Sat Oct 7 16:31:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050815 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/KKI_4/0050815/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0050815 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Actual FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux tars-551 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse 10485760 kbytes vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 65993948 56823204 9170744 1758704 0 53754960 -/+ buffers/cache: 3068244 62925704 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: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.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: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.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: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.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: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.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: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:31:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: ntraut Machine: tars-551 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/KKI_4/0050815/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/KKI_4/0050815/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/KKI_4/0050815/session_1/anat_1/mprage.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 16:31:09 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 16:31:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux tars-551 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 16:31:18 CEST 2017 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 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.9490 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9490/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9490/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9490/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:31:20 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9490/nu0.mnc ./tmp.mri_nu_correct.mni.9490/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9490/0/ -iterations 1000 -distance 50 [ntraut@tars-551:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/] [2017-10-07 16:31:20] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9490/0/ ./tmp.mri_nu_correct.mni.9490/nu0.mnc ./tmp.mri_nu_correct.mni.9490/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 31 CV of field change: 0.000979716 mri_convert ./tmp.mri_nu_correct.mni.9490/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9490/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.9490/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat Oct 7 16:32:20 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Oct 7 16:32:20 CEST 2017 Ended at Sat Oct 7 16:32:50 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 16:32:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7422, pval=0.6675 >= threshold=0.0050) awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/transforms/talairach_avi.log TalAviQA: 0.97461 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 16:32:52 CEST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux tars-551 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 16:32:52 CEST 2017 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 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.10164 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10164/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10164/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10164/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:32:54 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10164/nu0.mnc ./tmp.mri_nu_correct.mni.10164/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10164/0/ [ntraut@tars-551:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/] [2017-10-07 16:32:54] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10164/0/ ./tmp.mri_nu_correct.mni.10164/nu0.mnc ./tmp.mri_nu_correct.mni.10164/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000993847 -------------------------------------------------------- Iteration 2 Sat Oct 7 16:33:34 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10164/nu1.mnc ./tmp.mri_nu_correct.mni.10164/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10164/1/ [ntraut@tars-551:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/] [2017-10-07 16:33:34] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10164/1/ ./tmp.mri_nu_correct.mni.10164/nu1.mnc ./tmp.mri_nu_correct.mni.10164/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 14 CV of field change: 0.000973781 mri_binarize --i ./tmp.mri_nu_correct.mni.10164/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10164/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10164/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10164/ones.mgz sysname Linux hostname tars-551 