439168) : difference with theory (-25) = 0 CORRECTING DEFECT 145 (vertices=10, convex hull=16, v0=567859) After retessellation of defect 145 (v0=567859), euler #=-24 (720140,2159339,1439175) : difference with theory (-24) = 0 CORRECTING DEFECT 146 (vertices=174, convex hull=119, v0=568722) After retessellation of defect 146 (v0=568722), euler #=-22 (720150,2159432,1439260) : difference with theory (-23) = -1 CORRECTING DEFECT 147 (vertices=83, convex hull=82, v0=570426) After retessellation of defect 147 (v0=570426), euler #=-21 (720157,2159488,1439310) : difference with theory (-22) = -1 CORRECTING DEFECT 148 (vertices=2328, convex hull=453, v0=570748) After retessellation of defect 148 (v0=570748), euler #=-20 (720289,2160110,1439801) : difference with theory (-21) = -1 CORRECTING DEFECT 149 (vertices=54, convex hull=34, v0=577609) After retessellation of defect 149 (v0=577609), euler #=-19 (720292,2160131,1439820) : difference with theory (-20) = -1 CORRECTING DEFECT 150 (vertices=27, convex hull=59, v0=579806) After retessellation of defect 150 (v0=579806), euler #=-19 (720296,2160170,1439855) : difference with theory (-19) = 0 CORRECTING DEFECT 151 (vertices=18, convex hull=34, v0=579991) After retessellation of defect 151 (v0=579991), euler #=-18 (720298,2160189,1439873) : difference with theory (-18) = 0 CORRECTING DEFECT 152 (vertices=81, convex hull=30, v0=580355) After retessellation of defect 152 (v0=580355), euler #=-17 (720300,2160206,1439889) : difference with theory (-17) = 0 CORRECTING DEFECT 153 (vertices=51, convex hull=81, v0=582713) After retessellation of defect 153 (v0=582713), euler #=-16 (720308,2160268,1439944) : difference with theory (-16) = 0 CORRECTING DEFECT 154 (vertices=2702, convex hull=485, v0=584907) After retessellation of defect 154 (v0=584907), euler #=-15 (720413,2160825,1440397) : difference with theory (-15) = 0 CORRECTING DEFECT 155 (vertices=106, convex hull=31, v0=588479) After retessellation of defect 155 (v0=588479), euler #=-14 (720417,2160849,1440418) : difference with theory (-14) = 0 CORRECTING DEFECT 156 (vertices=54, convex hull=90, v0=590270) After retessellation of defect 156 (v0=590270), euler #=-13 (720422,2160906,1440471) : difference with theory (-13) = 0 CORRECTING DEFECT 157 (vertices=74, convex hull=35, v0=596906) After retessellation of defect 157 (v0=596906), euler #=-12 (720423,2160921,1440486) : difference with theory (-12) = 0 CORRECTING DEFECT 158 (vertices=24, convex hull=41, v0=612516) After retessellation of defect 158 (v0=612516), euler #=-11 (720423,2160938,1440504) : difference with theory (-11) = 0 CORRECTING DEFECT 159 (vertices=543, convex hull=168, v0=612562) After retessellation of defect 159 (v0=612562), euler #=-10 (720430,2161043,1440603) : difference with theory (-10) = 0 CORRECTING DEFECT 160 (vertices=75, convex hull=32, v0=622779) After retessellation of defect 160 (v0=622779), euler #=-9 (720432,2161062,1440621) : difference with theory (-9) = 0 CORRECTING DEFECT 161 (vertices=65, convex hull=28, v0=636075) After retessellation of defect 161 (v0=636075), euler #=-8 (720433,2161075,1440634) : difference with theory (-8) = 0 CORRECTING DEFECT 162 (vertices=46, convex hull=69, v0=640207) After retessellation of defect 162 (v0=640207), euler #=-7 (720438,2161123,1440678) : difference with theory (-7) = 0 CORRECTING DEFECT 163 (vertices=31, convex hull=31, v0=651107) After retessellation of defect 163 (v0=651107), euler #=-6 (720439,2161136,1440691) : difference with theory (-6) = 0 CORRECTING DEFECT 164 (vertices=6, convex hull=15, v0=652839) After retessellation of defect 164 (v0=652839), euler #=-5 (720440,2161143,1440698) : difference with theory (-5) = 0 CORRECTING DEFECT 165 (vertices=13, convex hull=28, v0=658329) After retessellation of defect 165 (v0=658329), euler #=-4 (720441,2161157,1440712) : difference with theory (-4) = 0 CORRECTING DEFECT 166 (vertices=121, convex hull=42, v0=663635) After retessellation of defect 166 (v0=663635), euler #=-3 (720443,2161181,1440735) : difference with theory (-3) = 0 CORRECTING DEFECT 167 (vertices=194, convex hull=48, v0=677128) After retessellation of defect 167 (v0=677128), euler #=-2 (720446,2161211,1440763) : difference with theory (-2) = 0 CORRECTING DEFECT 168 (vertices=86, convex hull=120, v0=692493) After retessellation of defect 168 (v0=692493), euler #=-1 (720458,2161297,1440838) : difference with theory (-1) = 0 CORRECTING DEFECT 169 (vertices=7, convex hull=19, v0=726017) After retessellation of defect 169 (v0=726017), euler #=0 (720459,2161306,1440847) : difference with theory (0) = 0 CORRECTING DEFECT 170 (vertices=38, convex hull=69, v0=745499) After retessellation of defect 170 (v0=745499), euler #=1 (720464,2161349,1440886) : difference with theory (1) = 0 CORRECTING DEFECT 171 (vertices=41, convex hull=85, v0=758045) After retessellation of defect 171 (v0=758045), euler #=2 (720470,2161404,1440936) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.41 +- 0.16 (0.04-->19.21) (max @ vno 540172 --> 619868) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.41 +- 0.16 (0.04-->19.21) (max @ vno 540172 --> 619868) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 561 mutations (36.8%), 962 crossovers (63.2%), 334 vertices were eliminated building final representation... 