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 rh -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 15665716 109490932 225100 6758972 114334732 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: 2019/01/13-01:08:12-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 rh Sun Jan 13 01:08:12 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 1 found - 1 modified | TOTAL: 6 pass 2 (xz-): 0 found - 1 modified | TOTAL: 6 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 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 9 (out of 2832289: 0.000318) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.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: 599 vertices, 656 faces slice 80: 4124 vertices, 4299 faces slice 90: 11848 vertices, 12195 faces slice 100: 23590 vertices, 24093 faces slice 110: 39975 vertices, 40634 faces slice 120: 61239 vertices, 62110 faces slice 130: 84682 vertices, 85519 faces slice 140: 107788 vertices, 108626 faces slice 150: 132294 vertices, 133197 faces slice 160: 156871 vertices, 157675 faces slice 170: 182191 vertices, 183125 faces slice 180: 207845 vertices, 208748 faces slice 190: 234219 vertices, 235115 faces slice 200: 260182 vertices, 261073 faces slice 210: 288155 vertices, 289221 faces slice 220: 320588 vertices, 321748 faces slice 230: 350081 vertices, 351145 faces slice 240: 379414 vertices, 380599 faces slice 250: 410626 vertices, 411854 faces slice 260: 439613 vertices, 440836 faces slice 270: 468015 vertices, 469201 faces slice 280: 496002 vertices, 497277 faces slice 290: 523091 vertices, 524307 faces slice 300: 553252 vertices, 554641 faces slice 310: 580448 vertices, 581678 faces slice 320: 605514 vertices, 606808 faces slice 330: 628584 vertices, 629752 faces slice 340: 650264 vertices, 651434 faces slice 350: 671385 vertices, 672528 faces slice 360: 689829 vertices, 690942 faces slice 370: 707864 vertices, 708913 faces slice 380: 723786 vertices, 724756 faces slice 390: 738386 vertices, 739363 faces slice 400: 751577 vertices, 752476 faces slice 410: 762295 vertices, 763122 faces slice 420: 771375 vertices, 772115 faces slice 430: 776816 vertices, 777381 faces slice 440: 777446 vertices, 777912 faces slice 450: 777446 vertices, 777912 faces slice 460: 777446 vertices, 777912 faces slice 470: 777446 vertices, 777912 faces slice 480: 777446 vertices, 777912 faces slice 490: 777446 vertices, 777912 faces slice 500: 777446 vertices, 777912 faces slice 510: 777446 vertices, 777912 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.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-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 777446 voxel in cpt #1: X=-466 [v=777446,e=2333736,f=1555824] located at (23.601702, -5.529474, 33.934162) For the whole surface: X=-466 [v=777446,e=2333736,f=1555824] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Sun Jan 13 01:10:24 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Sun Jan 13 01:12:00 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_inflate -no-save-sulc -n 50 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix niterations = 50 Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.1 mm, total surface area = 93804 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 79.1 minutes step 000: RMS=0.120 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.062 (target=0.015) step 030: RMS=0.058 (target=0.015) step 035: RMS=0.055 (target=0.015) step 040: RMS=0.053 (target=0.015) step 045: RMS=0.051 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.049 (target=0.015) step 060: RMS=0.048 (target=0.015) step 065: RMS=0.048 (target=0.015) step 070: RMS=0.047 (target=0.015) step 075: RMS=0.047 (target=0.015) step 080: RMS=0.047 (target=0.015) step 085: RMS=0.046 (target=0.015) step 090: RMS=0.046 (target=0.015) step 095: RMS=0.045 (target=0.015) step 100: RMS=0.045 (target=0.015) step 105: RMS=0.045 (target=0.015) step 110: RMS=0.045 (target=0.015) step 115: RMS=0.044 (target=0.015) step 120: RMS=0.044 (target=0.015) step 125: RMS=0.044 (target=0.015) step 130: RMS=0.044 (target=0.015) step 135: RMS=0.044 (target=0.015) step 140: RMS=0.043 (target=0.015) step 145: RMS=0.043 (target=0.015) step 150: RMS=0.043 (target=0.015) step 155: RMS=0.043 (target=0.015) step 160: RMS=0.043 (target=0.015) step 165: RMS=0.043 (target=0.015) step 170: RMS=0.043 (target=0.015) step 175: RMS=0.043 (target=0.015) step 180: RMS=0.043 (target=0.015) step 185: RMS=0.042 (target=0.015) step 190: RMS=0.042 (target=0.015) step 195: RMS=0.042 (target=0.015) step 200: RMS=0.042 (target=0.015) step 205: RMS=0.042 (target=0.015) step 210: RMS=0.042 (target=0.015) step 215: RMS=0.042 (target=0.015) step 220: RMS=0.042 (target=0.015) step 225: RMS=0.042 (target=0.015) step 230: RMS=0.042 (target=0.015) step 235: RMS=0.042 (target=0.015) step 240: RMS=0.042 (target=0.015) step 245: RMS=0.042 (target=0.015) step 250: RMS=0.042 (target=0.015) step 255: RMS=0.043 (target=0.015) step 260: RMS=0.044 (target=0.015) step 265: RMS=0.045 (target=0.015) step 270: RMS=0.045 (target=0.015) step 275: RMS=0.045 (target=0.015) step 280: RMS=0.045 (target=0.015) step 285: RMS=0.045 (target=0.015) step 290: RMS=0.044 (target=0.015) step 295: RMS=0.044 (target=0.015) step 300: RMS=0.044 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 2153.874952 mris_inflate stimesec 3.957477 mris_inflate ru_maxrss 1217716 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 3056345 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 73980 mris_inflate ru_nivcsw 192178 #-------------------------------------------- #@# QSphere rh Sun Jan 13 02:31:06 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.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 0.42 +- 0.28 (0.00-->3.99) (max @ vno 325835 --> 328791) face area 0.00 +- 0.01 (-0.10-->0.16) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.276... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.780, avgs=0 005/300: dt: 0.9000, rms radial error=176.519, avgs=0 010/300: dt: 0.9000, rms radial error=175.956, avgs=0 015/300: dt: 0.9000, rms radial error=175.217, avgs=0 020/300: dt: 0.9000, rms radial error=174.379, avgs=0 025/300: dt: 0.9000, rms radial error=173.484, avgs=0 030/300: dt: 0.9000, rms radial error=172.556, avgs=0 035/300: dt: 0.9000, rms radial error=171.612, avgs=0 040/300: dt: 0.9000, rms radial error=170.659, avgs=0 045/300: dt: 0.9000, rms radial error=169.705, avgs=0 050/300: dt: 0.9000, rms radial error=168.751, avgs=0 055/300: dt: 0.9000, rms radial error=167.800, avgs=0 060/300: dt: 0.9000, rms radial error=166.852, avgs=0 065/300: dt: 0.9000, rms radial error=165.909, avgs=0 070/300: dt: 0.9000, rms radial error=164.971, avgs=0 075/300: dt: 0.9000, rms radial error=164.038, avgs=0 080/300: dt: 0.9000, rms radial error=163.109, avgs=0 085/300: dt: 0.9000, rms radial error=162.186, avgs=0 090/300: dt: 0.9000, rms radial error=161.268, avgs=0 095/300: dt: 0.9000, rms radial error=160.356, avgs=0 100/300: dt: 0.9000, rms radial error=159.448, avgs=0 105/300: dt: 0.9000, rms radial error=158.545, avgs=0 110/300: dt: 0.9000, rms radial error=157.648, avgs=0 115/300: dt: 0.9000, rms radial error=156.755, avgs=0 120/300: dt: 0.9000, rms radial error=155.867, avgs=0 125/300: dt: 0.9000, rms radial error=154.985, avgs=0 130/300: dt: 0.9000, rms radial error=154.107, avgs=0 135/300: dt: 0.9000, rms radial error=153.234, avgs=0 140/300: dt: 0.9000, rms radial error=152.367, avgs=0 145/300: dt: 0.9000, rms radial error=151.504, avgs=0 150/300: dt: 0.9000, rms radial error=150.645, avgs=0 155/300: dt: 0.9000, rms radial error=149.792, avgs=0 160/300: dt: 0.9000, rms radial error=148.944, avgs=0 165/300: dt: 0.9000, rms radial error=148.101, avgs=0 170/300: dt: 0.9000, rms radial error=147.262, avgs=0 175/300: dt: 0.9000, rms radial error=146.428, avgs=0 180/300: dt: 0.9000, rms radial error=145.599, avgs=0 185/300: dt: 0.9000, rms radial error=144.774, avgs=0 190/300: dt: 0.9000, rms radial error=143.954, avgs=0 195/300: dt: 0.9000, rms radial error=143.139, avgs=0 200/300: dt: 0.9000, rms radial error=142.328, avgs=0 205/300: dt: 0.9000, rms radial error=141.522, avgs=0 210/300: dt: 0.9000, rms radial error=140.720, avgs=0 215/300: dt: 0.9000, rms radial error=139.923, avgs=0 220/300: dt: 0.9000, rms radial error=139.130, avgs=0 225/300: dt: 0.9000, rms radial error=138.342, avgs=0 230/300: dt: 0.9000, rms radial error=137.558, avgs=0 235/300: dt: 0.9000, rms radial error=136.778, avgs=0 240/300: dt: 0.9000, rms radial error=136.003, avgs=0 245/300: dt: 0.9000, rms radial error=135.232, avgs=0 250/300: dt: 0.9000, rms radial error=134.465, avgs=0 255/300: dt: 0.9000, rms radial error=133.703, avgs=0 260/300: dt: 0.9000, rms radial error=132.945, avgs=0 265/300: dt: 0.9000, rms radial error=132.192, avgs=0 270/300: dt: 0.9000, rms radial error=131.442, avgs=0 275/300: dt: 0.9000, rms radial error=130.697, avgs=0 280/300: dt: 0.9000, rms radial error=129.956, avgs=0 285/300: dt: 0.9000, rms radial error=129.220, avgs=0 290/300: dt: 0.9000, rms radial error=128.488, avgs=0 295/300: dt: 0.9000, rms radial error=127.760, avgs=0 300/300: dt: 0.9000, rms radial error=127.037, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 104402.49 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 = 23828.90 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 = 4454.17 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 = 554.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00208 final distance error %30.95 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 1.39 hours mris_sphere utimesec 2250.270053 mris_sphere stimesec 5.235035 mris_sphere ru_maxrss 1218184 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 5081542 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 60041 mris_sphere ru_nivcsw 204859 FSRUNTIME@ mris_sphere 1.3867 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy rh Sun Jan 13 03:54:19 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology rh Sun Jan 13 03:54:19 UTC 2019 mris_fix_topology -rusage /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-ADS5115 rh 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=-466 (nv=777446, nf=1555824, ne=2333736, g=234) 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... 100494 ambiguous faces found in tessellation segmenting defects... 