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.10164/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.10164/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10164/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10164/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10164/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10164/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10164/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10164/input.mean.dat sysname Linux hostname tars-551 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10164/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.10164/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10164/ones.mgz --i ./tmp.mri_nu_correct.mni.10164/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10164/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10164/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10164/ones.mgz --i ./tmp.mri_nu_correct.mni.10164/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10164/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10164/output.mean.dat sysname Linux hostname tars-551 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10164/ones.mgz Loading ./tmp.mri_nu_correct.mni.10164/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.10164/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.10164/nu2.mnc ./tmp.mri_nu_correct.mni.10164/nu2.mnc mul 1.04055382522017564117 Saving result to './tmp.mri_nu_correct.mni.10164/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.10164/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.10164/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.10164/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping (10, 129) to ( 3, 110) Sat Oct 7 16:34:41 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 16:34:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.06606 0.03765 0.00917 10.83012; -0.03083 0.95548 0.29125 1.84535; -0.02558 -0.24101 1.11999 -27.52129; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 6 Starting OpenSpline(): npoints = 6 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 58 (58), valley at 43 (43) csf peak at 29, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 89 gm peak at 55 (55), valley at 25 (25) csf peak at 14, setting threshold to 41 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 6 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 16:36:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (48, 46, 26) --> (208, 193, 228) using (101, 95, 127) as brain centroid... mean wm in atlas = 108, using box (81,77,102) --> (120, 113,151) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 105 +- 13.1 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.474 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.474477 @ (0.000, 0.000, 0.000) max log p = -4.264393 @ (-4.545, -4.545, -13.636) max log p = -4.264393 @ (0.000, 0.000, 0.000) max log p = -4.251993 @ (1.136, -1.136, -1.136) max log p = -4.201511 @ (-1.705, 1.705, -3.977) max log p = -4.201511 @ (0.000, 0.000, 0.000) Found translation: (-5.1, -4.0, -18.8): log p = -4.202 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.994, old_max_log_p =-4.202 (thresh=-4.2) 1.06375 0.00000 0.00000 -13.40042; 0.00000 1.11081 0.29764 -51.26917; 0.00000 -0.27532 1.02750 17.92177; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.994, old_max_log_p =-3.994 (thresh=-4.0) 1.06375 0.00000 0.00000 -13.40042; 0.00000 1.11081 0.29764 -51.26917; 0.00000 -0.27532 1.02750 17.92177; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.901, old_max_log_p =-3.994 (thresh=-4.0) 1.04334 0.00515 -0.03461 -5.24322; -0.00266 1.18381 0.27400 -55.98196; 0.03779 -0.23433 1.01592 8.88465; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.901, old_max_log_p =-3.901 (thresh=-3.9) 1.04334 0.00515 -0.03461 -5.24322; -0.00266 1.18381 0.27400 -55.98196; 0.03779 -0.23433 1.01592 8.88465; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.875, old_max_log_p =-3.901 (thresh=-3.9) 1.04604 -0.00668 -0.02873 -4.70422; 0.00634 1.18322 0.28240 -58.12589; 0.02934 -0.24461 1.01627 11.81291; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.871, old_max_log_p =-3.875 (thresh=-3.9) 1.04359 -0.00667 -0.02867 -4.40052; 0.00633 1.18184 0.28207 -57.89116; 0.02934 -0.24461 1.01627 11.81291; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.869, old_max_log_p =-3.871 (thresh=-3.9) 1.04359 -0.00667 -0.02867 -4.40052; 0.00656 1.17841 0.29003 -57.99115; 0.02929 -0.25427 1.01393 13.45299; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04359 -0.00667 -0.02867 -4.40052; 0.00656 1.17841 0.29003 -57.99115; 0.02929 -0.25427 1.01393 13.45299; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.04359 -0.00667 -0.02867 -4.40052; 0.00656 1.17841 0.29003 -57.99115; 0.02929 -0.25427 1.01393 13.45299; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04359 -0.00667 -0.02867 -4.40052; 0.00656 1.17841 0.29003 -57.99115; 0.02929 -0.25427 1.01393 13.45299; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.869 (old=-4.474) transform before final EM align: 1.04359 -0.00667 -0.02867 -4.40052; 0.00656 1.17841 0.29003 -57.99115; 0.02929 -0.25427 1.01393 13.45299; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04359 -0.00667 -0.02867 -4.40052; 0.00656 1.17841 0.29003 -57.99115; 0.02929 -0.25427 1.01393 