42952 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=720470, nf=1440936, ne=2161404, g=0) writing corrected surface to /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/lh.orig... defective orientation at vertex 272436(272444) with faces 543543 and 1432771 defective orientation at vertex 272436(272445) with faces 543543 and 1432783 defective orientation at vertex 272444(272436) with faces 543543 and 1432771 defective orientation at vertex 272444(272445) with faces 543543 and 1432782 defective orientation at vertex 272445(272444) with faces 543543 and 1432782 defective orientation at vertex 272445(272436) with faces 543543 and 1432783 0.001 % of the vertices (6 vertices) exhibit an orientation change topology fixing took 821.8 minutes 0 defective edges removing intersecting faces 000: 3862 intersecting 001: 244 intersecting 002: 176 intersecting 003: 88 intersecting 004: 45 intersecting 005: 36 intersecting 006: 22 intersecting 007: 15 intersecting expanding nbhd size to 2 008: 15 intersecting expanding nbhd size to 3 009: 15 intersecting expanding nbhd size to 4 010: 20 intersecting 011: 11 intersecting 012: 9 intersecting mris_fix_topology utimesec 21965.127088 mris_fix_topology stimesec 4.342794 mris_fix_topology ru_maxrss 2402752 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 832407 mris_fix_topology ru_majflt 4 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 740 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 46854 mris_fix_topology ru_nivcsw 1955148 FSRUNTIME@ mris_fix_topology lh 13.6972 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 720470 - 2161404 + 1440936 = 2 --> 0 holes F =2V-4: 1440936 = 1440940-4 (0) 2E=3F: 4322808 = 4322808 (0) total defect index = 0 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.06 hours removing intersecting faces 000: 987 intersecting 001: 223 intersecting 002: 159 intersecting 003: 69 intersecting 004: 43 intersecting 005: 38 intersecting 006: 20 intersecting 007: 19 intersecting 008: 14 intersecting expanding nbhd size to 2 009: 14 intersecting expanding nbhd size to 3 010: 16 intersecting expanding nbhd size to 4 011: 27 intersecting 012: 10 intersecting expanding nbhd size to 5 013: 10 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Jan 13 17:36:44 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-ADS5115 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 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/filled.mgz... reading volume /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/brain.finalsurfs.mgz... reading volume /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/../mri/aseg.presurf.mgz... reading volume /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/mri/wm.mgz... 38196 bright wm thresholded. 57 bright non-wm voxels segmented. reading original surface position from /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/lh.orig... computing class statistics... border white: 1581264 voxels (1.18%) border gray 1637655 voxels (1.22%) WM (99.0): 99.7 +- 4.8 [70.0 --> 110.0] GM (89.0) : 88.8 +- 5.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 77.4 (was 70) setting MAX_BORDER_WHITE to 114.8 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 71.8 (was 40) setting MAX_GRAY to 105.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 66.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.39 +- 0.11 (0.01-->7.34) (max @ vno 129266 --> 718874) face area 0.06 +- 0.04 (0.00-->6.61) mean absolute distance = 0.45 +- 0.80 35232 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... spring scale = 2.23 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=110+-1.7, GM=83+-5.2 mean inside = 101.9, mean outside = 86.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=96.7, 759 (759) missing vertices, mean dist -0.3 [0.5 (%71.9)->0.2 (%28.1))] %81 local maxima, %13 large gradients and % 2 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= n018, nav=4, nbrs=2, l_repulse=5.000, l_tspring=4.955, l_nspring=1.113, 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 0.47 +- 0.17 (0.02-->6.46) (max @ vno 129266 --> 718874) face area 0.06 +- 0.04 (0.00-->4.46) mean absolute distance = 0.30 +- 0.54 19808 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=9982201.0, rms=4.638 001: dt: 0.5000, sse=7554906.5, rms=3.519 (24.130%) 002: dt: 0.5000, sse=7620752.5, rms=3.203 (8.998%) 003: dt: 0.5000, sse=7837328.0, rms=2.971 (7.244%) 004: dt: 0.5000, sse=8109901.5, rms=2.889 (2.758%) 005: dt: 0.5000, sse=7982542.0, rms=2.814 (2.592%) rms = 2.78, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=7890703.0, rms=2.783 (1.090%) 007: dt: 0.2500, sse=7798551.0, rms=2.658 (4.504%) 008: dt: 0.2500, sse=7532609.0, rms=2.606 (1.940%) rms = 2.56, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=7482780.5, rms=2.560 (1.762%) rms = 2.54, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=7038456.5, rms=2.541 (0.770%) positioning took 15.