181 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 15 into 7 -merging segment 37 into 19 -merging segment 74 into 41 -merging segment 90 into 41 -merging segment 78 into 41 -merging segment 89 into 41 -merging segment 102 into 86 -merging segment 106 into 86 -merging segment 131 into 86 -merging segment 128 into 108 -merging segment 139 into 108 -merging segment 121 into 116 169 defects to be corrected 0 vertices coincident reading input surface /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1362 (-4.5681) -vertex loglikelihood: -5.2073 (-2.6037) -normal dot loglikelihood: -3.4483 (-3.4483) -quad curv loglikelihood: -6.8395 (-3.4198) Total Loglikelihood : -24.6313 CORRECTING DEFECT 0 (vertices=48, convex hull=53, v0=599) After retessellation of defect 0 (v0=599), euler #=-148 (722251,2157453,1435054) : difference with theory (-166) = -18 CORRECTING DEFECT 1 (vertices=3592, convex hull=525, v0=2885) After retessellation of defect 1 (v0=2885), euler #=-147 (722387,2158131,1435597) : difference with theory (-165) = -18 CORRECTING DEFECT 2 (vertices=2647, convex hull=474, v0=8061) After retessellation of defect 2 (v0=8061), euler #=-146 (722487,2158668,1436035) : difference with theory (-164) = -18 CORRECTING DEFECT 3 (vertices=19, convex hull=26, v0=18471) After retessellation of defect 3 (v0=18471), euler #=-145 (722488,2158678,1436045) : difference with theory (-163) = -18 CORRECTING DEFECT 4 (vertices=54, convex hull=53, v0=23803) After retessellation of defect 4 (v0=23803), euler #=-144 (722491,2158709,1436074) : difference with theory (-162) = -18 CORRECTING DEFECT 5 (vertices=21, convex hull=24, v0=25136) After retessellation of defect 5 (v0=25136), euler #=-143 (722491,2158715,1436081) : difference with theory (-161) = -18 CORRECTING DEFECT 6 (vertices=64, convex hull=45, v0=26510) After retessellation of defect 6 (v0=26510), euler #=-142 (722492,2158732,1436098) : difference with theory (-160) = -18 CORRECTING DEFECT 7 (vertices=560, convex hull=258, v0=38105) After retessellation of defect 7 (v0=38105), euler #=-140 (722502,2158913,1436271) : difference with theory (-159) = -19 CORRECTING DEFECT 8 (vertices=6, convex hull=35, v0=45138) After retessellation of defect 8 (v0=45138), euler #=-139 (722503,2158924,1436282) : difference with theory (-158) = -19 CORRECTING DEFECT 9 (vertices=182, convex hull=83, v0=45556) After retessellation of defect 9 (v0=45556), euler #=-138 (722509,2158986,1436339) : difference with theory (-157) = -19 CORRECTING DEFECT 10 (vertices=30, convex hull=69, v0=46910) After retessellation of defect 10 (v0=46910), euler #=-137 (722510,2159018,1436371) : difference with theory (-156) = -19 CORRECTING DEFECT 11 (vertices=30, convex hull=46, v0=48607) After retessellation of defect 11 (v0=48607), euler #=-136 (722512,2159044,1436396) : difference with theory (-155) = -19 CORRECTING DEFECT 12 (vertices=52, convex hull=61, v0=52951) After retessellation of defect 12 (v0=52951), euler #=-135 (722513,2159072,1436424) : difference with theory (-154) = -19 CORRECTING DEFECT 13 (vertices=8, convex hull=25, v0=56452) After retessellation of defect 13 (v0=56452), euler #=-134 (722514,2159082,1436434) : difference with theory (-153) = -19 CORRECTING DEFECT 14 (vertices=8, convex hull=27, v0=56459) After retessellation of defect 14 (v0=56459), euler #=-133 (722515,2159095,1436447) : difference with theory (-152) = -19 CORRECTING DEFECT 15 (vertices=115, convex hull=101, v0=62571) After retessellation of defect 15 (v0=62571), euler #=-132 (722520,2159149,1436497) : difference with theory (-151) = -19 CORRECTING DEFECT 16 (vertices=421, convex hull=133, v0=63474) After retessellation of defect 16 (v0=63474), euler #=-131 (722536,2159256,1436589) : difference with theory (-150) = -19 CORRECTING DEFECT 17 (vertices=10, convex hull=24, v0=64628) After retessellation of defect 17 (v0=64628), euler #=-130 (722537,2159267,1436600) : difference with theory (-149) = -19 CORRECTING DEFECT 18 (vertices=5166, convex hull=1313, v0=81424) XL defect detected... After retessellation of defect 18 (v0=81424), euler #=-129 (722788,2160707,1437790) : difference with theory (-148) = -19 CORRECTING DEFECT 19 (vertices=416, convex hull=131, v0=88345) After retessellation of defect 19 (v0=88345), euler #=-128 (722806,2160820,1437886) : difference with theory (-147) = -19 CORRECTING DEFECT 20 (vertices=27, convex hull=42, v0=98094) After retessellation of defect 20 (v0=98094), euler #=-127 (722808,2160844,1437909) : difference with theory (-146) = -19 CORRECTING DEFECT 21 (vertices=116, convex hull=101, v0=102591) After retessellation of defect 21 (v0=102591), euler #=-126 (722815,2160907,1437966) : difference with theory (-145) = -19 CORRECTING DEFECT 22 (vertices=349, convex hull=112, v0=107243) After retessellation of defect 22 (v0=107243), euler #=-125 (722822,2160979,1438032) : difference with theory (-144) = -19 CORRECTING DEFECT 23 (vertices=18, convex hull=24, v0=109511) After retessellation of defect 23 (v0=109511), euler #=-124 (722822,2160984,1438038) : difference with theory (-143) = -19 CORRECTING DEFECT 24 (vertices=101, convex hull=80, v0=109589) After retessellation of defect 24 (v0=109589), euler #=-123 (722827,2161035,1438085) : difference with theory (-142) = -19 CORRECTING DEFECT 25 (vertices=115, convex hull=87, v0=113782) After retessellation of defect 25 (v0=113782), euler #=-122 (722832,2161089,1438135) : difference with theory (-141) = -19 CORRECTING DEFECT 26 (vertices=173, convex hull=103, v0=124509) After retessellation of defect 26 (v0=124509), euler #=-121 (722841,2161161,1438199) : difference with theory (-140) = -19 CORRECTING DEFECT 27 (vertices=20, convex hull=35, v0=131464) After retessellation of defect 27 (v0=131464), euler #=-120 (722842,2161176,1438214) : difference with theory (-139) = -19 CORRECTING DEFECT 28 (vertices=10, convex hull=34, v0=131475) After retessellation of defect 28 (v0=131475), euler #=-119 (722843,2161190,1438228) : difference with theory (-138) = -19 CORRECTING DEFECT 29 (vertices=224, convex hull=133, v0=136283) After retessellation of defect 29 (v0=136283), euler #=-118 (722851,2161275,1438306) : difference with theory (-137) = -19 CORRECTING DEFECT 30 (vertices=54, convex hull=76, v0=139117) After retessellation of defect 30 (v0=139117), euler #=-117 (722856,2161322,1438349) : difference with theory (-136) = -19 CORRECTING DEFECT 31 (vertices=84, convex hull=42, v0=144898) After retessellation of defect 31 (v0=144898), euler #=-116 (722860,2161348,1438372) : difference with theory (-135) = -19 CORRECTING DEFECT 32 (vertices=27, convex hull=52, v0=149204) After retessellation of defect 32 (v0=149204), euler #=-115 (722863,2161379,1438401) : difference with theory (-134) = -19 CORRECTING DEFECT 33 (vertices=13, convex hull=31, v0=151354) After retessellation of defect 33 (v0=151354), euler #=-114 (722865,2161395,1438416) : difference with theory (-133) = -19 CORRECTING DEFECT 34 (vertices=80, convex hull=121, v0=160701) After retessellation of defect 34 (v0=160701), euler #=-113 (722877,2161485,1438495) : difference with theory (-132) = -19 CORRECTING DEFECT 35 (vertices=234, convex hull=103, v0=161006) After retessellation of defect 35 (v0=161006), euler #=-112 (722887,2161558,1438559) : difference with theory (-131) = -19 CORRECTING DEFECT 36 (vertices=23, convex hull=42, v0=168380) After retessellation of defect 36 (v0=168380), euler #=-111 (722888,2161575,1438576) : difference with theory (-130) = -19 CORRECTING DEFECT 37 (vertices=107, convex hull=58, v0=199721) After retessellation of defect 37 (v0=199721), euler #=-110 (722890,2161604,1438604) : difference with theory (-129) = -19 CORRECTING DEFECT 38 (vertices=36, convex hull=47, v0=231319) After retessellation of defect 38 (v0=231319), euler #=-109 (722893,2161630,1438628) : difference with theory (-128) = -19 CORRECTING DEFECT 39 (vertices=6414, convex hull=1923, v0=244330) XL defect detected... After retessellation of defect 39 (v0=244330), euler #=-105 (723237,2163711,1440369) : difference with theory (-127) = -22 CORRECTING DEFECT 40 (vertices=23, convex hull=27, v0=256785) After retessellation of defect 40 (v0=256785), euler #=-104 (723238,2163723,1440381) : difference with theory (-126) = -22 CORRECTING DEFECT 41 (vertices=61, convex hull=86, v0=260427) After retessellation of defect 41 (v0=260427), euler #=-103 (723246,2163784,1440435) : difference with theory (-125) = -22 CORRECTING DEFECT 42 (vertices=1115, convex hull=459, v0=262094) After retessellation of defect 42 (v0=262094), euler #=-104 (723279,2164122,1440739) : difference with theory (-124) = -20 CORRECTING DEFECT 43 (vertices=36, convex hull=56, v0=262928) After retessellation of defect 43 (v0=262928), euler #=-103 (723282,2164148,1440763) : difference with theory (-123) = -20 CORRECTING DEFECT 44 (vertices=42, convex hull=45, v0=274099) After retessellation of defect 44 (v0=274099), euler #=-102 (723284,2164172,1440786) : difference with theory (-122) = -20 CORRECTING DEFECT 45 (vertices=60, convex hull=46, v0=278548) After retessellation of defect 45 (v0=278548), euler #=-101 (723289,2164203,1440813) : difference with theory (-121) = -20 CORRECTING DEFECT 46 (vertices=68, convex hull=91, v0=280003) After retessellation of defect 46 (v0=280003), euler #=-100 (723295,2164261,1440866) : difference with theory (-120) = -20 CORRECTING DEFECT 47 (vertices=6, convex hull=24, v0=281603) After retessellation of defect 47 (v0=281603), euler #=-99 (723296,2164271,1440876) : difference with theory (-119) = -20 CORRECTING DEFECT 48 (vertices=22, convex hull=48, v0=283991) After retessellation of defect 48 (v0=283991), euler #=-98 (723301,2164303,1440904) : difference with theory (-118) = -20 CORRECTING DEFECT 49 (vertices=136, convex hull=150, v0=287954) After retessellation of defect 49 (v0=287954), euler #=-97 (723311,2164413,1441005) : difference with theory (-117) = -20 CORRECTING DEFECT 50 (vertices=181, convex hull=92, v0=291465) After retessellation of defect 50 (v0=291465), euler #=-96 (723319,2164484,1441069) : difference with theory (-116) = -20 CORRECTING DEFECT 51 (vertices=134, convex hull=121, v0=294557) After retessellation of defect 51 (v0=294557), euler #=-95 (723327,2164568,1441146) : difference with theory (-115) = -20 CORRECTING DEFECT 52 (vertices=485, convex hull=101, v0=296215) After retessellation of defect 52 (v0=296215), euler #=-94 (723335,2164642,1441213) : difference with theory (-114) = -20 CORRECTING DEFECT 53 (vertices=81, convex hull=106, v0=299616) After retessellation of defect 53 (v0=299616), euler #=-93 (723345,2164717,1441279) : difference with theory (-113) = -20 CORRECTING DEFECT 54 (vertices=30, convex hull=27, v0=300605) After retessellation of defect 54 (v0=300605), euler #=-92 (723346,2164728,1441290) : difference with theory (-112) = -20 CORRECTING DEFECT 55 (vertices=246, convex hull=77, v0=302857) After retessellation of defect 