13.45299; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.04359 -0.00667 -0.02867 -4.40052; 0.00656 1.17841 0.29003 -57.99115; 0.02929 -0.25427 1.01393 13.45299; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.3 tol 0.000000 final transform: 1.04359 -0.00667 -0.02867 -4.40052; 0.00656 1.17841 0.29003 -57.99115; 0.02929 -0.25427 1.01393 13.45299; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1256.175032 mri_em_register stimesec 1.586758 mri_em_register ru_maxrss 609824 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157598 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 2347 mri_em_register ru_nivcsw 7714 registration took 10 minutes and 55 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=130 y=112 z=125 r=69 first estimation of the main basin volume: 1404763 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=105, y=96, z=119, Imax=255 CSF=15, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=8543849093 voxels, voxel volume =1.000 = 8543849093 mmm3 = 8543848.960 cm3 done. PostAnalyze...Basin Prior 237 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=121, z=116, r=10470 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=50 , nb = 43856 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=47 , nb = -1038944217 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=44 , nb = -1039104202 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=48 , nb = -1056263196 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=52 , nb = 1060165302 OTHER CSF_MIN=0, CSF_intensity=23, CSF_MAX=55 , nb = 1077832686 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 50, 33, 21, 50 after analyzing : 26, 33, 33, 37 RIGHT_CER before analyzing : 47, 32, 21, 50 after analyzing : 26, 32, 32, 36 LEFT_CER before analyzing : 44, 31, 21, 50 after analyzing : 25, 31, 31, 35 RIGHT_BRAIN before analyzing : 48, 32, 21, 51 after analyzing : 26, 32, 32, 36 LEFT_BRAIN before analyzing : 52, 33, 23, 49 after analyzing : 26, 33, 33, 37 OTHER before analyzing : 55, 37, 21, 50 after analyzing : 32, 37, 37, 40 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 69.921, std = 8.370 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.01, sigma = 4.34 after rotation: sse = 3.01, sigma = 4.34 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.12, its var is 3.99 before Erosion-Dilatation 0.31% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...30 iterations mri_strip_skull: done peeling brain Brain Size = 1615982 voxels, voxel volume = 1.000 mm3 = 1615982 mmm3 = 1615.982 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 22.542573 mri_watershed stimesec 0.361944 mri_watershed ru_maxrss 820348 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212414 mri_watershed ru_majflt 2 mri_watershed ru_nswap 0 mri_watershed ru_inblock 12640 mri_watershed ru_oublock 2864 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1114 mri_watershed ru_nivcsw 919 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 16:48:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (56, 63, 42) --> (199, 187, 216) using (104, 104, 129) as brain centroid... mean wm in atlas = 107, using box (86,89,108) --> (121, 119,150) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 105 +- 11.8 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.304 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.212747 @ (-9.091, -9.091, -9.091) max log p = -3.981273 @ (4.545, 4.545, -4.545) max log p = -3.903367 @ (2.273, 2.273, -2.273) max log p = -3.903367 @ (0.000, 0.000, 0.000) max log p = -3.879127 @ (0.568, 2.841, 2.841) max log p = -3.879127 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 0.6, -13.1): log p = -3.879 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.725, old_max_log_p =-3.879 (thresh=-3.9) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.11081 0.29764 -47.86224; 0.00000 -0.25882 0.96593 21.69751; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.725, old_max_log_p =-3.725 (thresh=-3.7) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.11081 0.29764 -47.86224; 0.00000 -0.25882 0.96593 21.69751; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.585, old_max_log_p =-3.725 (thresh=-3.7) 1.01734 0.00419 -0.03569 -0.19136; 0.00404 1.13178 0.29815 -52.72718; 0.02945 -0.25930 0.94563 22.50247; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.578, old_max_log_p =-3.585 (thresh=-3.6) 1.01583 0.01267 -0.06661 2.59038; 0.00404 1.13178 0.29815 -52.72718; 0.06155 -0.25417 0.92625 20.02610; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.578, old_max_log_p =-3.578 (thresh=-3.6) 1.01583 0.01267 -0.06661 2.59038; 0.00404 1.13178 0.29815 -52.72718; 0.06155 -0.25417 0.92625 20.02610; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.544, old_max_log_p =-3.578 (thresh=-3.6) 1.01630 0.01054 -0.05903 1.43200; 0.00398 1.12784 0.29698 -52.10687; 0.05344 -0.25501 0.93007 20.25334; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.542, old_max_log_p =-3.544 (thresh=-3.5) 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.542 (old=-4.304) transform before final EM align: 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1169.888149 