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=97.3, 2035 (201) missing vertices, mean dist -0.1 [0.3 (%64.3)->0.2 (%35.7))] %86 local maxima, % 7 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= n018, nav=2, nbrs=2, l_repulse=5.000, l_tspring=4.955, l_nspring=1.113, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.47 +- 0.17 (0.03-->6.16) (max @ vno 129266 --> 718874) face area 0.08 +- 0.06 (0.00-->5.69) mean absolute distance = 0.25 +- 0.42 18790 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8105643.0, rms=2.676 011: dt: 0.5000, sse=8480835.0, rms=2.453 (8.325%) rms = 2.43, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=8262144.5, rms=2.426 (1.128%) 013: dt: 0.2500, sse=8017561.0, rms=2.260 (6.805%) 014: dt: 0.2500, sse=7771903.5, rms=2.189 (3.172%) rms = 2.14, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=7670537.5, rms=2.140 (2.233%) rms = 2.11, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=7239245.0, rms=2.113 (1.271%) positioning took 9.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=97.6, 2187 (120) missing vertices, mean dist -0.1 [0.3 (%57.6)->0.2 (%42.4))] %88 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= n018, nav=1, nbrs=2, l_repulse=5.000, l_tspring=4.955, l_nspring=1.113, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.46 +- 0.16 (0.03-->5.99) (max @ vno 129266 --> 718874) face area 0.08 +- 0.05 (0.00-->5.64) mean absolute distance = 0.24 +- 0.36 18775 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7350108.5, rms=2.305 017: dt: 0.5000, sse=8115985.5, rms=2.249 (2.429%) rms = 2.28, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=6313597.0, rms=2.113 (6.032%) 019: dt: 0.2500, sse=7705203.0, rms=1.990 (5.813%) rms = 2.00, time step reduction 2 of 3 to 0.125... rms = 1.95, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=6653874.0, rms=1.950 (2.042%) positioning took 7.8 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 4 vertex label from ripped group mean border=97.7, 2310 (89) missing vertices, mean dist -0.0 [0.3 (%55.2)->0.2 (%44.8))] %89 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= n018, nav=0, nbrs=2, l_repulse=5.000, l_tspring=4.955, l_nspring=1.113, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/lh.white.preaparc... 000: dt: 0.0000, sse=6638540.5, rms=2.063 rms = 2.05, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=7749933.0, rms=2.051 (0.560%) 022: dt: 0.2500, sse=7391298.0, rms=1.954 (4.749%) 023: dt: 0.2500, sse=7269278.5, rms=1.879 (3.853%) rms = 1.85, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=7311025.0, rms=1.848 (1.645%) rms = 1.80, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=6946341.5, rms=1.799 (2.643%) positioning took 7.0 minutes generating cortex label... 175 non-cortical segments detected only using segment with 36238 vertices erasing segment 0 (vno[0] = 10324) erasing segment 1 (vno[0] = 13915) erasing segment 2 (vno[0] = 21045) erasing segment 3 (vno[0] = 28847) erasing segment 4 (vno[0] = 30303) erasing segment 5 (vno[0] = 35321) erasing segment 6 (vno[0] = 41641) erasing segment 7 (vno[0] = 44528) erasing segment 8 (vno[0] = 55688) erasing segment 9 (vno[0] = 57664) erasing segment 10 (vno[0] = 64473) erasing segment 11 (vno[0] = 66716) erasing segment 12 (vno[0] = 66742) erasing segment 13 (vno[0] = 69097) erasing segment 14 (vno[0] = 71379) erasing segment 15 (vno[0] = 73528) erasing segment 16 (vno[0] = 129182) erasing segment 17 (vno[0] = 133712) erasing segment 18 (vno[0] = 140683) erasing segment 19 (vno[0] = 155605) erasing segment 20 (vno[0] = 156986) erasing segment 21 (vno[0] = 164307) erasing segment 22 (vno[0] = 164380) erasing segment 23 (vno[0] = 164530) erasing segment 24 (vno[0] = 174705) erasing segment 25 (vno[0] = 175645) erasing segment 26 (vno[0] = 175721) erasing segment 27 (vno[0] = 177315) erasing segment 28 (vno[0] = 188764) erasing segment 29 (vno[0] = 189593) erasing segment 30 (vno[0] = 195171) erasing segment 31 (vno[0] = 200554) erasing segment 33 (vno[0] = 252567) erasing segment 34 (vno[0] = 264405) erasing segment 35 (vno[0] = 268280) erasing segment 36 (vno[0] = 270648) erasing segment 37 (vno[0] = 276031) erasing segment 38 (vno[0] = 278856) erasing segment 39 (vno[0] = 279365) erasing segment 40 (vno[0] = 280366) erasing segment 41 (vno[0] = 280377) erasing segment 42 (vno[0] = 281551) erasing segment 43 (vno[0] = 281581) erasing segment 44 (vno[0] = 282193) erasing segment 45 (vno[0] = 285015) erasing segment 46 (vno[0] = 285201) erasing segment 47 (vno[0] = 285892) erasing segment 48 (vno[0] = 285895) erasing segment 49 (vno[0] = 287834) erasing segment 50 (vno[0] = 289762) erasing segment 51 (vno[0] = 290430) erasing segment 52 (vno[0] = 297975) erasing segment 53 (vno[0] = 300494) erasing segment 54 (vno[0] = 303047) erasing segment 55 (vno[0] = 306494) erasing segment 56 (vno[0] = 310103) erasing segment 57 (vno[0] = 313248) erasing segment 58 (vno[0] = 319205) erasing segment 59 (vno[0] = 319290) erasing segment 60 (vno[0] = 332163) erasing segment 61 (vno[0] = 334973) erasing segment 62 (vno[0] = 335015) erasing segment 