55 (v0=302857), euler #=-91 (723348,2164777,1441338) : difference with theory (-111) = -20 CORRECTING DEFECT 56 (vertices=37, convex hull=55, v0=306559) After retessellation of defect 56 (v0=306559), euler #=-90 (723352,2164811,1441369) : difference with theory (-110) = -20 CORRECTING DEFECT 57 (vertices=50, convex hull=49, v0=307648) After retessellation of defect 57 (v0=307648), euler #=-89 (723356,2164837,1441392) : difference with theory (-109) = -20 CORRECTING DEFECT 58 (vertices=6, convex hull=28, v0=322486) After retessellation of defect 58 (v0=322486), euler #=-88 (723358,2164851,1441405) : difference with theory (-108) = -20 CORRECTING DEFECT 59 (vertices=70, convex hull=84, v0=323662) After retessellation of defect 59 (v0=323662), euler #=-87 (723367,2164915,1441461) : difference with theory (-107) = -20 CORRECTING DEFECT 60 (vertices=115, convex hull=111, v0=326914) After retessellation of defect 60 (v0=326914), euler #=-86 (723378,2165003,1441539) : difference with theory (-106) = -20 CORRECTING DEFECT 61 (vertices=23, convex hull=36, v0=327139) After retessellation of defect 61 (v0=327139), euler #=-85 (723383,2165030,1441562) : difference with theory (-105) = -20 CORRECTING DEFECT 62 (vertices=6, convex hull=14, v0=334298) After retessellation of defect 62 (v0=334298), euler #=-84 (723384,2165037,1441569) : difference with theory (-104) = -20 CORRECTING DEFECT 63 (vertices=93, convex hull=76, v0=352965) After retessellation of defect 63 (v0=352965), euler #=-83 (723390,2165091,1441618) : difference with theory (-103) = -20 CORRECTING DEFECT 64 (vertices=51, convex hull=20, v0=355325) After retessellation of defect 64 (v0=355325), euler #=-82 (723390,2165096,1441624) : difference with theory (-102) = -20 CORRECTING DEFECT 65 (vertices=135, convex hull=93, v0=358125) After retessellation of defect 65 (v0=358125), euler #=-81 (723402,2165171,1441688) : difference with theory (-101) = -20 CORRECTING DEFECT 66 (vertices=54, convex hull=86, v0=359742) After retessellation of defect 66 (v0=359742), euler #=-80 (723408,2165222,1441734) : difference with theory (-100) = -20 CORRECTING DEFECT 67 (vertices=44, convex hull=64, v0=364134) After retessellation of defect 67 (v0=364134), euler #=-79 (723414,2165265,1441772) : difference with theory (-99) = -20 CORRECTING DEFECT 68 (vertices=32, convex hull=62, v0=374260) After retessellation of defect 68 (v0=374260), euler #=-78 (723421,2165312,1441813) : difference with theory (-98) = -20 CORRECTING DEFECT 69 (vertices=276, convex hull=41, v0=375074) After retessellation of defect 69 (v0=375074), euler #=-77 (723424,2165336,1441835) : difference with theory (-97) = -20 CORRECTING DEFECT 70 (vertices=27, convex hull=20, v0=377344) After retessellation of defect 70 (v0=377344), euler #=-76 (723424,2165340,1441840) : difference with theory (-96) = -20 CORRECTING DEFECT 71 (vertices=71, convex hull=91, v0=381365) After retessellation of defect 71 (v0=381365), euler #=-76 (723431,2165407,1441900) : difference with theory (-95) = -19 CORRECTING DEFECT 72 (vertices=115, convex hull=32, v0=386097) After retessellation of defect 72 (v0=386097), euler #=-75 (723433,2165424,1441916) : difference with theory (-94) = -19 CORRECTING DEFECT 73 (vertices=27, convex hull=64, v0=386242) After retessellation of defect 73 (v0=386242), euler #=-74 (723438,2165463,1441951) : difference with theory (-93) = -19 CORRECTING DEFECT 74 (vertices=329, convex hull=246, v0=387135) After retessellation of defect 74 (v0=387135), euler #=-73 (723447,2165611,1442091) : difference with theory (-92) = -19 CORRECTING DEFECT 75 (vertices=117, convex hull=109, v0=392671) After retessellation of defect 75 (v0=392671), euler #=-72 (723455,2165684,1442157) : difference with theory (-91) = -19 CORRECTING DEFECT 76 (vertices=433, convex hull=190, v0=396975) After retessellation of defect 76 (v0=396975), euler #=-71 (723482,2165857,1442304) : difference with theory (-90) = -19 CORRECTING DEFECT 77 (vertices=79, convex hull=80, v0=406238) After retessellation of defect 77 (v0=406238), euler #=-70 (723488,2165910,1442352) : difference with theory (-89) = -19 CORRECTING DEFECT 78 (vertices=270, convex hull=76, v0=408247) After retessellation of defect 78 (v0=408247), euler #=-70 (723500,2165985,1442415) : difference with theory (-88) = -18 CORRECTING DEFECT 79 (vertices=34, convex hull=65, v0=411356) After retessellation of defect 79 (v0=411356), euler #=-69 (723506,2166030,1442455) : difference with theory (-87) = -18 CORRECTING DEFECT 80 (vertices=59, convex hull=34, v0=417115) After retessellation of defect 80 (v0=417115), euler #=-68 (723507,2166048,1442473) : difference with theory (-86) = -18 CORRECTING DEFECT 81 (vertices=67, convex hull=77, v0=418086) After retessellation of defect 81 (v0=418086), euler #=-67 (723515,2166108,1442526) : difference with theory (-85) = -18 CORRECTING DEFECT 82 (vertices=12708, convex hull=2465, v0=419193) XL defect detected... After retessellation of defect 82 (v0=419193), euler #=-78 (723974,2168934,1444882) : difference with theory (-84) = -6 CORRECTING DEFECT 83 (vertices=6, convex hull=23, v0=420481) After retessellation of defect 83 (v0=420481), euler #=-77 (723975,2168942,1444890) : difference with theory (-83) = -6 CORRECTING DEFECT 84 (vertices=259, convex hull=61, v0=421300) After retessellation of defect 84 (v0=421300), euler #=-76 (723983,2168989,1444930) : difference with theory (-82) = -6 CORRECTING DEFECT 85 (vertices=1073, convex hull=121, v0=422428) After retessellation of defect 85 (v0=422428), euler #=-75 (723993,2169070,1445002) : difference with theory (-81) = -6 CORRECTING DEFECT 86 (vertices=97, convex hull=28, v0=428227) After retessellation of defect 86 (v0=428227), euler #=-74 (723996,2169091,1445021) : difference with theory (-80) = -6 CORRECTING DEFECT 87 (vertices=111, convex hull=62, v0=433974) After retessellation of defect 87 (v0=433974), euler #=-73 (723997,2169117,1445047) : difference with theory (-79) = -6 CORRECTING DEFECT 88 (vertices=33, convex hull=42, v0=448019) After retessellation of defect 88 (v0=448019), euler #=-72 (723999,2169138,1445067) : difference with theory (-78) = -6 CORRECTING DEFECT 89 (vertices=41, convex hull=79, v0=455580) After retessellation of defect 89 (v0=455580), euler #=-71 (724005,2169189,1445113) : difference with theory (-77) = -6 CORRECTING DEFECT 90 (vertices=18, convex hull=49, v0=456416) After retessellation of defect 90 (v0=456416), euler #=-70 (724009,2169218,1445139) : difference with theory (-76) = -6 CORRECTING DEFECT 91 (vertices=41, convex hull=56, v0=456809) After retessellation of defect 91 (v0=456809), euler #=-69 (724014,2169257,1445174) : difference with theory (-75) = -6 CORRECTING DEFECT 92 (vertices=16, convex hull=29, v0=464884) After retessellation of defect 92 (v0=464884), euler #=-68 (724015,2169270,1445187) : difference with theory (-74) = -6 CORRECTING DEFECT 93 (vertices=24, convex hull=31, v0=466934) After retessellation of defect 93 (v0=466934), euler #=-67 (724018,2169291,1445206) : difference with theory (-73) = -6 CORRECTING DEFECT 94 (vertices=25, convex hull=23, v0=471119) After retessellation of defect 94 (v0=471119), euler #=-66 (724020,2169304,1445218) : difference with theory (-72) = -6 CORRECTING DEFECT 95 (vertices=211, convex hull=43, v0=475966) After retessellation of defect 95 (v0=475966), euler #=-65 (724024,2169333,1445244) : difference with theory (-71) = -6 CORRECTING DEFECT 96 (vertices=37, convex hull=21, v0=481665) After retessellation of defect 96 (v0=481665), euler #=-64 (724024,2169339,1445251) : difference with theory (-70) = -6 CORRECTING DEFECT 97 (vertices=23, convex hull=54, v0=489454) After retessellation of defect 97 (v0=489454), euler #=-63 (724025,2169363,1445275) : difference with theory (-69) = -6 CORRECTING DEFECT 98 (vertices=52, convex hull=74, v0=497689) After retessellation of defect 98 (v0=497689), euler #=-62 (724033,2169414,1445319) : difference with theory (-68) = -6 CORRECTING DEFECT 99 (vertices=60, convex hull=27, v0=505815) After retessellation of defect 99 (v0=505815), euler #=-61 (724034,2169424,1445329) : difference with theory (-67) = -6 CORRECTING DEFECT 100 (vertices=1244, convex hull=193, v0=513649) After retessellation of defect 100 (v0=513649), euler #=-63 (724061,2169620,1445496) : difference with theory (-66) = -3 CORRECTING DEFECT 101 (vertices=311, convex hull=96, v0=513734) After retessellation of defect 101 (v0=513734), euler #=-62 (724066,2169683,1445555) : difference with theory (-65) = -3 CORRECTING DEFECT 102 (vertices=90, convex hull=22, v0=513966) After retessellation of defect 102 (v0=513966), euler #=-61 (724069,2169700,1445570) : difference with theory (-64) = -3 CORRECTING DEFECT 103 (vertices=78, convex hull=45, v0=517582) After retessellation of defect 103 (v0=517582), euler #=-60 (724071,2169725,1445594) : difference with theory (-63) = -3 CORRECTING DEFECT 104 (vertices=88, convex hull=82, v0=521070) After retessellation of defect 104 (v0=521070), euler #=-59 (724079,2169784,1445646) : difference with theory (-62) = -3 CORRECTING DEFECT 105 (vertices=12, convex hull=29, v0=524728) After retessellation of defect 105 (v0=524728), euler #=-58 (724081,2169801,1445662) : difference with theory (-61) = -3 CORRECTING DEFECT 106 (vertices=95, convex hull=36, v0=527215) After retessellation of defect 106 (v0=527215), euler #=-57 (724084,2169822,1445681) : difference with theory (-60) = -3 CORRECTING DEFECT 107 (vertices=186, convex hull=52, v0=528157) After retessellation of defect 107 (v0=528157), euler #=-56 (724086,2169851,1445709) : difference with theory (-59) = -3 CORRECTING DEFECT 108 (vertices=622, convex hull=472, v0=530218) After retessellation of defect 108 (v0=530218), euler #=-54 (724125,2170249,1446070) : difference with theory (-58) = -4 CORRECTING DEFECT 109 (vertices=382, convex hull=262, v0=530344) After retessellation of defect 109 (v0=530344), euler #=-53 (724156,2170476,1446267) : difference with theory (-57) = -4 CORRECTING DEFECT 110 (vertices=16, convex hull=20, v0=532797) After retessellation of defect 110 (v0=532797), euler #=-52 (724157,2170485,1446276) : difference with theory (-56) = -4 CORRECTING DEFECT 111 (vertices=309, convex hull=147, v0=533537) After retessellation of defect 111 (v0=533537), euler #=-51 (724176,2170617,1446390) : difference with theory (-55) = -4 CORRECTING DEFECT 112 (vertices=6, convex hull=15, v0=533949) After retessellation of defect 112 (v0=533949), euler #=-50 (724177,2170625,1446398) : difference with theory (-54) = -4 CORRECTING DEFECT 113 (vertices=37, convex hull=40, v0=543404) After retessellation