mri_em_register stimesec 1.654748 mri_em_register ru_maxrss 599052 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158949 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 13268 mri_em_register ru_nivcsw 4370 registration took 10 minutes and 17 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 16:58:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (56, 63, 42) --> (199, 187, 216) using (104, 104, 129) as brain centroid... mean wm in atlas = 107, using box (86,89,108) --> (121, 119,150) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 105 +- 11.8 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.01749 0.01056 -0.05910 1.28517; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15351; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 63, 39) --> (193, 167, 208) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 62, 39) --> (132, 159, 209) Right_Cerebral_White_Matter: limiting intensities to 108.0 --> 132.0 11 of 14 (78.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 144, 68) --> (176, 182, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 8 (87.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 144, 67) --> (127, 180, 126) finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 130, 105) --> (146, 191, 136) Brain_Stem: limiting intensities to 103.0 --> 132.0 8 of 9 (88.9%) samples deleted using 47 total control points for intensity normalization... bias field = 0.983 +- 0.065 0 of 21 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 63, 39) --> (193, 167, 208) Left_Cerebral_White_Matter: limiting intensities to 120.0 --> 132.0 75 of 83 (90.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 62, 39) --> (132, 159, 209) Right_Cerebral_White_Matter: limiting intensities to 113.0 --> 132.0 49 of 80 (61.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 144, 68) --> (176, 182, 124) finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 144, 67) --> (127, 180, 126) finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 130, 105) --> (146, 191, 136) Brain_Stem: limiting intensities to 109.0 --> 132.0 38 of 41 (92.7%) samples deleted using 204 total control points for intensity normalization... bias field = 0.876 +- 0.050 0 of 42 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 63, 39) --> (193, 167, 208) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 183 (13.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 62, 39) --> (132, 159, 209) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 36 of 182 (19.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 144, 68) --> (176, 182, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 11 of 11 (100.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 144, 67) --> (127, 180, 126) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 9 (100.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 130, 105) --> (146, 191, 136) Brain_Stem: limiting intensities to 88.0 --> 132.0 58 of 61 (95.1%) samples deleted using 446 total control points for intensity normalization... bias field = 1.072 +- 0.075 0 of 303 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 49 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 17:00:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.15 (predicted orig area = 7.0) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.877, neg=0, invalid=762 0001: dt=223.019973, rms=0.809 (7.812%), neg=0, invalid=762 0002: dt=228.155844, rms=0.794 (1.855%), neg=0, invalid=762 0003: dt=168.106667, rms=0.784 (1.174%), neg=0, invalid=762 0004: dt=295.936000, rms=0.778 (0.794%), neg=0, invalid=762 0005: dt=156.190476, rms=0.773 (0.635%), neg=0, invalid=762 0006: dt=369.920000, rms=0.769 (0.529%), neg=0, invalid=762 0007: dt=137.513514, rms=0.765 (0.454%), neg=0, invalid=762 0008: dt=517.888000, rms=0.762 (0.481%), neg=0, invalid=762 0009: dt=129.472000, rms=0.759 (0.367%), neg=0, invalid=762 0010: dt=517.888000, rms=0.756 (0.371%), neg=0, invalid=762 0011: dt=129.472000, rms=0.755 (0.210%), neg=0, invalid=762 0012: dt=129.472000, rms=0.754 (0.101%), neg=0, invalid=762 0013: dt=129.472000, rms=0.753 (0.174%), neg=0, invalid=762 0014: dt=129.472000, rms=0.751 (0.243%), neg=0, invalid=762 0015: dt=129.472000, rms=0.749 (0.283%), neg=0, invalid=762 0016: dt=129.472000, rms=0.746 (0.300%), neg=0, invalid=762 0017: dt=129.472000, rms=0.744 (0.310%), neg=0, invalid=762 0018: dt=129.472000, rms=0.742 (0.295%), neg=0, invalid=762 0019: dt=129.472000, rms=0.740 (0.264%), neg=0, invalid=762 0020: dt=129.472000, rms=0.738 (0.217%), neg=0, invalid=762 0021: dt=129.472000, rms=0.737 (0.184%), neg=0, invalid=762 0022: dt=129.472000, rms=0.736 (0.181%), neg=0, invalid=762 0023: dt=129.472000, rms=0.734 (0.187%), neg=0, invalid=762 0024: dt=129.472000, rms=0.733 (0.184%), neg=0, invalid=762 0025: dt=129.472000, rms=0.731 (0.181%), neg=0, invalid=762 0026: dt=129.472000, rms=0.730 (0.159%), neg=0, invalid=762 0027: dt=129.472000, rms=0.729 (0.158%), neg=0, invalid=762 0028: dt=129.472000, rms=0.728 (0.164%), neg=0, invalid=762 0029: dt=129.472000, rms=0.727 (0.141%), neg=0, invalid=762 0030: dt=129.472000, rms=0.726 (0.133%), neg=0, invalid=762 0031: dt=129.472000, rms=0.725 (0.120%), neg=0, invalid=762 0032: dt=129.472000, rms=0.724 (0.114%), neg=0, invalid=762 0033: dt=517.888000, rms=0.724 (0.079%), neg=0, invalid=762 0034: dt=517.888000, rms=0.724 (-0.140%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.725, neg=0, invalid=762 0035: dt=221.952000, rms=0.723 (0.308%), neg=0, invalid=762 0036: dt=369.920000, rms=0.722 (0.091%), neg=0, invalid=762 0037: dt=369.920000, rms=0.722 (0.057%), neg=0, invalid=762 0038: dt=369.920000, rms=0.721 (0.142%), neg=0, invalid=762 0039: dt=369.920000, rms=0.720 (0.074%), neg=0, invalid=762 0040: dt=369.920000, rms=0.719 (0.129%), neg=0, invalid=762 0041: dt=369.920000, rms=0.718 (0.118%), neg=0, invalid=762 0042: dt=369.920000, rms=0.718 (0.042%), neg=0, invalid=762 0043: dt=129.472000, rms=0.718 (0.042%), neg=0, invalid=762 0044: dt=129.472000, rms=0.718 (0.011%), neg=0, invalid=762 0045: dt=129.472000, rms=0.718 (0.016%), neg=0, invalid=762 0046: dt=129.472000, rms=0.717 (0.023%), neg=0, invalid=762 0047: dt=129.472000, rms=0.717 (0.024%), neg=0, invalid=762 0048: dt=129.472000, rms=0.717 (0.029%), neg=0, invalid=762 0049: dt=129.472000, rms=0.717 (0.017%), neg=0, invalid=762 0050: dt=129.472000, rms=0.717 (0.022%), neg=0, invalid=762 0051: dt=129.472000, rms=0.717 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.724, neg=0, invalid=762 0052: dt=200.373832, rms=0.715 (1.273%), neg=0, invalid=762 0053: dt=182.582583, rms=0.705 (1.423%), neg=0, invalid=762 0054: dt=73.076364, rms=0.700 (0.657%), neg=0, invalid=762 0055: dt=248.832000, rms=0.695 (0.674%), neg=0, invalid=762 0056: dt=65.607306, rms=0.691 (0.627%), neg=0, invalid=762 0057: dt=145.152000, rms=0.689 (0.333%), neg=0, invalid=762 0058: dt=78.147368, rms=0.686 (0.358%), neg=0, invalid=762 0059: dt=87.317829, rms=0.685 (0.163%), neg=0, invalid=762 0060: dt=87.317829, rms=0.683 (0.280%), neg=0, invalid=762 0061: dt=87.317829, rms=0.681 (0.360%), neg=0, invalid=762 0062: dt=87.317829, rms=0.678 (0.448%), neg=0, invalid=762 0063: dt=87.317829, rms=0.674 (0.511%), neg=0, invalid=762 0064: dt=87.317829, rms=0.670 (0.610%), neg=0, invalid=762 0065: dt=87.317829, rms=0.667 (0.508%), neg=0, invalid=762 0066: dt=87.317829, rms=0.664 (0.391%), neg=0, invalid=762 0067: dt=87.317829, rms=0.662 (0.373%), neg=0, invalid=762 0068: dt=87.317829, rms=0.659 (0.379%), neg=0, invalid=762 0069: dt=87.317829, rms=0.657 (0.288%), neg=0, invalid=762 0070: dt=87.317829, rms=0.656 (0.199%), neg=0, invalid=762 0071: dt=87.317829, rms=0.655 (0.194%), neg=0, invalid=762 0072: dt=87.317829, rms=0.653 (0.189%), neg=0, invalid=762 0073: dt=87.317829, rms=0.653 (0.117%), neg=0, invalid=762 0074: dt=87.317829, rms=0.652 (0.085%), neg=0, invalid=762 0075: dt=124.416000, rms=0.652 (0.093%), neg=0, invalid=762 0076: dt=20.736000, rms=0.651 (0.013%), neg=0, invalid=762 0077: dt=20.736000, rms=0.652 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0078: dt=36.288000, rms=0.651 (0.291%), neg=0, invalid=762 0079: dt=36.288000, rms=0.651 (0.023%), neg=0, invalid=762 0080: dt=36.288000, rms=0.651 (0.006%), neg=0, invalid=762 0081: dt=36.288000, rms=0.651 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0082: dt=6.400000, rms=0.682 (0.281%), neg=0, invalid=762 0083: dt=2.000000, rms=0.682 (0.004%), neg=0, invalid=762 0084: dt=2.000000, rms=0.682 (0.004%), neg=0, invalid=762 0085: dt=2.000000, rms=0.682 (-0.018%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.683, neg=0, invalid=762 0086: dt=0.000000, rms=0.682 (0.211%), neg=0, invalid=762 0087: dt=0.000000, rms=0.682 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.765, neg=0, invalid=762 0088: dt=6.255319, rms=0.739 (3.374%), neg=0, invalid=762 0089: dt=5.200000, rms=0.736 (0.345%), neg=0, invalid=762 0090: dt=3.456000, rms=0.736 (0.041%), neg=0, invalid=762 0091: dt=3.456000, rms=0.736 (0.015%), neg=0, invalid=762 0092: dt=3.456000, rms=0.736 (-0.103%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.737, neg=0, invalid=762 0093: dt=0.000000, rms=0.736 (0.164%), neg=0, invalid=762 0094: dt=0.000000, rms=0.736 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.792, neg=0, invalid=762 0095: dt=0.000000, rms=0.791 (0.142%), neg=0, invalid=762 0096: dt=0.000000, rms=0.791 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.792, neg=0, invalid=762 0097: dt=0.112000, rms=0.790 (0.151%), neg=0, invalid=762 0098: dt=0.112000, rms=0.790 (0.002%), neg=0, invalid=762 0099: dt=0.112000, rms=0.790 (0.003%), neg=0, invalid=762 0100: dt=0.112000, rms=0.790 (-0.010%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.704, neg=0, invalid=762 0101: dt=0.842030, rms=0.684 (2.793%), neg=0, invalid=762 0102: dt=0.080000, rms=0.683 (0.136%), neg=0, invalid=762 0103: dt=0.080000, rms=0.683 (-0.083%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0104: dt=0.028000, rms=0.683 (0.205%), neg=0, invalid=762 0105: dt=0.016000, rms=0.683 (0.002%), neg=0, invalid=762 0106: dt=0.016000, rms=0.683 (-0.004%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.06531 (55) Left_Lateral_Ventricle (4): linear fit = 2.60 x + 0.0 (628 