63 (vno[0] = 338009) erasing segment 64 (vno[0] = 344814) erasing segment 65 (vno[0] = 351676) erasing segment 66 (vno[0] = 355386) erasing segment 67 (vno[0] = 359322) erasing segment 68 (vno[0] = 360142) erasing segment 69 (vno[0] = 366352) erasing segment 70 (vno[0] = 367052) erasing segment 71 (vno[0] = 368304) erasing segment 72 (vno[0] = 368306) erasing segment 73 (vno[0] = 370160) erasing segment 74 (vno[0] = 372975) erasing segment 75 (vno[0] = 380970) erasing segment 76 (vno[0] = 383909) erasing segment 77 (vno[0] = 404238) erasing segment 78 (vno[0] = 404248) erasing segment 79 (vno[0] = 406591) erasing segment 80 (vno[0] = 407168) erasing segment 81 (vno[0] = 420698) erasing segment 82 (vno[0] = 424808) erasing segment 83 (vno[0] = 428018) erasing segment 84 (vno[0] = 434166) erasing segment 85 (vno[0] = 446392) erasing segment 86 (vno[0] = 451702) erasing segment 87 (vno[0] = 451783) erasing segment 88 (vno[0] = 456903) erasing segment 89 (vno[0] = 457161) erasing segment 90 (vno[0] = 458286) erasing segment 91 (vno[0] = 463369) erasing segment 92 (vno[0] = 467229) erasing segment 93 (vno[0] = 470842) erasing segment 94 (vno[0] = 472193) erasing segment 95 (vno[0] = 476177) erasing segment 96 (vno[0] writing smoothed curvature to lh.curv = 476768) erasing segment 97 (vno[0] = 479719) erasing segment 98 (vno[0] = 480160) erasing segment 99 (vno[0] = 480245) erasing segment 100 (vno[0] = 480273) erasing segment 101 (vno[0] = 481690) erasing segment 102 (vno[0] = 482727) erasing segment 103 (vno[0] = 484177) erasing segment 104 (vno[0] = 484828) erasing segment 105 (vno[0] = 484978) erasing segment 106 (vno[0] = 485644) erasing segment 107 (vno[0] = 492424) erasing segment 108 (vno[0] = 493729) erasing segment 109 (vno[0] = 493827) erasing segment 110 (vno[0] = 495762) erasing segment 111 (vno[0] = 497755) erasing segment 112 (vno[0] = 498504) erasing segment 113 (vno[0] = 500579) erasing segment 114 (vno[0] = 500637) erasing segment 115 (vno[0] = 504323) erasing segment 116 (vno[0] = 504457) erasing segment 117 (vno[0] = 504563) erasing segment 118 (vno[0] = 507265) erasing segment 119 (vno[0] = 507297) erasing segment 120 (vno[0] = 509984) erasing segment 121 (vno[0] = 510494) erasing segment 122 (vno[0] = 512441) erasing segment 123 (vno[0] = 512983) erasing segment 124 (vno[0] = 515246) erasing segment 125 (vno[0] = 515393) erasing segment 126 (vno[0] = 515408) erasing segment 127 (vno[0] = 517574) erasing segment 128 (vno[0] = 519375) erasing segment 129 (vno[0] = 521340) erasing segment 130 (vno[0] = 521668) erasing segment 131 (vno[0] = 521735) erasing segment 132 (vno[0] = 525733) erasing segment 133 (vno[0] = 526041) erasing segment 134 (vno[0] = 528143) erasing segment 135 (vno[0] = 528492) erasing segment 136 (vno[0] = 537065) erasing segment 137 (vno[0] = 537410) erasing segment 138 (vno[0] = 537427) erasing segment 139 (vno[0] = 537434) erasing segment 140 (vno[0] = 554776) erasing segment 141 (vno[0] = 566251) erasing segment 142 (vno[0] = 567840) erasing segment 143 (vno[0] = 568469) erasing segment 144 (vno[0] = 572486) erasing segment 145 (vno[0] = 589662) erasing segment 146 (vno[0] = 590159) erasing segment 147 (vno[0] = 599147) erasing segment 148 (vno[0] = 601097) erasing segment 149 (vno[0] = 601821) erasing segment 150 (vno[0] = 603551) erasing segment 151 (vno[0] = 606999) erasing segment 152 (vno[0] = 609176) erasing segment 153 (vno[0] = 612614) erasing segment 154 (vno[0] = 620786) erasing segment 155 (vno[0] = 620991) erasing segment 156 (vno[0] = 621290) erasing segment 157 (vno[0] = 622488) erasing segment 158 (vno[0] = 622600) erasing segment 159 (vno[0] = 624622) erasing segment 160 (vno[0] = 629235) erasing segment 161 (vno[0] = 630448) erasing segment 162 (vno[0] = 637800) erasing segment 163 (vno[0] = 642763) erasing segment 164 (vno[0] = 644390) erasing segment 165 (vno[0] = 646821) erasing segment 166 (vno[0] = 647206) erasing segment 167 (vno[0] = 653244) erasing segment 168 (vno[0] = 666786) erasing segment 169 (vno[0] = 668558) erasing segment 170 (vno[0] = 668573) erasing segment 171 (vno[0] = 669882) erasing segment 172 (vno[0] = 670074) erasing segment 173 (vno[0] = 719372) erasing segment 174 (vno[0] = 719407) writing cortex label to /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/label/lh.cortex.label... writing curvature file /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/lh.curv writing smoothed area to lh.area writing curvature file /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/lh.area vertex spacing 0.46 +- 0.17 (0.01-->6.27) (max @ vno 73554 --> 75668) face area 0.08 +- 0.06 (0.00-->5.55) refinement took 57.3 minutes #-------------------------------------------- #@# Smooth2 lh Sun Jan 13 18:34:05 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 Sun Jan 13 18:35:10 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_inflate -rusage /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/touch/rusage.mris_inflate.lh.dat -n 50 ../surf/lh.smoothwm ../surf/lh.inflated niterations = 50 Reading ../surf/lh.smoothwm avg radius = 46.4 mm, total