of defect 113 (v0=543404), euler #=-49 (724180,2170648,1446419) : difference with theory (-53) = -4 CORRECTING DEFECT 114 (vertices=28, convex hull=73, v0=545513) After retessellation of defect 114 (v0=545513), euler #=-48 (724186,2170692,1446458) : difference with theory (-52) = -4 CORRECTING DEFECT 115 (vertices=13, convex hull=23, v0=548976) After retessellation of defect 115 (v0=548976), euler #=-47 (724187,2170703,1446469) : difference with theory (-51) = -4 CORRECTING DEFECT 116 (vertices=30, convex hull=22, v0=549121) After retessellation of defect 116 (v0=549121), euler #=-46 (724188,2170713,1446479) : difference with theory (-50) = -4 CORRECTING DEFECT 117 (vertices=165, convex hull=95, v0=551695) After retessellation of defect 117 (v0=551695), euler #=-45 (724195,2170782,1446542) : difference with theory (-49) = -4 CORRECTING DEFECT 118 (vertices=12, convex hull=25, v0=551999) After retessellation of defect 118 (v0=551999), euler #=-44 (724198,2170798,1446556) : difference with theory (-48) = -4 CORRECTING DEFECT 119 (vertices=651, convex hull=232, v0=555613) After retessellation of defect 119 (v0=555613), euler #=-43 (724219,2170972,1446710) : difference with theory (-47) = -4 CORRECTING DEFECT 120 (vertices=25, convex hull=27, v0=558598) After retessellation of defect 120 (v0=558598), euler #=-42 (724220,2170983,1446721) : difference with theory (-46) = -4 CORRECTING DEFECT 121 (vertices=9, convex hull=26, v0=567135) After retessellation of defect 121 (v0=567135), euler #=-41 (724221,2170994,1446732) : difference with theory (-45) = -4 CORRECTING DEFECT 122 (vertices=166, convex hull=106, v0=567186) After retessellation of defect 122 (v0=567186), euler #=-40 (724232,2171075,1446803) : difference with theory (-44) = -4 CORRECTING DEFECT 123 (vertices=8, convex hull=37, v0=571981) After retessellation of defect 123 (v0=571981), euler #=-39 (724234,2171092,1446819) : difference with theory (-43) = -4 CORRECTING DEFECT 124 (vertices=11, convex hull=37, v0=572223) After retessellation of defect 124 (v0=572223), euler #=-38 (724235,2171107,1446834) : difference with theory (-42) = -4 CORRECTING DEFECT 125 (vertices=14, convex hull=20, v0=572256) After retessellation of defect 125 (v0=572256), euler #=-37 (724236,2171116,1446843) : difference with theory (-41) = -4 CORRECTING DEFECT 126 (vertices=151, convex hull=46, v0=572546) After retessellation of defect 126 (v0=572546), euler #=-36 (724238,2171139,1446865) : difference with theory (-40) = -4 CORRECTING DEFECT 127 (vertices=22, convex hull=21, v0=575651) After retessellation of defect 127 (v0=575651), euler #=-35 (724239,2171152,1446878) : difference with theory (-39) = -4 CORRECTING DEFECT 128 (vertices=156, convex hull=84, v0=578068) After retessellation of defect 128 (v0=578068), euler #=-34 (724244,2171204,1446926) : difference with theory (-38) = -4 CORRECTING DEFECT 129 (vertices=38, convex hull=57, v0=584138) After retessellation of defect 129 (v0=584138), euler #=-33 (724247,2171237,1446957) : difference with theory (-37) = -4 CORRECTING DEFECT 130 (vertices=870, convex hull=269, v0=586700) After retessellation of defect 130 (v0=586700), euler #=-36 (724273,2171482,1447173) : difference with theory (-36) = 0 CORRECTING DEFECT 131 (vertices=89, convex hull=85, v0=588866) After retessellation of defect 131 (v0=588866), euler #=-35 (724280,2171539,1447224) : difference with theory (-35) = 0 CORRECTING DEFECT 132 (vertices=47, convex hull=77, v0=589305) After retessellation of defect 132 (v0=589305), euler #=-34 (724286,2171589,1447269) : difference with theory (-34) = 0 CORRECTING DEFECT 133 (vertices=205, convex hull=78, v0=592065) After retessellation of defect 133 (v0=592065), euler #=-33 (724294,2171644,1447317) : difference with theory (-33) = 0 CORRECTING DEFECT 134 (vertices=2544, convex hull=434, v0=594398) After retessellation of defect 134 (v0=594398), euler #=-32 (724385,2172144,1447727) : difference with theory (-32) = 0 CORRECTING DEFECT 135 (vertices=48, convex hull=40, v0=599840) After retessellation of defect 135 (v0=599840), euler #=-31 (724386,2172165,1447748) : difference with theory (-31) = 0 CORRECTING DEFECT 136 (vertices=97, convex hull=44, v0=600410) After retessellation of defect 136 (v0=600410), euler #=-30 (724389,2172193,1447774) : difference with theory (-30) = 0 CORRECTING DEFECT 137 (vertices=13, convex hull=29, v0=601766) After retessellation of defect 137 (v0=601766), euler #=-29 (724390,2172205,1447786) : difference with theory (-29) = 0 CORRECTING DEFECT 138 (vertices=299, convex hull=76, v0=614658) After retessellation of defect 138 (v0=614658), euler #=-28 (724398,2172263,1447837) : difference with theory (-28) = 0 CORRECTING DEFECT 139 (vertices=222, convex hull=129, v0=616779) After retessellation of defect 139 (v0=616779), euler #=-27 (724407,2172350,1447916) : difference with theory (-27) = 0 CORRECTING DEFECT 140 (vertices=78, convex hull=24, v0=616954) After retessellation of defect 140 (v0=616954), euler #=-26 (724407,2172356,1447923) : difference with theory (-26) = 0 CORRECTING DEFECT 141 (vertices=5, convex hull=22, v0=617654) After retessellation of defect 141 (v0=617654), euler #=-25 (724408,2172364,1447931) : difference with theory (-25) = 0 CORRECTING DEFECT 142 (vertices=195, convex hull=60, v0=619130) After retessellation of defect 142 (v0=619130), euler #=-24 (724412,2172402,1447966) : difference with theory (-24) = 0 CORRECTING DEFECT 143 (vertices=129, convex hull=50, v0=621520) After retessellation of defect 143 (v0=621520), euler #=-23 (724416,2172431,1447992) : difference with theory (-23) = 0 CORRECTING DEFECT 144 (vertices=814, convex hull=286, v0=623504) After retessellation of defect 144 (v0=623504), euler #=-22 (724449,2172672,1448201) : difference with theory (-22) = 0 CORRECTING DEFECT 145 (vertices=65, convex hull=33, v0=624244) After retessellation of defect 145 (v0=624244), euler #=-21 (724451,2172689,1448217) : difference with theory (-21) = 0 CORRECTING DEFECT 146 (vertices=137, convex hull=65, v0=627972) After retessellation of defect 146 (v0=627972), euler #=-20 (724453,2172722,1448249) : difference with theory (-20) = 0 CORRECTING DEFECT 147 (vertices=106, convex hull=115, v0=629425) After retessellation of defect 147 (v0=629425), euler #=-19 (724465,2172810,1448326) : difference with theory (-19) = 0 CORRECTING DEFECT 148 (vertices=5, convex hull=25, v0=639237) After retessellation of defect 148 (v0=639237), euler #=-18 (724466,2172819,1448335) : difference with theory (-18) = 0 CORRECTING DEFECT 149 (vertices=16, convex hull=18, v0=642420) After retessellation of defect 149 (v0=642420), euler #=-17 (724466,2172825,1448342) : difference with theory (-17) = 0 CORRECTING DEFECT 150 (vertices=98, convex hull=81, v0=647757) After retessellation of defect 150 (v0=647757), euler #=-16 (724472,2172878,1448390) : difference with theory (-16) = 0 CORRECTING DEFECT 151 (vertices=9, convex hull=18, v0=654482) After retessellation of defect 151 (v0=654482), euler #=-15 (724473,2172886,1448398) : difference with theory (-15) = 0 CORRECTING DEFECT 152 (vertices=39, convex hull=33, v0=659295) After retessellation of defect 152 (v0=659295), euler #=-14 (724475,2172901,1448412) : difference with theory (-14) = 0 CORRECTING DEFECT 153 (vertices=38, convex hull=46, v0=660685) After retessellation of defect 153 (v0=660685), euler #=-13 (724476,2172921,1448432) : difference with theory (-13) = 0 CORRECTING DEFECT 154 (vertices=135, convex hull=98, v0=669036) After retessellation of defect 154 (v0=669036), euler #=-12 (724485,2172995,1448498) : difference with theory (-12) = 0 CORRECTING DEFECT 155 (vertices=318, convex hull=86, v0=672959) After retessellation of defect 155 (v0=672959), euler #=-11 (724489,2173050,1448550) : difference with theory (-11) = 0 CORRECTING DEFECT 156 (vertices=275, convex hull=187, v0=683861) After retessellation of defect 156 (v0=683861), euler #=-10 (724505,2173193,1448678) : difference with theory (-10) = 0 CORRECTING DEFECT 157 (vertices=607, convex hull=188, v0=687323) After retessellation of defect 157 (v0=687323), euler #=-9 (724526,2173359,1448824) : difference with theory (-9) = 0 CORRECTING DEFECT 158 (vertices=46, convex hull=41, v0=687762) After retessellation of defect 158 (v0=687762), euler #=-8 (724526,2173373,1448839) : difference with theory (-8) = 0 CORRECTING DEFECT 159 (vertices=20, convex hull=34, v0=693639) After retessellation of defect 159 (v0=693639), euler #=-7 (724526,2173385,1448852) : difference with theory (-7) = 0 CORRECTING DEFECT 160 (vertices=259, convex hull=44, v0=701017) After retessellation of defect 160 (v0=701017), euler #=-6 (724532,2173420,1448882) : difference with theory (-6) = 0 CORRECTING DEFECT 161 (vertices=24, convex hull=55, v0=702164) After retessellation of defect 161 (v0=702164), euler #=-5 (724536,2173453,1448912) : difference with theory (-5) = 0 CORRECTING DEFECT 162 (vertices=28, convex hull=38, v0=716202) After retessellation of defect 162 (v0=716202), euler #=-4 (724538,2173472,1448930) : difference with theory (-4) = 0 CORRECTING DEFECT 163 (vertices=50, convex hull=47, v0=719400) After retessellation of defect 163 (v0=719400), euler #=-3 (724539,2173489,1448947) : difference with theory (-3) = 0 CORRECTING DEFECT 164 (vertices=114, convex hull=46, v0=735183) After retessellation of defect 164 (v0=735183), euler #=-2 (724540,2173509,1448967) : difference with theory (-2) = 0 CORRECTING DEFECT 165 (vertices=123, convex hull=33, v0=736687) After retessellation of defect 165 (v0=736687), euler #=-1 (724541,2173525,1448983) : difference with theory (-1) = 0 CORRECTING DEFECT 166 (vertices=46, convex hull=59, v0=751562) After retessellation of defect 166 (v0=751562), euler #=0 (724543,2173553,1449010) : difference with theory (0) = 0 CORRECTING DEFECT 167 (vertices=22, convex hull=57, v0=770183) After retessellation of defect 167 (v0=770183), euler #=1 (724546,2173583,1449038) : difference with theory (1) = 0 CORRECTING DEFECT 168 (vertices=93, convex hull=114, v0=771360) After retessellation of defect 168 (v0=771360), euler #=2 (724552,2173650,1449100) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.41 +- 0.15 (0.02-->19.28) (max @ vno 506895 --> 512720) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.41 +- 0.15 (0.02-->19.28) (max @ vno 506895 --> 512720) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 531 mutations (35.9%), 948 crossovers (64.1%), 176 vertices were eliminated building final representation... 