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (628 voxels, peak = 52), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.05468 (10) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (612 voxels, overlap=0.589) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (612 voxels, peak = 17), gca=16.6 gca peak = 0.26829 (96) mri peak = 0.15773 (75) Right_Pallidum (52): linear fit = 0.80 x + 0.0 (819 voxels, overlap=0.023) Right_Pallidum (52): linear fit = 0.80 x + 0.0 (819 voxels, peak = 76), gca=76.3 gca peak = 0.20183 (93) mri peak = 0.12536 (80) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (678 voxels, overlap=0.029) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (678 voxels, peak = 79), gca=78.6 gca peak = 0.21683 (55) mri peak = 0.08081 (53) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (312 voxels, overlap=0.862) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (312 voxels, peak = 52), gca=52.0 gca peak = 0.30730 (58) mri peak = 0.09426 (51) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (332 voxels, overlap=0.661) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (332 voxels, peak = 53), gca=53.1 gca peak = 0.11430 (101) mri peak = 0.05330 (98) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52250 voxels, overlap=0.977) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52250 voxels, peak = 102), gca=101.5 gca peak = 0.12076 (102) mri peak = 0.04863 (101) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (49871 voxels, overlap=0.978) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (49871 voxels, peak = 104), gca=103.5 gca peak = 0.14995 (59) mri peak = 0.03623 (51) Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (13542 voxels, overlap=0.434) Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (13542 voxels, peak = 53), gca=52.8 gca peak = 0.15082 (58) mri peak = 0.03666 (46) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (16248 voxels, overlap=0.755) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (16248 voxels, peak = 52), gca=51.9 gca peak = 0.14161 (67) mri peak = 0.10063 (53) Right_Caudate (50): linear fit = 0.80 x + 0.0 (654 voxels, overlap=0.038) Right_Caudate (50): linear fit = 0.80 x + 0.0 (654 voxels, peak = 53), gca=53.3 gca peak = 0.15243 (71) mri peak = 0.05525 (63) Left_Caudate (11): linear fit = 0.86 x + 0.0 (936 voxels, overlap=0.279) Left_Caudate (11): linear fit = 0.86 x + 0.0 (936 voxels, peak = 61), gca=60.7 gca peak = 0.13336 (57) mri peak = 0.03524 (47) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (12624 voxels, overlap=0.912) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (12624 voxels, peak = 54), gca=53.9 gca peak = 0.13252 (56) mri peak = 0.03549 (53) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (13914 voxels, overlap=0.905) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (13914 voxels, peak = 53), gca=52.9 gca peak = 0.18181 (84) mri peak = 0.03432 (80) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (4698 voxels, overlap=0.473) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (4698 voxels, peak = 78), gca=77.7 gca peak = 0.20573 (83) mri peak = 0.03744 (80) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (3666 voxels, overlap=0.986) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (3666 voxels, peak = 81), gca=80.9 gca peak = 0.21969 (57) mri peak = 0.07488 (50) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (139 voxels, overlap=0.771) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (139 voxels, peak = 51), gca=51.0 gca peak = 0.39313 (56) mri peak = 0.11765 (53) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (106 voxels, overlap=0.913) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (106 voxels, peak = 52), gca=52.4 gca peak = 0.14181 (85) mri peak = 0.10199 (75) Left_Thalamus_Proper (10): linear fit = 0.89 x + 0.0 (5458 voxels, overlap=0.756) Left_Thalamus_Proper (10): linear fit = 0.89 x + 0.0 (5458 voxels, peak = 76), gca=76.1 gca peak = 0.11978 (83) mri peak = 0.14411 (75) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4433 voxels, overlap=0.787) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4433 voxels, peak = 79), gca=79.3 gca peak = 0.13399 (79) mri peak = 0.05287 (76) Left_Putamen (12): linear fit = 0.94 x + 0.0 (2068 voxels, overlap=0.945) Left_Putamen (12): linear fit = 0.94 x + 0.0 (2068 voxels, peak = 75), gca=74.7 gca peak = 0.14159 (79) mri peak = 0.08464 (63) Right_Putamen (51): linear fit = 0.82 x + 0.0 (2377 voxels, overlap=0.348) Right_Putamen (51): linear fit = 0.82 x + 0.0 (2377 voxels, peak = 65), gca=65.2 gca peak = 0.10025 (80) mri peak = 0.11595 (80) Brain_Stem (16): linear fit = 1.07 x + 0.0 (6270 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.07 x + 0.0 (6270 voxels, peak = 85), gca=85.2 gca peak = 0.13281 (86) mri peak = 0.11982 (80) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (645 voxels, overlap=0.614) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (645 voxels, peak = 88), gca=88.2 gca peak = 0.12801 (89) mri peak = 0.11842 (80) Left_VentralDC (28): linear fit = 0.93 x + 0.0 (879 voxels, overlap=0.817) Left_VentralDC (28): linear fit = 0.93 x + 0.0 (879 voxels, peak = 82), gca=82.3 gca peak = 0.20494 (23) mri peak = 0.04285 (10) gca peak = 0.15061 (21) mri peak = 0.07369 (12) Fourth_Ventricle (15): linear fit = 0.62 x + 0.0 (279 voxels, overlap=0.345) Fourth_Ventricle (15): linear fit = 0.62 x + 0.0 (279 voxels, peak = 13), gca=13.