surface area = 97667 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.133 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.078 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.034 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.030 (target=0.015) step 060: RMS=0.028 (target=0.015) step 065: RMS=0.026 (target=0.015) step 070: RMS=0.025 (target=0.015) step 075: RMS=0.024 (target=0.015) step 080: RMS=0.023 (target=0.015) step 085: RMS=0.022 (target=0.015) step 090: RMS=0.021 (target=0.015) step 095: RMS=0.020 (target=0.015) step 100: RMS=0.020 (target=0.015) step 105: RMS=0.019 (target=0.015) step 110: RMS=0.018 (target=0.015) step 115: RMS=0.018 (target=0.015) step 120: RMS=0.017 (target=0.015) step 125: RMS=0.017 (target=0.015) step 130: RMS=0.016 (target=0.015) step 135: RMS=0.016 (target=0.015) step 140: RMS=0.016 (target=0.015) step 145: RMS=0.015 (target=0.015) inflation complete. inflation took 21.2 minutes mris_inflate utimesec 948.618861 mris_inflate stimesec 3.020396 mris_inflate ru_maxrss 1129564 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 2836618 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 53359 mris_inflate ru_nivcsw 79498 #-------------------------------------------- #@# Curv .H and .K lh Sun Jan 13 18:56:24 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf mris_curvature -w lh.white.preaparc total integrated curvature = 1301.187*4pi (16351.194) --> -1300 handles ICI = 2411.6, FI = 11686.0, variation=210074.377 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 1521 vertices thresholded to be in k1 ~ [-0.57 0.69], k2 ~ [-0.19 0.13] total integrated curvature = 0.280*4pi (3.517) --> 1 handles ICI = 2.7, FI = 32.7, variation=496.948 969 vertices thresholded to be in [-0.04 0.04] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 916 vertices thresholded to be in [-0.22 0.33] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.041 done. #----------------------------------------- #@# Curvature Stats lh Sun Jan 13 19:08:46 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-ADS5115 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-ADS5115/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 [ 1979 ] Gb_filter = 0 WARN: S lookup min: -1.996402 WARN: S explicit min: 0.000000 vertex = 319 WARN: C lookup max: 339.569580 WARN: C explicit max: 166.791534 vertex = 155582 #-------------------------------------------- #@# Sphere lh Sun Jan 13 19:09:32 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_sphere -rusage /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 0.272... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= n018, 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 %20.81 pass 1: epoch 2 of 3 starting distance error %20.32 unfolding complete - removing small folds... starting distance error %19.41 removing remaining folds... final distance error %19.45 MRISunfold() return, current seed 1234 -01: dt=0.0000, 12879 negative triangles 223: dt=0.9900, 12879 negative triangles 224: dt=0.9900, 10348 negative triangles 225: dt=0.9900, 9946 negative triangles 226: dt=0.9900, 9505 negative triangles 227: dt=0.9900, 9291 negative triangles 228: dt=0.9900, 9161 negative triangles 229: dt=0.9900, 9006 negative triangles 230: dt=0.9900, 8911 negative triangles 231: dt=0.9900, 8804 negative triangles 232: dt=0.9900, 8792 negative triangles 233: dt=0.9900, 8671 negative triangles 234: dt=0.9900, 8631 negative triangles 235: dt=0.9900, 8558 negative triangles 236: dt=0.9900, 8480 negative triangles 237: dt=0.9900, 8459 negative triangles 238: dt=0.9900, 8405 negative triangles 239: dt=0.9900, 8363 negative triangles 240: dt=0.9900, 8327 negative triangles 241: dt=0.9900, 8307 negative triangles 242: dt=0.9900, 8292 negative triangles 243: dt=0.9900, 8169 negative triangles 244: dt=0.9900, 8214 negative triangles 245: dt=0.9900, 8184 negative triangles 246: dt=0.9900, 8129 negative triangles 247: dt=0.9900, 8090 negative triangles 248: dt=0.9900, 8092 negative triangles 249: dt=0.9900, 8031 negative triangles 250: dt=0.9900, 8002 negative triangles 251: dt=0.9900, 8036 negative triangles 252: dt=0.9900, 7988 negative triangles 253: dt=0.9900, 7971 negative triangles 254: dt=0.9900, 7954 negative triangles 255: dt=0.9900, 7922 negative triangles 256: dt=0.9900, 7966 negative triangles 257: dt=0.9900, 7930 negative triangles 258: dt=0.9900, 7877 negative triangles 259: dt=0.9900, 7837 negative triangles 260: dt=0.9900, 7858 negative triangles 261: dt=0.9900, 7832 negative triangles 262: dt=0.9900, 7836 negative triangles 263: dt=0.9900, 7817 negative triangles 264: dt=0.9900, 7799 negative triangles 265: dt=0.9900, 7786 negative triangles 266: dt=0.9900, 7773 negative triangles 267: dt=0.9900, 7706 negative triangles 268: dt=0.9900, 7688 negative triangles 269: dt=0.9900, 7687 negative triangles 270: dt=0.9900, 7694 negative triangles 271: dt=0.9900, 7671 negative triangles 272: dt=0.9900, 7666 negative triangles 273: dt=0.9900, 7620 negative triangles 274: dt=0.9900, 7614 negative triangles 275: dt=0.9900, 7583 negative triangles 276: dt=0.9900, 7567 negative