52894 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=724552, nf=1449100, ne=2173650, g=0) writing corrected surface to /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change 0 defective edges removing intersecting faces 000: 3806 intersecting 001: 200 intersecting 002: 111 intersecting 003: 90 intersecting expanding nbhd size to 2 004: 93 intersecting 005: 80 intersecting 006: 75 intersecting 007: 71 intersecting 008: 69 intersecting 009: 65 intersecting 010: 55 intersecting expanding nbhd size to 3 011: 58 intersecting expanding nbhd size to 4 012: 65 intersecting 013: 58 intersecting expanding nbhd size to 5 014: 63 intersecting expanding nbhd size to 6 015: 69 intersecting expanding nbhd size to 7 016: 74 intersecting expanding nbhd size to 8 017: 77 intersecting 018: 70 intersecting expanding nbhd size to 9 019: 70 intersecting 020: 62 intersecting expanding nbhd size to 10 021: 66 intersecting expanding nbhd size to 11 022: 66 intersecting 023: 65 intersecting 024: 56 intersecting expanding nbhd size to 12 025: 61 intersecting 026: 60 intersecting 027: 54 intersecting expanding nbhd size to 13 028: 57 intersecting 029: 56 intersecting expanding nbhd size to 14 030: 57 intersecting 031: 44 intersecting 032: 17 intersecting 033: 10 intersecting expanding nbhd size to 15 034: 10 intersecting 035: 6 intersecting expanding nbhd size to 16 036: 10 intersecting expanding nbhd size to 17 037: 13 intersecting expanding nbhd size to 18 038: 16 intersecting expanding nbhd size to 19 039: 20 intersecting expanding nbhd size to 20 040: 23 intersecting expanding nbhd size to 21 041: 25 intersecting expanding nbhd size to 22 042: 31 intersecting expanding nbhd size to 23 043: 31 intersecting expanding nbhd size to 24 044: 34 intersecting expanding nbhd size to 25 045: 34 intersecting expanding nbhd size to 26 046: 44 intersecting expanding nbhd size to 27 047: 51 intersecting expanding nbhd size to 28 048: 57 intersecting expanding nbhd size to 29 049: 73 intersecting expanding nbhd size to 30 050: 89 intersecting 051: 74 intersecting 052: 69 intersecting 053: 61 intersecting 054: 53 intersecting expanding nbhd size to 31 055: 53 intersecting 056: 51 intersecting expanding nbhd size to 32 057: 51 intersecting 058: 50 intersecting 059: 45 intersecting 060: 43 intersecting 061: 41 intersecting expanding nbhd size to 33 062: 42 intersecting 063: 39 intersecting 064: 35 intersecting expanding nbhd size to 34 065: 36 intersecting expanding nbhd size to 35 066: 40 intersecting expanding nbhd size to 36 067: 41 intersecting 068: 40 intersecting expanding nbhd size to 37 069: 43 intersecting expanding nbhd size to 38 070: 46 intersecting expanding nbhd size to 39 071: 46 intersecting expanding nbhd size to 40 072: 46 intersecting expanding nbhd size to 41 073: 46 intersecting expanding nbhd size to 42 074: 47 intersecting expanding nbhd size to 43 075: 51 intersecting expanding nbhd size to 44 076: 52 intersecting expanding nbhd size to 45 077: 53 intersecting expanding nbhd size to 46 078: 55 intersecting expanding nbhd size to 47 079: 56 intersecting expanding nbhd size to 48 080: 56 intersecting expanding nbhd size to 49 081: 57 intersecting expanding nbhd size to 50 082: 58 intersecting expanding nbhd size to 51 083: 58 intersecting expanding nbhd size to 52 084: 58 intersecting expanding nbhd size to 53 085: 59 intersecting 086: 58 intersecting expanding nbhd size to 54 087: 60 intersecting expanding nbhd size to 55 088: 60 intersecting expanding nbhd size to 56 089: 65 intersecting 090: 64 intersecting expanding nbhd size to 57 091: 65 intersecting expanding nbhd size to 58 092: 68 intersecting 093: 67 intersecting expanding nbhd size to 59 094: 67 intersecting expanding nbhd size to 60 095: 68 intersecting expanding nbhd size to 61 096: 68 intersecting expanding nbhd size to 62 097: 73 intersecting 098: 68 intersecting expanding nbhd size to 63 099: 68 intersecting expanding nbhd size to 64 100: 69 intersecting 101: 68 intersecting mris_fix_topology utimesec 23370.388742 mris_fix_topology stimesec 4.868440 mris_fix_topology ru_maxrss 2439720 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 1075364 mris_fix_topology ru_topology fixing took 873.2 minutes majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 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 11934 mris_fix_topology ru_nivcsw 2077679 FSRUNTIME@ mris_fix_topology rh 14.5540 hours 1 threads mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 724552 - 2173650 + 1449100 = 2 --> 0 holes F =2V-4: 1449100 = 1449104-4 (0) 2E=3F: 4347300 = 4347300 (0) total defect index = 0 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.62 hours removing intersecting faces 000: 1028 intersecting 001: 206 intersecting 002: 113 intersecting 003: 88 intersecting expanding nbhd size to 2 004: 89 intersecting 005: 73 intersecting expanding nbhd size to 3 006: 84 intersecting 007: 56 intersecting expanding nbhd size to 4 008: 58 intersecting 009: 45 intersecting expanding nbhd size to 5 010: 47 intersecting expanding nbhd size to 6 011: 50 intersecting expanding nbhd size to 7 012: 74 intersecting 013: 62 intersecting expanding nbhd size to 8 014: 64 intersecting 015: 62 intersecting expanding nbhd size to 9 016: 65 intersecting 017: 63 intersecting 018: 59 intersecting expanding nbhd size to 10 019: 63 intersecting expanding nbhd size to 11 020: 65 intersecting expanding nbhd size to 12 021: 68 intersecting 022: 58 intersecting expanding nbhd size to 13 023: 62 intersecting 024: 57 intersecting 025: 55 intersecting expanding nbhd size to 14 026: 61 intersecting 027: 56 intersecting 028: 40 intersecting 029: 17 intersecting 030: 9 intersecting 031: 8 intersecting 032: 6 intersecting expanding nbhd size to 15 033: 10 intersecting expanding nbhd size to 16 034: 12 intersecting expanding nbhd size to 17 035: 17 intersecting expanding nbhd size to 18 036: 19 intersecting expanding nbhd size to 19 037: 23 intersecting expanding nbhd size to 20 038: 24 intersecting expanding nbhd size to 21 039: 28 intersecting expanding nbhd size to 22 040: 28 intersecting expanding nbhd size to 23 041: 31 intersecting expanding nbhd size to 24 042: 36 intersecting expanding nbhd size to 25 043: 44 intersecting expanding nbhd size to 26 044: 49 intersecting expanding nbhd size to 27 045: 57 intersecting expanding nbhd size to 28 046: 67 intersecting expanding nbhd size to 29 047: 80 intersecting 048: 76 intersecting 049: 69 intersecting 050: 63 intersecting 051: 59 intersecting 052: 54 intersecting 053: 52 intersecting 054: 51 intersecting 055: 49 intersecting 056: 44 intersecting 057: 42 intersecting expanding nbhd size to 30 058: 42 intersecting 059: 40 intersecting 060: 39 intersecting 061: 38 intersecting expanding nbhd size to 31 062: 38 intersecting expanding nbhd size to 32 063: 39 intersecting expanding nbhd size to 33 064: 40 intersecting expanding nbhd size to 34 065: 41 intersecting expanding nbhd size to 35 066: 44 intersecting expanding nbhd size to 36 067: 46 intersecting expanding nbhd size to 37 068: 46 intersecting expanding nbhd size to 38 069: 46 intersecting 070: 45 intersecting expanding nbhd size to 39 071: 49 intersecting expanding nbhd size to 40 072: 70 intersecting 073: 50 intersecting expanding nbhd size to 41 074: 52 intersecting expanding nbhd size to 42 075: 55 intersecting expanding nbhd size to 43 076: 56 intersecting expanding nbhd size to 44 077: 57 intersecting expanding nbhd size to 45 078: 57 intersecting expanding nbhd size to 46 079: 57 intersecting expanding nbhd size to 47 080: 57 intersecting expanding nbhd size to 48 081: 58 intersecting expanding nbhd size to 49 082: 59 intersecting expanding nbhd size to 50 083: 61 intersecting expanding nbhd size to 51 084: 61 intersecting expanding nbhd size to 52 085: 62 intersecting expanding nbhd size to 53 086: 66 intersecting 087: 64 intersecting expanding nbhd size to 54 088: 65 intersecting expanding nbhd size to 55 089: 67 intersecting 090: 66 intersecting expanding nbhd size to 56 091: 66 intersecting expanding nbhd size to 57 092: 67 intersecting expanding nbhd size to 58 093: 80 intersecting 094: 69 intersecting expanding nbhd size to 59 095: 69 intersecting expanding nbhd size to 60 096: 71 intersecting expanding nbhd size to 61 097: 72 intersecting 098: 69 intersecting 099: 68 intersecting expanding nbhd size to 62 100: 69 intersecting 101: 68 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sun Jan 13 19:05:03 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 rh 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/rh.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 (0.00-->5.41) (max @ vno 722662 --> 722721) face area 0.06 +- 0.04 (0.00-->7.05) mean absolute distance = 0.47 +- 0.82 33887 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 = 101.7, mean outside = 87.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=96.8, 636 (636) missing vertices, mean dist -0.3 [0.5 (%72.0)->0.3 (%28.0))] %84 local maxima, %10 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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.47 +- 0.17 (0.03-->4.84) (max @ vno 722662 --> 722721) face area 0.06 +- 0.04 (0.00-->4.18) mean absolute distance = 0.32 +- 0.58 20044 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=30300560.0, rms=4.648 001: dt: 0.5000, sse=17075426.0, rms=3.693 (20.539%) 002: dt: 0.5000, sse=13744059.0, rms=3.420 (7.397%) 003: dt: 0.5000, sse=11995114.0, rms=3.211 (6.098%) 004: dt: 0.5000, sse=10696161.0, rms=3.127 (2.627%) 005: dt: 0.5000, sse=10291783.0, rms=3.053 (2.375%) rms = 3.01, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=9618405.0, rms=3.014 (1.257%) 007: dt: 0.2500, sse=9192848.0, rms=2.896 (3.944%) 008: dt: 0.2500, sse=8855472.0, rms=2.839 (1.956%) rms = 2.79, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=8654809.0, rms=2.790 (1.725%) rms = 2.76, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=8259278.0, rms=2.763 (0.962%) positioning took 60.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=97.3, 2461 (202) missing vertices, mean dist -0.1 [0.4 (%64.7)->0.2 (%35.3))] %89 local maxima, % 5 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-->4.50) (max @ vno 722662 --> 722721) face area 0.08 +- 0.06 (0.00-->4.99) mean absolute distance = 0.26 +- 0.44 20068 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=9291842.0, rms=2.854 011: dt: 0.5000, sse=9512744.0, rms=2.636 (7.628%) rms = 2.60, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=9298715.0, rms=2.598 (1.450%) 013: dt: 0.2500, sse=8981049.0, rms=2.430 (6.473%) 014: dt: 0.2500, sse=8711739.0, rms=2.357 (2.982%) 015: dt: 0.2500, sse=8724775.0, rms=2.306 (2.163%) rms = 2.27, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=8656814.0, rms=2.266 (1.730%) rms = 2.23, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=8028926.0, rms=2.233 (1.462%) positioning took 41.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=97.6, 2986 (138) missing vertices, mean dist -0.1 [0.3 (%57.1)->0.2 (%42.9))] %90 local maxima, % 4 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-->4.43) (max @ vno 147652 --> 722721) face area 0.08 +- 0.05 (0.00-->4.96) mean absolute distance = 0.25 +- 0.38 20725 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8087776.0, rms=2.376 018: dt: 0.5000, sse=8657817.0, rms=2.320 (2.343%) rms = 2.34, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=6871182.5, rms=2.198 (5.282%) 020: dt: 0.2500, sse=8475894.0, rms=2.083 (5.203%) rms = 2.09, time step reduction 2 of 3 to 0.125... rms = 2.05, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=7225442.5, rms=2.048 (1.697%) positioning took 32.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=97.7, 3461 (90) missing vertices, mean dist -0.0 [0.3 (%54.6)->0.2 (%45.4))] %90 local maxima, % 3 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/rh.white.preaparc... 000: dt: 0.0000, sse=7205912.0, rms=2.139 rms = 2.12, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=8577095.0, rms=2.119 (0.967%) 023: dt: 0.2500, sse=7876081.5, rms=2.020 (4.673%) 024: dt: 0.2500, sse=8002568.0, rms=1.949 (3.521%) rms = 1.91, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=7807126.5, rms=1.912 (1.895%) rms = 1.86, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=7515273.0, rms=1.865 (2.460%) positioning took 28.1 minutes generating cortex label... 196 non-cortical segments detected only using segment with 32854 vertices erasing segment 0 (vno[0] = 22100) erasing segment 1 (vno[0] = 23730) erasing segment 2 (vno[0] = 24727) erasing segment 3 (vno[0] = 40633) erasing segment 4 (vno[0] = 44522) erasing segment 5 (vno[0] = 46768) erasing segment 6 (vno[0] = 48655) erasing segment 7 (vno[0] = 49137) erasing segment 8 (vno[0] = 50878) erasing segment 9 (vno[0] = 71408) erasing segment 10 (vno[0] = 71466) erasing segment 11 (vno[0] = 71564) erasing segment 12 (vno[0] = 83932) erasing segment 13 (vno[0] = 84036) erasing segment 14 (vno[0] = 89115) erasing segment 15 (vno[0] = 91327) erasing segment 16 (vno[0] = 91599) erasing segment 17 (vno[0] = 93435) erasing segment 18 (vno[0] = 99264) erasing segment 19 (vno[0] = 103085) erasing segment 20 (vno[0] = 103128) erasing segment 21 (vno[0] = 104175) erasing segment 22 (vno[0] = 104250) erasing segment 23 (vno[0] = 113339) erasing segment 24 (vno[0] = 114667) erasing segment 25 (vno[0] = 115707) erasing segment 26 (vno[0] = 115759) erasing segment 27 (vno[0] = 126513) erasing segment 28 (vno[0] = 130237) erasing segment 29 (vno[0] = 133951) erasing segment 30 (vno[0] = 134004) erasing segment 31 (vno[0] = 139371) erasing segment 32 (vno[0] = 142536) erasing segment 33 (vno[0] = 149322) erasing segment 34 (vno[0] = 153450) erasing segment 35 (vno[0] = 154711) erasing segment 36 (vno[0] = 157124) erasing segment 37 (vno[0] = 158841) erasing segment 38 (vno[0] = 162053) erasing segment 39 (vno[0] = 168771) erasing segment 40 (vno[0] = 169537) erasing segment 41 (vno[0] = 173758) erasing segment 42 (vno[0] = 188651) erasing segment 43 (vno[0] = 191200) erasing segment 44 (vno[0] = 192178) erasing segment 45 (vno[0] = 192540) erasing segment 46 (vno[0] = 194732) erasing segment 47 (vno[0] = 207165) erasing segment 48 (vno[0] = 217624) erasing segment 49 (vno[0] = 226526) erasing segment 50 (vno[0] = 228118) erasing segment 51 (vno[0] = 230901) erasing segment 52 (vno[0] = 232630) erasing segment 53 (vno[0] = 233499) erasing segment 54 (vno[0] = 233516) erasing segment 55 (vno[0] = 235768) erasing segment 56 (vno[0] = 238187) erasing segment 57 (vno[0] = 243388) erasing segment 58 (vno[0] = 248859) erasing segment 60 (vno[0] = 256361) erasing segment 61 (vno[0] = 259027) erasing segment 62 (vno[0] = 262468) erasing segment 63 (vno[0] = 265109) erasing segment 64 (vno[0] = 275663) erasing segment 65 (vno[0] = 282519) erasing segment 66 (vno[0] = 289426) erasing segment 67 (vno[0] = 292107) erasing segment 68 (vno[0] = 312050) erasing segment 69 (vno[0] = 312090) erasing segment 70 (vno[0] = 321353) erasing segment 71 (vno[0] = 349804) erasing segment 72 (vno[0] = 350520) erasing segment 73 (vno[0] = 360444) erasing segment 74 (vno[0] = 363119) erasing segment 75 (vno[0] = 378240) erasing segment 76 (vno[0] = 391963) erasing segment 77 (vno[0] = 392781) erasing segment 78 (vno[0] = 397390) erasing segment 79 (vno[0] = 403582) erasing segment 80 (vno[0] = 405043) erasing segment 81 (vno[0] = 419088) erasing segment 82 (vno[0] = 424467) erasing segment 83 (vno[0] = 436123) erasing segment 84 (vno[0] = 439615) erasing segment 85 (vno[0] = 444572) erasing segment 86 (vno[0] = 448329) erasing segment 87 (vno[0] = 454359) erasing segment 88 (vno[0] = 459006) erasing segment 89 (vno[0] = 459073) erasing segment 90 (vno[0] = 461633) erasing segment 91 (vno[0] = 463004) erasing segment 92 (vno[0] = 466839) erasing segment 93 (vno[0] = 469076) erasing segment 94 (vno[0] = 471317) erasing segment 95 (vno[0] = 471346) erasing segment 96 (vno[0] = writing smoothed curvature to rh.curv 483008) erasing segment 97 (vno[0] = 484584) erasing segment 98 (vno[0] = 488649) erasing segment 99 (vno[0] = 491050) erasing segment 100 (vno[0] = 491152) erasing segment 101 (vno[0] = 492999) erasing segment 102 (vno[0] = 493044) erasing segment 103 (vno[0] = 495913) erasing segment 104 (vno[0] = 495928) erasing segment 105 (vno[0] = 498471) erasing segment 106 (vno[0] = 498666) erasing segment 107 (vno[0] = 500960) erasing segment 108 (vno[0] = 500967) erasing segment 109 (vno[0] = 501296) erasing segment 110 (vno[0] = 501455) erasing segment 111 (vno[0] = 503909) erasing segment 112 (vno[0] = 506345) erasing segment 113 (vno[0] = 511684) erasing segment 114 (vno[0] = 511723) erasing segment 115 (vno[0] = 511786) erasing segment 116 (vno[0] = 512183) erasing segment 117 (vno[0] = 514343) erasing segment 118 (vno[0] = 514597) erasing segment 119 (vno[0] = 515021) erasing segment 120 (vno[0] = 515041) erasing segment 121 (vno[0] = 516233) erasing segment 122 (vno[0] = 517328) erasing segment 123 (vno[0] = 519869) erasing segment 124 (vno[0] = 520044) erasing segment 125 (vno[0] = 522705) erasing segment 126 (vno[0] = 524641) erasing segment 127 (vno[0] = 524730) erasing segment 128 (vno[0] = 524906) erasing segment 129 (vno[0] = 524935) erasing segment 130 (vno[0] = 525214) erasing segment 131 (vno[0] = 527235) erasing segment 132 (vno[0] = 528818) erasing segment 133 (vno[0] = 530803) erasing segment 134 (vno[0] = 531611) erasing segment 135 (vno[0] = 533154) erasing segment 136 (vno[0] = 534913) erasing segment 137 (vno[0] = 535718) erasing segment 138 (vno[0] = 541907) erasing segment 139 (vno[0] = 542151) erasing segment 140 (vno[0] = 542167) erasing segment 141 (vno[0] = 542177) erasing segment 142 (vno[0] = 543703) erasing segment 143 (vno[0] = 544295) erasing segment 144 (vno[0] = 546330) erasing segment 145 (vno[0] = 555939) erasing segment 146 (vno[0] = 562809) erasing segment 147 (vno[0] = 564970) erasing segment 148 (vno[0] = 576905) erasing segment 149 (vno[0] = 581229) erasing segment 150 (vno[0] = 582885) erasing segment 151 (vno[0] = 586892) erasing segment 152 (vno[0] = 586947) erasing segment 153 (vno[0] = 593368) erasing segment 154 (vno[0] = 595319) erasing segment 155 (vno[0] = 598984) erasing segment 156 (vno[0] = 603061) erasing segment 157 (vno[0] = 607786) erasing segment 158 (vno[0] = 612285) erasing segment 159 (vno[0] = 612616) erasing segment 160 (vno[0] = 616677) erasing segment 161 (vno[0] = 621660) erasing segment 162 (vno[0] = 623207) erasing segment 163 (vno[0] = 624863) erasing segment 164 (vno[0] = 628278) erasing segment 165 (vno[0] = 629424) erasing segment 166 (vno[0] = 629462) erasing segment 167 (vno[0] = 631399) erasing segment 168 (vno[0] = 631754) erasing segment 169 (vno[0] = 633789) erasing segment 170 (vno[0] = 633819) erasing segment 171 (vno[0] = 635323) erasing segment 172 (vno[0] = 635771) erasing segment 173 (vno[0] = 637117) erasing segment 174 (vno[0] = 644518) erasing segment 175 (vno[0] = 649261) erasing segment 176 (vno[0] = 651506) erasing segment 177 (vno[0] = 652715) erasing segment 178 (vno[0] = 654185) erasing segment 179 (vno[0] = 654496) erasing segment 180 (vno[0] = 657743) erasing segment 181 (vno[0] = 660917) erasing segment 182 (vno[0] = 661154) erasing segment 183 (vno[0] = 672936) erasing segment 184 (vno[0] = 674697) erasing segment 185 (vno[0] = 676094) erasing segment 186 (vno[0] = 677319) erasing segment 187 (vno[0] = 678626) erasing segment 188 (vno[0] = 690901) erasing segment 189 (vno[0] = 692198) erasing segment 190 (vno[0] = 723794) erasing segment 191 (vno[0] = 723798) erasing segment 192 (vno[0] = 723872) erasing segment 193 (vno[0] = 723891) erasing segment 194 (vno[0] = 724062) erasing segment 195 (vno[0] = 724173) writing cortex label to /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/label/rh.cortex.label... writing curvature file /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/rh.curv writing smoothed area to rh.area writing curvature file /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf/rh.area vertex spacing 0.46 +- 0.17 (0.00-->4.35) (max @ vno 147652 --> 722721) face area 0.08 +- 0.06 (0.00-->5.00) refinement took 212.4 minutes #-------------------------------------------- #@# Smooth2 rh Sun Jan 13 22:37:28 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Sun Jan 13 22:41:07 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.rh.dat -n 50 ../surf/rh.smoothwm ../surf/rh.inflated niterations = 50 Reading ../surf/rh.smoothwm avg radius = 46.1 mm, total surface area = 96875 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.133 (target=0.015) step 005: RMS=0.097 (target=0.015) step 010: RMS=0.078 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.049 (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=0.033 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.026 (target=0.015) step 065: RMS=0.025 (target=0.015) step 070: RMS=0.024 (target=0.015) step 075: RMS=0.023 (target=0.015) step 080: RMS=0.022 (target=0.015) step 085: RMS=0.021 (target=0.015) step 090: RMS=0.020 (target=0.015) step 095: RMS=0.019 (target=0.015) step 100: RMS=0.019 (target=0.015) step 105: RMS=0.018 (target=0.015) step 110: RMS=0.018 (target=0.015) step 115: RMS=0.017 (target=0.015) step 120: RMS=0.017 (target=0.015) step 125: RMS=0.016 (target=0.015) step 130: RMS=0.016 (target=0.015) step 135: RMS=0.015 (target=0.015) step 140: RMS=0.015 (target=0.015) inflation complete. inflation took 37.4 minutes mris_inflate utimesec 866.447853 mris_inflate stimesec 2.654390 mris_inflate ru_maxrss 1135952 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 2584320 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 52504 mris_inflate ru_nivcsw 74135 #-------------------------------------------- #@# Curv .H and .K rh Sun Jan 13 23:18:34 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf mris_curvature -w rh.white.preaparc total integrated curvature = 1641.523*4pi (20627.984) --> -1641 handles ICI = 2787.4, FI = 12999.2, variation=235218.698 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 1737 vertices thresholded to be in k1 ~ [-0.55 0.51], k2 ~ [-0.11 0.09] total integrated curvature = 0.214*4pi (2.688) --> 1 handles ICI = 2.9, FI = 35.1, variation=533.839 927 vertices thresholded to be in [-0.02 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 782 vertices thresholded to be in [-0.25 0.25] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.043 done. #----------------------------------------- #@# Curvature Stats rh Mon Jan 14 00:01:21 UTC 2019 /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS5115/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-ADS5115 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-ADS5115/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 2033 ] Gb_filter = 0 #-------------------------------------------- #@# Sphere rh Mon Jan 14 00:03:48 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.