triangles 277: dt=0.9900, 7519 negative triangles 278: dt=0.9900, 7524 negative triangles 279: dt=0.9900, 7514 negative triangles 280: dt=0.9900, 7509 negative triangles 281: dt=0.9900, 7472 negative triangles 282: dt=0.9900, 7429 negative triangles 283: dt=0.9900, 7420 negative triangles 284: dt=0.9900, 7429 negative triangles 285: dt=0.9900, 7388 negative triangles 286: dt=0.9900, 7359 negative triangles 287: dt=0.9900, 7354 negative triangles 288: dt=0.9900, 7345 negative triangles 289: dt=0.9900, 7322 negative triangles 290: dt=0.9900, 7318 negative triangles 291: dt=0.9900, 7309 negative triangles 292: dt=0.9900, 7262 negative triangles 293: dt=0.9900, 7255 negative triangles 294: dt=0.9900, 7227 negative triangles 295: dt=0.9900, 7180 negative triangles 296: dt=0.9900, 7184 negative triangles 297: dt=0.9900, 7194 negative triangles 298: dt=0.9900, 7168 negative triangles 299: dt=0.9900, 7145 negative triangles 300: dt=0.9900, 7161 negative triangles 301: dt=0.9900, 7113 negative triangles 302: dt=0.9900, 7090 negative triangles 303: dt=0.9900, 7052 negative triangles 304: dt=0.9900, 7056 negative triangles 305: dt=0.9900, 7036 negative triangles 306: dt=0.9900, 7042 negative triangles 307: dt=0.9900, 7033 negative triangles 308: dt=0.9900, 7026 negative triangles 309: dt=0.9900, 7004 negative triangles 310: dt=0.9900, 6970 negative triangles 311: dt=0.9900, 6919 negative triangles 312: dt=0.9900, 6893 negative triangles 313: dt=0.9900, 6896 negative triangles 314: dt=0.9900, 6924 negative triangles 315: dt=0.9900, 6855 negative triangles 316: dt=0.9900, 6862 negative triangles 317: dt=0.9900, 6815 negative triangles 318: dt=0.9900, 6821 negative triangles 319: dt=0.9900, 6773 negative triangles 320: dt=0.9900, 6767 negative triangles 321: dt=0.9900, 6766 negative triangles 322: dt=0.9900, 6769 negative triangles 323: dt=0.9900, 6729 negative triangles 324: dt=0.9900, 6710 negative triangles 325: dt=0.9900, 6681 negative triangles 326: dt=0.9900, 6683 negative triangles 327: dt=0.9900, 6655 negative triangles 328: dt=0.9900, 6662 negative triangles 329: dt=0.9900, 6669 negative triangles 330: dt=0.9900, 6645 negative triangles 331: dt=0.9900, 6623 negative triangles 332: dt=0.9900, 6599 negative triangles 333: dt=0.9900, 6559 negative triangles 334: dt=0.9900, 6544 negative triangles 335: dt=0.9900, 6519 negative triangles 336: dt=0.9900, 6459 negative triangles 337: dt=0.9900, 6476 negative triangles 338: dt=0.9900, 6464 negative triangles 339: dt=0.9900, 6440 negative triangles 340: dt=0.9900, 6408 negative triangles 341: dt=0.9900, 6425 negative triangles 342: dt=0.9900, 6405 negative triangles 343: dt=0.9900, 6373 negative triangles 344: dt=0.9900, 6381 negative triangles 345: dt=0.9900, 6353 negative triangles 346: dt=0.9900, 6305 negative triangles 347: dt=0.9900, 6308 negative triangles 348: dt=0.9900, 6306 negative triangles 349: dt=0.9900, 6286 negative triangles 350: dt=0.9900, 6264 negative triangles 351: dt=0.9900, 6279 negative triangles 352: dt=0.9900, 6258 negative triangles 353: dt=0.9900, 6207 negative triangles 354: dt=0.9900, 6172 negative triangles 355: dt=0.9900, 6180 negative triangles 356: dt=0.9900, 6139 negative triangles 357: dt=0.9900, 6092 negative triangles 358: dt=0.9900, 6132 negative triangles 359: dt=0.9900, 6085 negative triangles 360: dt=0.9900, 6081 negative triangles 361: dt=0.9900, 6034 negative triangles 362: dt=0.9900, 6044 negative triangles 363: dt=0.9900, 6054 negative triangles 364: dt=0.9900, 6062 negative triangles 365: dt=0.9900, 6022 negative triangles 366: dt=0.9900, 5979 negative triangles 367: dt=0.9900, 5952 negative triangles 368: dt=0.9900, 5971 negative triangles 369: dt=0.9900, 5952 negative triangles 370: dt=0.9900, 5952 negative triangles 371: dt=0.9900, 5937 negative triangles 372: dt=0.9900, 5932 negative triangles 373: dt=0.9900, 5891 negative triangles 374: dt=0.9900, 5880 negative triangles 375: dt=0.9900, 5824 negative triangles 376: dt=0.9900, 5807 negative triangles 377: dt=0.9900, 5839 negative triangles 378: dt=0.9900, 5796 negative triangles 379: dt=0.9900, 5802 negative triangles 380: dt=0.9900, 5780 negative triangles 381: dt=0.9900, 5776 negative triangles 382: dt=0.9900, 5785 negative triangles 383: dt=0.9900, 5774 negative triangles 384: dt=0.9900, 5745 negative triangles 385: dt=0.9900, 5720 negative triangles 386: dt=0.9900, 5700 negative triangles 387: dt=0.9900, 5689 negative triangles 388: dt=0.9900, 5686 negative triangles 389: dt=0.9900, 5669 negative triangles 390: dt=0.9900, 5648 negative triangles 391: dt=0.9900, 5619 negative triangles 392: dt=0.9900, 5612 negative triangles 393: dt=0.9900, 5620 negative triangles 394: dt=0.9900, 5594 negative triangles 395: dt=0.9900, 5576 negative triangles 396: dt=0.9900, 5548 negative triangles 397: dt=0.9900, 5549 negative triangles 398: dt=0.9900, 5496 negative triangles 399: dt=0.9900, 5526 negative triangles 400: dt=0.9900, 5501 negative triangles 401: dt=0.9900, 5516 negative triangles 402: dt=0.9900, 5471 negative triangles 403: dt=0.9900, 5476 negative triangles 404: dt=0.9900, 5455 negative