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.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 0.275... 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 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.34 pass 1: epoch 2 of 3 starting distance error %20.06 unfolding complete - removing small folds... starting distance error %19.57 removing remaining folds... final distance error %19.59 MRISunfold() return, current seed 1234 -01: dt=0.0000, 4975 negative triangles 190: dt=0.9900, 4975 negative triangles 191: dt=0.9900, 3455 negative triangles 192: dt=0.9900, 3312 negative triangles 193: dt=0.9900, 3150 negative triangles 194: dt=0.9900, 3120 negative triangles 195: dt=0.9900, 3069 negative triangles 196: dt=0.9900, 3056 negative triangles 197: dt=0.9900, 3016 negative triangles 198: dt=0.9900, 2985 negative triangles 199: dt=0.9900, 2914 negative triangles 200: dt=0.9900, 2911 negative triangles 201: dt=0.9900, 2887 negative triangles 202: dt=0.9900, 2842 negative triangles 203: dt=0.9900, 2818 negative triangles 204: dt=0.9900, 2757 negative triangles 205: dt=0.9900, 2770 negative triangles 206: dt=0.9900, 2756 negative triangles 207: dt=0.9900, 2755 negative triangles 208: dt=0.9900, 2728 negative triangles 209: dt=0.9900, 2725 negative triangles 210: dt=0.9900, 2700 negative triangles 211: dt=0.9900, 2705 negative triangles 212: dt=0.9900, 2656 negative triangles 213: dt=0.9900, 2649 negative triangles 214: dt=0.9900, 2629 negative triangles 215: dt=0.9900, 2629 negative triangles 216: dt=0.9900, 2599 negative triangles 217: dt=0.9900, 2621 negative triangles 218: dt=0.9900, 2611 negative triangles 219: dt=0.9900, 2614 negative triangles 220: dt=0.9900, 2582 negative triangles 221: dt=0.9900, 2589 negative triangles 222: dt=0.9900, 2561 negative triangles 223: dt=0.9900, 2546 negative triangles 224: dt=0.9900, 2549 negative triangles 225: dt=0.9900, 2534 negative triangles 226: dt=0.9900, 2500 negative triangles 227: dt=0.9900, 2515 negative triangles 228: dt=0.9900, 2497 negative triangles 229: dt=0.9900, 2486 negative triangles 230: dt=0.9900, 2477 negative triangles 231: dt=0.9900, 2428 negative triangles 232: dt=0.9900, 2433 negative triangles 233: dt=0.9900, 2418 negative triangles 234: dt=0.9900, 2399 negative triangles 235: dt=0.9900, 2385 negative triangles 236: dt=0.9900, 2382 negative triangles 237: dt=0.9900, 2381 negative triangles 238: dt=0.9900, 2348 negative triangles 239: dt=0.9900, 2343 negative triangles 240: dt=0.9900, 2307 negative triangles 241: dt=0.9900, 2315 negative triangles 242: dt=0.9900, 2288 negative triangles 243: dt=0.9900, 2290 negative triangles 244: dt=0.9900, 2287 negative triangles 245: dt=0.9900, 2278 negative triangles 246: dt=0.9900, 2318 negative triangles 247: dt=0.9900, 2269 negative triangles 248: dt=0.9900, 2264 negative triangles 249: dt=0.9900, 2252 negative triangles 250: dt=0.9900, 2257 negative triangles 251: dt=0.9900, 2244 negative triangles 252: dt=0.9900, 2267 negative triangles 253: dt=0.9900, 2254 negative triangles 254: dt=0.9900, 2241 negative triangles 255: dt=0.9900, 2242 negative triangles 256: dt=0.9900, 2243 negative triangles 257: dt=0.9900, 2213 negative triangles 258: dt=0.9900, 2222 negative triangles 259: dt=0.9900, 2222 negative triangles 260: dt=0.9900, 2205 negative triangles 261: dt=0.9900, 2218 negative triangles 262: dt=0.9900, 2196 negative triangles 263: dt=0.9900, 2185 negative triangles 264: dt=0.9900, 2193 negative triangles 265: dt=0.9900, 2186 negative triangles 266: dt=0.9900, 2193 negative triangles 267: dt=0.9900, 2187 negative triangles 268: dt=0.9900, 2197 negative triangles 269: dt=0.9900, 2188 negative triangles 270: dt=0.9900, 2186 negative triangles 271: dt=0.9900, 2162 negative triangles 272: dt=0.9900, 2155 negative triangles 273: dt=0.9900, 2151 negative triangles 274: dt=0.9900, 2126 negative triangles 275: dt=0.9900, 2137 negative triangles 276: dt=0.9900, 2117 negative triangles 277: dt=0.9900, 2085 negative triangles 278: dt=0.9900, 2115 negative triangles 279: dt=0.9900, 2118 negative triangles 280: dt=0.9900, 2101 negative triangles 281: dt=0.9900, 2093 negative triangles 282: dt=0.9900, 2101 negative triangles 283: dt=0.9900, 2084 negative triangles 284: dt=0.9900, 2082 negative triangles 285: dt=0.9900, 2058 negative triangles 286: dt=0.9900, 2035 negative triangles 287: dt=0.9900, 2052 negative triangles 288: dt=0.9900, 2006 negative triangles 289: dt=0.9900, 2036 negative triangles 290: dt=0.9900, 2009 negative triangles 291: dt=0.9900, 1993 negative triangles 292: dt=0.9900, 1999 negative triangles 293: dt=0.9900, 2003 negative triangles 294: dt=0.9900, 1979 negative triangles 295: dt=0.9900, 1956 negative triangles 296: dt=0.9900, 1949 negative triangles 297: dt=0.9900, 1946 negative triangles 298: dt=0.9900, 1948 negative triangles 299: dt=0.9900, 1956 negative triangles 300: dt=0.9900, 1925 negative triangles 301: dt=0.9900, 1924 negative triangles 302: dt=0.9900, 1928 negative triangles 303: dt=0.9900, 1918 negative triangles 304: dt=0.9900, 1891 negative triangles 305: dt=0.9900, 1893 negative triangles 306: dt=0.9900, 1880 negative triangles 307: dt=0.9900, 1901 negative triangles 308: dt=0.9900, 1869 negative triangles 309: dt=0.9900, 1863 negative triangles 310: dt=0.9900, 1842 negative triangles 311: dt=0.9900, 1848 negative triangles 312: dt=0.9900, 1842 negative triangles 313: dt=0.9900, 1810 negative triangles 314: dt=0.9900, 1825 negative triangles 315: dt=0.9900, 1803 negative triangles 316: dt=0.9900, 1804 negative triangles 317: dt=0.9900, 1797 negative triangles 318: dt=0.9900, 1779 negative triangles 319: dt=0.9900, 1789 negative triangles 320: dt=0.9900, 1779 negative triangles 321: dt=0.9900, 1758 negative triangles 322: dt=0.9900, 1758 negative triangles 323: dt=0.9900, 1744 negative triangles 324: dt=0.9900, 1758 negative triangles 325: dt=0.9900, 1762 negative triangles 326: dt=0.9900, 1744 negative triangles 327: dt=0.9900, 1729 negative triangles 328: dt=0.9900, 1720 negative triangles 329: dt=0.9900, 1718 negative triangles 330: dt=0.9900, 1682 negative triangles 331: dt=0.9900, 1685 negative triangles 332: dt=0.9900, 1681 negative triangles 333: dt=0.9900, 1685 negative triangles 334: dt=0.9900, 1686 negative triangles 335: dt=0.9900, 1672 negative triangles 336: dt=0.9900, 1676 negative triangles 337: dt=0.9900, 1649 negative triangles 338: dt=0.9900, 1649 negative triangles 339: dt=0.9900, 1629 negative triangles 340: dt=0.9900, 1634 negative triangles 341: dt=0.9900, 1633 negative triangles 342: dt=0.9900, 1626 negative triangles 343: dt=0.9900, 1595 negative triangles 344: dt=0.9900, 1604 negative triangles 345: dt=0.9900, 1586 negative triangles 346: dt=0.9900, 1568 negative triangles 347: dt=0.9900, 1572 negative triangles 348: dt=0.9900, 1564 negative triangles 349: dt=0.9900, 1570 negative triangles 350: dt=0.9900, 1532 negative triangles 351: dt=0.9900, 1546 negative triangles 352: dt=0.9900, 1512 negative triangles 353: dt=0.9900, 1538 negative triangles 354: dt=0.9900, 1513 negative triangles 355: dt=0.9900, 1498 negative triangles 356: dt=0.9900, 1475 negative triangles 357: dt=0.9900, 1452 negative triangles 358: dt=0.9900, 1448 negative triangles 359: dt=0.9900, 1445 negative triangles 360: dt=0.9900, 1460 negative triangles 361: dt=0.9900, 1439 negative triangles 362: dt=0.9900, 1406 negative triangles 363: dt=0.9900, 1403 negative triangles 364: dt=0.9900, 1388 negative triangles 365: dt=0.9900, 1394 negative triangles 366: dt=0.9900, 1394 negative triangles 367: dt=0.9900, 1373 negative triangles 368: dt=0.9900, 1362 negative triangles 369: dt=0.9900, 1333 negative triangles 370: dt=0.9900, 1329 negative triangles 371: dt=0.9900, 1315 negative triangles 372: dt=0.9900, 1299 negative triangles 373: dt=0.9900, 1296 negative triangles 374: dt=0.9900, 1279 negative triangles 375: dt=0.9900, 1273 negative triangles 376: dt=0.9900, 1252 negative triangles 377: dt=0.9900, 1239 negative triangles 378: dt=0.9900, 1239 negative triangles 379: dt=0.9900, 1234 negative triangles 380: dt=0.9900, 1204 negative triangles 381: dt=0.9900, 1206 negative triangles 382: dt=0.9900, 1191 negative triangles 383: dt=0.9900, 1183 negative triangles 384: dt=0.9900, 1162 negative triangles 385: dt=0.9900, 1143 negative triangles 386: dt=0.9900, 1145 negative triangles 387: dt=0.9900, 1135 negative triangles 388: dt=0.9900, 1121 negative triangles 389: dt=0.9900, 1096 negative triangles 390: dt=0.9900, 1084 negative triangles 391: dt=0.9900, 1088 negative triangles 392: dt=0.9900, 1044 negative triangles 393: dt=0.9900, 1067 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419: dt=0.9900, 824 negative triangles 420: dt=0.9900, 837 negative triangles 421: dt=0.9900, 815 negative triangles 422: dt=0.9900, 798 negative triangles 423: dt=0.9900, 789 negative triangles 424: dt=0.9900, 775 negative triangles 425: dt=0.9900, 784 negative triangles 426: dt=0.9900, 748 negative triangles 427: dt=0.9900, 740 negative triangles 428: dt=0.9900, 730 negative triangles 429: dt=0.9900, 715 negative triangles 430: dt=0.9900, 710 negative triangles 431: dt=0.9900, 682 negative triangles 432: dt=0.9900, 694 negative triangles 433: dt=0.9900, 660 negative triangles 434: dt=0.9900, 669 negative triangles 435: dt=0.9900, 652 negative triangles 436: dt=0.9900, 635 negative triangles 437: dt=0.9900, 625 negative triangles 438: dt=0.9900, 613 negative triangles 439: dt=0.9900, 623 negative triangles 440: dt=0.9900, 612 negative triangles 441: dt=0.9900, 597 negative triangles 442: dt=0.9900, 584 negative triangles 443: dt=0.9900, 577 negative triangles 444: dt=0.9900, 563 negative triangles 445: dt=0.9900, 568 negative triangles 446: dt=0.9900, 540 negative triangles 447: dt=0.9900, 540 negative triangles 448: dt=0.9900, 524 negative triangles 449: dt=0.9900, 521 negative triangles 450: dt=0.9900, 510 negative triangles 451: dt=0.9900, 493 negative triangles 452: dt=0.9900, 492 negative triangles 453: dt=0.9900, 486 negative triangles 454: dt=0.9900, 474 negative triangles 455: dt=0.9900, 467 negative triangles 456: dt=0.9900, 472 negative triangles 457: dt=0.9900, 452 negative triangles 458: dt=0.9900, 438 negative triangles 459: dt=0.9900, 436 negative triangles 460: dt=0.9900, 417 negative triangles 461: dt=0.9900, 436 negative triangles 462: dt=0.9900, 408 negative triangles 463: dt=0.9900, 402 negative triangles 464: dt=0.9900, 396 negative triangles 465: dt=0.9900, 377 negative triangles 466: dt=0.9900, 356 negative triangles 467: dt=0.9900, 348 negative triangles 468: dt=0.9900, 339 negative triangles 469: dt=0.9900, 323 negative triangles 470: dt=0.9900, 325 negative triangles 471: dt=0.9900, 311 negative triangles 472: dt=0.9900, 291 negative triangles 473: dt=0.9900, 283 negative triangles 474: dt=0.9900, 285 negative triangles 475: dt=0.9900, 276 negative triangles 476: dt=0.9900, 270 negative triangles 477: dt=0.9900, 255 negative triangles 478: dt=0.9900, 254 negative triangles 479: dt=0.9900, 247 negative triangles 480: dt=0.9900, 255 negative triangles 481: dt=0.9900, 242 negative triangles 482: dt=0.9900, 252 negative triangles 483: dt=0.9900, 250 negative triangles 484: dt=0.9900, 247 negative triangles 485: dt=0.9900, 242 negative triangles 486: dt=0.9900, 246 negative triangles 487: dt=0.9900, 236 negative triangles 488: dt=0.9900, 236 negative triangles 489: dt=0.9900, 231 negative triangles 490: dt=0.9900, 235 negative triangles 491: dt=0.9900, 236 negative triangles 492: dt=0.9900, 232 negative triangles 493: dt=0.9900, 235 negative triangles 494: dt=0.9900, 232 negative triangles 495: dt=0.9900, 234 negative triangles 496: dt=0.9900, 238 negative triangles 497: dt=0.9900, 229 negative triangles 498: dt=0.9900, 236 negative triangles 499: dt=0.9900, 231 negative triangles 500: dt=0.9900, 240 negative triangles 501: dt=0.9900, 232 negative triangles 502: dt=0.9900, 235 negative triangles 503: dt=0.9900, 239 negative triangles 504: dt=0.9900, 238 negative triangles 505: dt=0.9900, 228 negative triangles 506: dt=0.9900, 237 negative triangles 507: dt=0.9900, 231 negative triangles 508: dt=0.9900, 222 negative triangles 509: dt=0.9900, 231 negative triangles 510: dt=0.9900, 233 negative triangles 511: dt=0.9900, 228 negative triangles 512: dt=0.9900, 232 negative triangles 513: dt=0.9900, 222 negative triangles 514: dt=0.9900, 231 negative triangles 515: dt=0.9900, 222 negative triangles 516: dt=0.9900, 226 negative triangles 517: dt=0.9900, 225 negative triangles 518: dt=0.9900, 216 negative triangles 519: dt=0.9900, 224 negative triangles 520: dt=0.9900, 220 negative triangles 521: dt=0.9900, 216 negative triangles 522: dt=0.9900, 218 negative triangles 523: dt=0.9900, 206 negative triangles 524: dt=0.9900, 210 negative triangles 525: dt=0.9900, 210 negative triangles 526: dt=0.9900, 206 negative triangles 527: dt=0.9900, 211 negative triangles 528: dt=0.9900, 209 negative triangles 529: dt=0.9900, 195 negative triangles 530: dt=0.9900, 210 negative triangles 531: dt=0.9900, 211 negative triangles 532: dt=0.9900, 211 negative triangles 533: dt=0.9900, 211 negative triangles 534: dt=0.9900, 208 negative triangles 535: dt=0.9900, 208 negative triangles 536: dt=0.9900, 204 negative triangles 537: dt=0.9900, 213 negative triangles 538: dt=0.9900, 211 negative triangles 539: dt=0.9405, 217 negative triangles 540: dt=0.9405, 217 negative triangles 541: dt=0.9405, 211 negative triangles 542: dt=0.9405, 203 negative triangles 543: dt=0.9405, 213 negative triangles 544: dt=0.9405, 205 negative triangles 545: dt=0.9405, 203 negative triangles 546: dt=0.9405, 203 negative triangles 547: dt=0.9405, 204 negative triangles 548: dt=0.9405, 202 negative triangles 549: dt=0.8935, 200 negative triangles 550: dt=0.8935, 200 negative triangles 551: dt=0.8935, 207 negative triangles 552: dt=0.8935, 198 negative triangles 553: dt=0.8935, 201 negative triangles 554: dt=0.8935, 195 negative triangles 555: dt=0.8935, 192 negative triangles 556: dt=0.8935, 188 negative triangles 557: dt=0.8935, 197 negative triangles 558: dt=0.8935, 188 negative triangles 559: dt=0.8935, 188 negative triangles 560: dt=0.8935, 178 negative triangles 561: dt=0.8935, 184 negative triangles 562: dt=0.8935, 178 negative triangles 563: dt=0.8935, 179 negative triangles 564: dt=0.8935, 174 negative triangles 565: dt=0.8935, 169 negative triangles 566: dt=0.8935, 185 negative triangles 567: dt=0.8935, 165 negative triangles 568: dt=0.8935, 179 negative triangles 569: dt=0.8935, 171 negative triangles 570: dt=0.8935, 169 negative triangles 571: dt=0.8935, 172 negative triangles 572: dt=0.8935, 163 negative triangles 573: dt=0.8935, 160 negative triangles 574: dt=0.8935, 166 negative triangles 575: dt=0.8935, 167 negative triangles 576: dt=0.8935, 159 negative triangles 577: dt=0.8935, 161 negative triangles 578: dt=0.8935, 171 negative triangles 579: dt=0.8935, 156 negative triangles 580: dt=0.8935, 164 negative triangles 581: dt=0.8935, 164 negative triangles 582: dt=0.8935, 160 negative triangles 583: dt=0.8935, 155 negative triangles 584: dt=0.8935, 152 negative triangles 585: dt=0.8935, 158 negative triangles 586: dt=0.8935, 151 negative triangles 587: dt=0.8935, 156 negative triangles 588: dt=0.8935, 153 negative triangles 589: dt=0.8935, 156 negative triangles 590: dt=0.8935, 158 negative triangles 591: dt=0.8935, 158 negative triangles 592: dt=0.8935, 148 negative triangles 593: dt=0.8935, 154 negative triangles 594: dt=0.8935, 149 negative triangles 595: dt=0.8935, 136 negative triangles 596: dt=0.8935, 145 negative triangles 597: dt=0.8935, 144 negative triangles 598: dt=0.8935, 140 negative triangles 599: dt=0.8935, 138 negative triangles 600: dt=0.8935, 141 negative triangles 601: dt=0.8935, 126 negative triangles 602: dt=0.8935, 129 negative triangles 603: dt=0.8935, 130 negative triangles 604: dt=0.8935, 125 negative triangles 605: dt=0.8935, 124 negative triangles 606: dt=0.8935, 130 negative triangles 607: dt=0.8935, 125 negative triangles 608: dt=0.8935, 122 negative triangles 609: dt=0.8935, 119 negative triangles 610: dt=0.8935, 122 negative triangles 611: dt=0.8935, 125 negative triangles 612: dt=0.8935, 116 negative triangles 613: dt=0.8935, 119 negative triangles 614: dt=0.8935, 117 negative triangles 615: dt=0.8935, 115 negative triangles 616: dt=0.8935, 114 negative triangles 617: dt=0.8935, 110 negative triangles 618: dt=0.8935, 110 negative triangles 619: dt=0.8935, 106 negative triangles 620: dt=0.8935, 111 negative triangles 621: dt=0.8935, 101 negative triangles 622: dt=0.8935, 103 negative triangles 623: dt=0.8935, 93 negative triangles 624: dt=0.8935, 97 negative triangles 625: dt=0.8935, 103 negative triangles 626: dt=0.8935, 98 negative triangles 627: dt=0.8935, 93 negative triangles 628: dt=0.8935, 90 negative triangles 629: dt=0.8935, 90 negative triangles 630: dt=0.8935, 92 negative triangles 631: dt=0.8935, 86 negative triangles 632: dt=0.8935, 84 negative triangles 633: dt=0.8935, 88 negative triangles 634: dt=0.8935, 91 negative triangles 635: dt=0.8935, 84 negative triangles 636: dt=0.8935, 77 negative triangles 637: dt=0.8935, 72 negative triangles 638: dt=0.8935, 75 negative triangles 639: dt=0.8935, 69 negative triangles 640: dt=0.8935, 67 negative triangles 641: dt=0.8935, 65 negative triangles 642: dt=0.8935, 62 negative triangles 643: dt=0.8935, 64 negative triangles 644: dt=0.8935, 52 negative triangles 645: dt=0.8935, 61 negative triangles 646: dt=0.8935, 50 negative triangles 647: dt=0.8935, 52 negative triangles 648: dt=0.8935, 49 negative triangles 649: dt=0.8935, 46 negative triangles 650: dt=0.8935, 47 negative triangles 651: dt=0.8935, 49 negative triangles 652: dt=0.8935, 38 negative triangles 653: dt=0.8935, 33 negative triangles 654: dt=0.8935, 31 negative triangles 655: dt=0.8935, 19 negative triangles 656: dt=0.8935, 23 negative triangles 657: dt=0.8935, 18 negative triangles 658: dt=0.8935, 17 negative triangles 659: dt=0.8935, 13 negative triangles 660: dt=0.8935, 11 negative triangles 661: dt=0.8935, 9 negative triangles 662: dt=0.8935, 8 negative triangles 663: dt=0.8935, 3 negative triangles 664: dt=0.8935, 2 negative triangles 665: dt=0.8935, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 16.24 hours mris_sphere utimesec 28921.058545 mris_sphere stimesec 19.792387 mris_sphere ru_maxrss 1519924 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 4307040 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 2028932 mris_sphere ru_nivcsw 2421636 FSRUNTIME@ mris_sphere 16.2443 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Mon Jan 14 16:18:28 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.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.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.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.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/rh.sphere... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= 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 1 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 rh.sulc curvature mean = 0.000, std = 4.398 curvature mean = 0.020, std = 0.802 curvature mean = 0.019, std = 0.810 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 1990349.5, tmin=12.7549 d=32.00 min @ (0.00, -8.00, -8.00) sse = 1632727.8, tmin=25.6015 d=16.00 min @ (4.00, 4.00, 4.00) sse = 1478288.6, tmin=38.4917 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 1438112.4, tmin=51.5213 d=4.00 min @ (1.00, 0.00, 0.00) sse = 1434383.5, tmin=64.5803 d=2.00 min @ (-0.50, 0.00, -0.50) sse = 1433585.2, tmin=80.4693 d=1.00 min @ (0.00, 0.00, 0.25) sse = 1433142.1, tmin=133.9384 d=0.50 min @ (0.12, 0.00, 0.00) sse = 1433024.4, tmin=186.4348