triangles 405: dt=0.9900, 5430 negative triangles 406: dt=0.9900, 5414 negative triangles 407: dt=0.9900, 5370 negative triangles 408: dt=0.9900, 5376 negative triangles 409: dt=0.9900, 5377 negative triangles 410: dt=0.9900, 5370 negative triangles 411: dt=0.9900, 5343 negative triangles 412: dt=0.9900, 5315 negative triangles 413: dt=0.9900, 5293 negative triangles 414: dt=0.9900, 5278 negative triangles 415: dt=0.9900, 5280 negative triangles 416: dt=0.9900, 5272 negative triangles 417: dt=0.9900, 5260 negative triangles 418: dt=0.9900, 5232 negative triangles 419: dt=0.9900, 5229 negative triangles 420: dt=0.9900, 5201 negative triangles 421: dt=0.9900, 5187 negative triangles 422: dt=0.9900, 5180 negative triangles 423: dt=0.9900, 5166 negative triangles 424: dt=0.9900, 5160 negative triangles 425: dt=0.9900, 5149 negative triangles 426: dt=0.9900, 5115 negative triangles 427: dt=0.9900, 5155 negative triangles 428: dt=0.9900, 5155 negative triangles 429: dt=0.9900, 5136 negative triangles 430: dt=0.9900, 5114 negative triangles 431: dt=0.9900, 5103 negative triangles 432: dt=0.9900, 5108 negative triangles 433: dt=0.9900, 5103 negative triangles 434: dt=0.9900, 5087 negative triangles 435: dt=0.9900, 5094 negative triangles 436: dt=0.9900, 5094 negative triangles 437: dt=0.9900, 5080 negative triangles 438: dt=0.9900, 5061 negative triangles 439: dt=0.9900, 5045 negative triangles 440: dt=0.9900, 5059 negative triangles 441: dt=0.9900, 5046 negative triangles 442: dt=0.9900, 5031 negative triangles 443: dt=0.9900, 5038 negative triangles 444: dt=0.9900, 5020 negative triangles 445: dt=0.9900, 5031 negative triangles 446: dt=0.9900, 5011 negative triangles 447: dt=0.9900, 5020 negative triangles 448: dt=0.9900, 5027 negative triangles 449: dt=0.9900, 4997 negative triangles 450: dt=0.9900, 4995 negative triangles 451: dt=0.9900, 4997 negative triangles 452: dt=0.9900, 5000 negative triangles 453: dt=0.9900, 4936 negative triangles 454: dt=0.9900, 4985 negative triangles 455: dt=0.9900, 4963 negative triangles 456: dt=0.9900, 4953 negative triangles 457: dt=0.9900, 4938 negative triangles 458: dt=0.9900, 4962 negative triangles 459: dt=0.9900, 4947 negative triangles 460: dt=0.9900, 4942 negative triangles 461: dt=0.9900, 4934 negative triangles 462: dt=0.9900, 4933 negative triangles 463: dt=0.9900, 4926 negative triangles 464: dt=0.9900, 4892 negative triangles 465: dt=0.9900, 4932 negative triangles 466: dt=0.9900, 4914 negative triangles 467: dt=0.9900, 4920 negative triangles 468: dt=0.9900, 4903 negative triangles 469: dt=0.9900, 4886 negative triangles 470: dt=0.9900, 4877 negative triangles 471: dt=0.9900, 4887 negative triangles 472: dt=0.9900, 4875 negative triangles 473: dt=0.9900, 4841 negative triangles 474: dt=0.9900, 4839 negative triangles 475: dt=0.9900, 4846 negative triangles 476: dt=0.9900, 4856 negative triangles 477: dt=0.9900, 4811 negative triangles 478: dt=0.9900, 4839 negative triangles 479: dt=0.9900, 4829 negative triangles 480: dt=0.9900, 4809 negative triangles 481: dt=0.9900, 4793 negative triangles 482: dt=0.9900, 4821 negative triangles 483: dt=0.9900, 4795 negative triangles 484: dt=0.9900, 4792 negative triangles 485: dt=0.9900, 4791 negative triangles 486: dt=0.9900, 4791 negative triangles 487: dt=0.9900, 4754 negative triangles 488: dt=0.9900, 4757 negative triangles 489: dt=0.9900, 4724 negative triangles 490: dt=0.9900, 4751 negative triangles 491: dt=0.9900, 4698 negative triangles 492: dt=0.9900, 4693 negative triangles 493: dt=0.9900, 4706 negative triangles 494: dt=0.9900, 4721 negative triangles 495: dt=0.9900, 4698 negative triangles 496: dt=0.9900, 4693 negative triangles 497: dt=0.9900, 4663 negative triangles 498: dt=0.9900, 4643 negative triangles 499: dt=0.9900, 4622 negative triangles 500: dt=0.9900, 4625 negative triangles 501: dt=0.9900, 4583 negative triangles 502: dt=0.9900, 4602 negative triangles 503: dt=0.9900, 4580 negative triangles 504: dt=0.9900, 4589 negative triangles 505: dt=0.9900, 4565 negative triangles 506: dt=0.9900, 4568 negative triangles 507: dt=0.9900, 4555 negative triangles 508: dt=0.9900, 4557 negative triangles 509: dt=0.9900, 4536 negative triangles 510: dt=0.9900, 4535 negative triangles 511: dt=0.9900, 4502 negative triangles 512: dt=0.9900, 4537 negative triangles 513: dt=0.9900, 4497 negative triangles 514: dt=0.9900, 4474 negative triangles 515: dt=0.9900, 4503 negative triangles 516: dt=0.9900, 4497 negative triangles 517: dt=0.9900, 4502 negative triangles 518: dt=0.9900, 4459 negative triangles 519: dt=0.9900, 4467 negative triangles 520: dt=0.9900, 4475 negative triangles 521: dt=0.9900, 4432 negative triangles 522: dt=0.9900, 4447 negative triangles 523: dt=0.9900, 4435 negative triangles 524: dt=0.9900, 4462 negative triangles 525: dt=0.9900, 4418 negative triangles 526: dt=0.9900, 4439 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dt=0.9405, 265 negative triangles 1128: dt=0.8935, 261 negative triangles 1129: dt=0.8935, 264 negative triangles 1130: dt=0.8935, 263 negative triangles 1131: dt=0.8935, 270 negative triangles 1132: dt=0.8935, 268 negative triangles 1133: dt=0.8935, 259 negative triangles 1134: dt=0.8935, 262 negative triangles 1135: dt=0.8935, 264 negative triangles 1136: dt=0.8935, 264 negative triangles 1137: dt=0.8935, 267 negative triangles 1138: dt=0.8488, 257 negative triangles 1139: dt=0.8488, 260 negative triangles 1140: dt=0.8488, 262 negative triangles 1141: dt=0.8488, 259 negative triangles 1142: dt=0.8488, 258 negative triangles 1143: dt=0.8488, 254 negative triangles 1144: dt=0.8488, 260 negative triangles 1145: dt=0.8488, 256 negative triangles 1146: dt=0.8488, 258 negative triangles 1147: dt=0.8488, 259 negative triangles 1148: dt=0.8488, 261 negative triangles 1149: dt=0.8488, 253 negative triangles 1150: dt=0.8488, 262 negative triangles 1151: dt=0.8488, 259 negative triangles 1152: dt=0.8488, 249 negative triangles 1153: dt=0.8488, 256 negative triangles 1154: dt=0.8488, 252 negative triangles 1155: dt=0.8488, 257 negative triangles 1156: dt=0.8488, 250 negative triangles 1157: dt=0.8488, 256 negative triangles 1158: dt=0.8488, 244 negative triangles 1159: dt=0.8488, 242 negative triangles 1160: dt=0.8488, 250 negative triangles 1161: dt=0.8488, 249 negative triangles 1162: dt=0.8488, 242 negative triangles 1163: dt=0.8488, 254 negative triangles 1164: dt=0.8488, 242 negative triangles 1165: dt=0.8488, 245 negative triangles 1166: dt=0.8488, 253 negative triangles 1167: dt=0.8488, 247 negative triangles 1168: dt=0.8488, 243 negative triangles 1169: dt=0.8064, 245 negative triangles 1170: dt=0.8064, 240 negative triangles 1171: dt=0.8064, 240 negative triangles 1172: dt=0.8064, 237 negative triangles 1173: dt=0.8064, 247 negative triangles 1174: dt=0.8064, 233 negative triangles 1175: dt=0.8064, 241 negative triangles 1176: dt=0.8064, 240 negative triangles 1177: dt=0.8064, 241 negative triangles 1178: dt=0.8064, 239 negative triangles 1179: dt=0.8064, 244 negative triangles 1180: dt=0.8064, 235 negative triangles 1181: dt=0.8064, 235 negative triangles 1182: dt=0.8064, 240 negative triangles 1183: dt=0.8064, 239 negative triangles 1184: dt=0.8064, 229 negative triangles 1185: dt=0.8064, 238 negative triangles 1186: dt=0.8064, 226 negative triangles 1187: dt=0.8064, 237 negative triangles 1188: dt=0.8064, 233 negative triangles 1189: dt=0.8064, 233 negative triangles 1190: dt=0.8064, 231 negative triangles 1191: dt=0.8064, 237 negative triangles 1192: dt=0.8064, 226 negative triangles 1193: dt=0.8064, 237 negative triangles 1194: dt=0.8064, 232 negative triangles 1195: dt=0.8064, 231 negative triangles 1196: dt=0.8064, 224 negative triangles 1197: dt=0.8064, 234 negative triangles 1198: dt=0.8064, 226 negative triangles 1199: dt=0.8064, 235 negative triangles 1200: dt=0.8064, 220 negative triangles 1201: dt=0.8064, 241 negative triangles 1202: dt=0.8064, 230 negative triangles 1203: dt=0.8064, 232 negative triangles 1204: dt=0.8064, 217 negative triangles 1205: dt=0.8064, 224 negative triangles 1206: dt=0.8064, 213 negative triangles 1207: dt=0.8064, 225 negative triangles 1208: dt=0.8064, 213 negative triangles 1209: dt=0.8064, 223 negative triangles 1210: dt=0.8064, 217 negative triangles 1211: dt=0.8064, 219 negative triangles 1212: dt=0.8064, 213 negative triangles 1213: dt=0.8064, 220 negative triangles 1214: dt=0.8064, 212 negative triangles 1215: dt=0.8064, 217 negative triangles 1216: dt=0.8064, 211 negative triangles 1217: dt=0.8064, 216 negative triangles 1218: dt=0.8064, 209 negative triangles 1219: dt=0.8064, 214 negative triangles 1220: dt=0.8064, 207 negative triangles 1221: dt=0.8064, 211 negative triangles 1222: dt=0.8064, 197 negative triangles 1223: dt=0.8064, 213 negative triangles 1224: 200 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 19.54 hours mris_sphere utimesec 37906.640537 mris_sphere stimesec 30.513036 mris_sphere ru_maxrss 1569864 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 11889539 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2077288 mris_sphere ru_nivcsw 3269332 FSRUNTIME@ mris_sphere 19.5418 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Mon Jan 14 14:42:03 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_register -curv -rusage /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts cmdline mris_register -curv -rusage /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/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= n018, 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= n018, 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 = 4.487 curvature mean = 0.014, std = 0.811 curvature mean = 0.021, std = 0.809 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 1935222.2, tmin=47.3884 d=32.00 min @ (8.00, 8.00, 8.00) sse = 1508960.0, tmin=88.5816 d=16.00 min @ (0.00, -4.00, -4.00) sse = 1403706.4, tmin=101.3733 d=8.00 min @ (0.00, 0.00, 2.00) sse = 1401026.0, tmin=114.2426 d=4.00 min @ (1.00, 1.00, -1.00) sse = 1392896.1, tmin=127.1317 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 1392391.1, tmin=140.0159 d=1.00 min @ (0.25, 0.00, 0.00) sse = 1391893.1, tmin=152.8772 d=0.50 min @ (0.12, 0.12, -0.12) sse = 1391792.8, tmin=165.7476