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.27 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.682, neg=0, invalid=762 0107: dt=144.888889, rms=0.677 (0.703%), neg=0, invalid=762 0108: dt=369.920000, rms=0.674 (0.448%), neg=0, invalid=762 0109: dt=110.976000, rms=0.673 (0.148%), neg=0, invalid=762 0110: dt=129.472000, rms=0.672 (0.086%), neg=0, invalid=762 0111: dt=443.904000, rms=0.671 (0.163%), neg=0, invalid=762 0112: dt=73.984000, rms=0.671 (0.089%), neg=0, invalid=762 0113: dt=1183.744000, rms=0.669 (0.200%), neg=0, invalid=762 0114: dt=92.480000, rms=0.668 (0.133%), neg=0, invalid=762 0115: dt=295.936000, rms=0.668 (0.028%), neg=0, invalid=762 0116: dt=295.936000, rms=0.668 (0.006%), neg=0, invalid=762 0117: dt=295.936000, rms=0.668 (-0.121%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.670, neg=0, invalid=762 0118: dt=129.472000, rms=0.667 (0.408%), neg=0, invalid=762 0119: dt=129.472000, rms=0.666 (0.051%), neg=0, invalid=762 0120: dt=517.888000, rms=0.666 (0.108%), neg=0, invalid=762 0121: dt=129.472000, rms=0.665 (0.038%), neg=0, invalid=762 0122: dt=129.472000, rms=0.665 (0.022%), neg=0, invalid=762 0123: dt=129.472000, rms=0.665 (0.036%), neg=0, invalid=762 0124: dt=129.472000, rms=0.665 (0.050%), neg=0, invalid=762 0125: dt=129.472000, rms=0.664 (0.049%), neg=0, invalid=762 0126: dt=129.472000, rms=0.664 (0.052%), neg=0, invalid=762 0127: dt=129.472000, rms=0.664 (0.057%), neg=0, invalid=762 0128: dt=129.472000, rms=0.663 (0.060%), neg=0, invalid=762 0129: dt=129.472000, rms=0.663 (0.060%), neg=0, invalid=762 0130: dt=129.472000, rms=0.663 (0.061%), neg=0, invalid=762 0131: dt=129.472000, rms=0.662 (0.062%), neg=0, invalid=762 0132: dt=129.472000, rms=0.662 (0.069%), neg=0, invalid=762 0133: dt=129.472000, rms=0.661 (0.068%), neg=0, invalid=762 0134: dt=129.472000, rms=0.661 (0.065%), neg=0, invalid=762 0135: dt=129.472000, rms=0.660 (0.052%), neg=0, invalid=762 0136: dt=129.472000, rms=0.660 (0.055%), neg=0, invalid=762 0137: dt=129.472000, rms=0.660 (0.052%), neg=0, invalid=762 0138: dt=129.472000, rms=0.659 (0.054%), neg=0, invalid=762 0139: dt=129.472000, rms=0.659 (0.051%), neg=0, invalid=762 0140: dt=129.472000, rms=0.659 (0.042%), neg=0, invalid=762 0141: dt=129.472000, rms=0.658 (0.043%), neg=0, invalid=762 0142: dt=129.472000, rms=0.658 (0.041%), neg=0, invalid=762 0143: dt=129.472000, rms=0.658 (0.033%), neg=0, invalid=762 0144: dt=129.472000, rms=0.658 (0.034%), neg=0, invalid=762 0145: dt=129.472000, rms=0.658 (0.037%), neg=0, invalid=762 0146: dt=129.472000, rms=0.657 (0.038%), neg=0, invalid=762 0147: dt=129.472000, rms=0.657 (0.037%), neg=0, invalid=762 0148: dt=129.472000, rms=0.657 (0.033%), neg=0, invalid=762 0149: dt=129.472000, rms=0.657 (0.031%), neg=0, invalid=762 0150: dt=129.472000, rms=0.656 (0.029%), neg=0, invalid=762 0151: dt=129.472000, rms=0.656 (0.025%), neg=0, invalid=762 0152: dt=129.472000, rms=0.656 (0.025%), neg=0, invalid=762 0153: dt=129.472000, rms=0.656 (0.026%), neg=0, invalid=762 0154: dt=129.472000, rms=0.656 (0.021%), neg=0, invalid=762 0155: dt=129.472000, rms=0.656 (0.023%), neg=0, invalid=762 0156: dt=129.472000, rms=0.655 (0.020%), neg=0, invalid=762 0157: dt=517.888000, rms=0.655 (0.012%), neg=0, invalid=762 0158: dt=517.888000, rms=0.655 (-0.086%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.657, neg=0, invalid=762 0159: dt=117.800797, rms=0.652 (0.713%), neg=0, invalid=762 0160: dt=145.152000, rms=0.647 (0.852%), neg=0, invalid=762 0161: dt=103.680000, rms=0.645 (0.314%), neg=0, invalid=762 0162: dt=124.416000, rms=0.642 (0.401%), neg=0, invalid=762 0163: dt=78.181818, rms=0.640 (0.337%), neg=0, invalid=762 0164: dt=89.239437, rms=0.639 (0.190%), neg=0, invalid=762 0165: dt=118.421769, rms=0.637 (0.310%), neg=0, invalid=762 0166: dt=36.288000, rms=0.636 (0.152%), neg=0, invalid=762 0167: dt=414.720000, rms=0.633 (0.457%), neg=0, invalid=762 0168: dt=36.288000, rms=0.630 (0.400%), neg=0, invalid=762 0169: dt=145.152000, rms=0.629 (0.215%), neg=0, invalid=762 0170: dt=36.288000, rms=0.629 (0.086%), neg=0, invalid=762 0171: dt=331.776000, rms=0.627 (0.226%), neg=0, invalid=762 0172: dt=65.574944, rms=0.625 (0.280%), neg=0, invalid=762 0173: dt=36.288000, rms=0.625 (0.038%), neg=0, invalid=762 0174: dt=36.288000, rms=0.625 (0.048%), neg=0, invalid=762 0175: dt=36.288000, rms=0.624 (0.066%), neg=0, invalid=762 0176: dt=0.567000, rms=0.624 (0.001%), neg=0, invalid=762 0177: dt=0.035437, rms=0.624 (0.000%), neg=0, invalid=762 0178: dt=0.030375, rms=0.624 (0.000%), neg=0, invalid=762 0179: dt=0.001898, rms=0.624 (0.000%), neg=0, invalid=762 0180: dt=0.000237, rms=0.624 (0.000%), neg=0, invalid=762 0181: dt=0.000059, rms=0.624 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.626, neg=0, invalid=762 0182: dt=122.947368, rms=0.622 (0.551%), neg=0, invalid=762 0183: dt=103.680000, rms=0.621 (0.191%), neg=0, invalid=762 0184: dt=90.000000, rms=0.620 (0.167%), neg=0, invalid=762 0185: dt=62.208000, rms=0.619 (0.084%), neg=0, invalid=762 0186: dt=331.776000, rms=0.618 (0.228%), neg=0, invalid=762 0187: dt=36.288000, rms=0.617 (0.165%), neg=0, invalid=762 0188: dt=103.680000, rms=0.617 (0.053%), neg=0, invalid=762 0189: dt=124.416000, rms=0.616 (0.122%), neg=0, invalid=762 0190: dt=36.288000, rms=0.616 (0.044%), neg=0, invalid=762 0191: dt=36.288000, rms=0.616 (0.029%), neg=0, invalid=762 0192: dt=36.288000, rms=0.615 (0.040%), neg=0, invalid=762 0193: dt=36.288000, rms=0.615 (0.066%), neg=0, invalid=762 0194: dt=36.288000, rms=0.614 (0.088%), neg=0, invalid=762 0195: dt=36.288000, rms=0.614 (0.108%), neg=0, invalid=762 0196: dt=36.288000, rms=0.613 (0.114%), neg=0, invalid=762 0197: dt=36.288000, rms=0.612 (0.116%), neg=0, invalid=762 0198: dt=36.288000, rms=0.612 (0.110%), neg=0, invalid=762 0199: dt=36.288000, rms=0.611 (0.116%), neg=0, invalid=762 0200: dt=36.288000, rms=0.610 (0.114%), neg=0, invalid=762 0201: dt=36.288000, rms=0.609 (0.113%), neg=0, invalid=762 0202: dt=36.288000, rms=0.609 (0.114%), neg=0, invalid=762 0203: dt=36.288000, rms=0.608 (0.118%), neg=0, invalid=762 0204: dt=36.288000, rms=0.607 (0.115%), neg=0, invalid=762 0205: dt=36.288000, rms=0.607 (0.109%), neg=0, invalid=762 0206: dt=36.288000, rms=0.606 (0.119%), neg=0, invalid=762 0207: dt=36.288000, rms=0.605 (0.102%), neg=0, invalid=762 0208: dt=36.288000, rms=0.605 (0.102%), neg=0, invalid=762 0209: dt=36.288000, rms=0.604 (0.092%), neg=0, invalid=762 0210: dt=36.288000, rms=0.604 (0.086%), neg=0, invalid=762 0211: dt=36.288000, rms=0.603 (0.089%), neg=0, invalid=762 0212: dt=36.288000, rms=0.603 (0.096%), neg=0, invalid=762 0213: dt=36.288000, rms=0.602 (0.093%), neg=0, invalid=762 0214: dt=36.288000, rms=0.601 (0.087%), neg=0, invalid=762 0215: dt=36.288000, rms=0.601 (0.084%), neg=0, invalid=762 0216: dt=36.288000, rms=0.600 (0.083%), neg=0, invalid=762 0217: dt=36.288000, rms=0.600 (0.073%), neg=0, invalid=762 0218: dt=36.288000, rms=0.600 (0.072%), neg=0, invalid=762 0219: dt=36.288000, rms=0.599 (0.069%), neg=0, invalid=762 0220: dt=36.288000, rms=0.599 (0.067%), neg=0, invalid=762 0221: dt=36.288000, rms=0.598 (0.075%), neg=0, invalid=762 0222: dt=36.288000, rms=0.598 (0.063%), neg=0, invalid=762 0223: dt=36.288000, rms=0.598 (0.064%), neg=0, invalid=762 0224: dt=36.288000, rms=0.597 (0.058%), neg=0, invalid=762 0225: dt=36.288000, rms=0.597 (0.059%), neg=0, invalid=762 0226: dt=36.288000, rms=0.597 (0.054%), neg=0, invalid=762 0227: dt=36.288000, rms=0.596 (0.051%), neg=0, invalid=762 0228: dt=36.288000, rms=0.596 (0.050%), neg=0, invalid=762 0229: dt=36.288000, rms=0.596 (0.055%), neg=0, invalid=762 0230: dt=36.288000, rms=0.595 (0.047%), neg=0, invalid=762 0231: dt=36.288000, rms=0.595 (0.049%), neg=0, invalid=762 0232: dt=36.288000, rms=0.595 (0.044%), neg=0, invalid=762 0233: dt=36.288000, rms=0.595 (0.044%), neg=0, invalid=762 0234: dt=36.288000, rms=0.594 (0.042%), neg=0, invalid=762 0235: dt=36.288000, rms=0.594 (0.049%), neg=0, invalid=762 0236: dt=36.288000, rms=0.594 (0.041%), neg=0, invalid=762 0237: dt=36.288000, rms=0.594 (0.043%), neg=0, invalid=762 0238: dt=36.288000, rms=0.593 (0.041%), neg=0, invalid=762 0239: dt=36.288000, rms=0.593 (0.034%), neg=0, invalid=762 0240: dt=36.288000, rms=0.593 (0.036%), neg=0, invalid=762 0241: dt=36.288000, rms=0.593 (0.036%), neg=0, invalid=762 0242: dt=36.288000, rms=0.592 (0.034%), neg=0, invalid=762 0243: dt=36.288000, rms=0.592 (0.034%), neg=0, invalid=762 0244: dt=36.288000, rms=0.592 (0.032%), neg=0, invalid=762 0245: dt=36.288000, rms=0.592 (0.030%), neg=0, invalid=762 0246: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=762 0247: dt=36.288000, rms=0.592 (0.026%), neg=0, invalid=762 0248: dt=36.288000, rms=0.591 (0.033%), neg=0, invalid=762 0249: dt=36.288000, rms=0.591 (0.027%), neg=0, invalid=762 0250: dt=36.288000, rms=0.591 (0.023%), neg=0, invalid=762 0251: dt=36.288000, rms=0.591 (0.030%), neg=0, invalid=762 0252: dt=36.288000, rms=0.591 (0.028%), neg=0, invalid=762 0253: dt=36.288000, rms=0.591 (0.023%), neg=0, invalid=762 0254: dt=36.288000, rms=0.590 (0.026%), neg=0, invalid=762 0255: dt=36.288000, rms=0.590 (0.030%), neg=0, invalid=762 0256: dt=36.288000, rms=0.590 (0.025%), neg=0, invalid=762 0257: dt=36.288000, rms=0.590 (0.026%), neg=0, invalid=762 0258: dt=36.288000, rms=0.590 (0.029%), neg=0, invalid=762 0259: dt=36.288000, rms=0.590 (0.027%), neg=0, invalid=762 0260: dt=36.288000, rms=0.590 (0.020%), neg=0, invalid=762 0261: dt=36.288000, rms=0.589 (0.021%), neg=0, invalid=762 0262: dt=36.288000, rms=0.589 (0.002%), neg=0, invalid=762 0263: dt=2.268000, rms=0.589 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.596, neg=0, invalid=762 0264: dt=11.200000, rms=0.593 (0.446%), neg=0, invalid=762 0265: dt=9.600000, rms=0.592 (0.155%), neg=0, invalid=762 0266: dt=0.700000, rms=0.592 (0.011%), neg=0, invalid=762 0267: dt=0.043750, rms=0.592 (0.000%), neg=0, invalid=762 0268: dt=0.021875, rms=0.592 (0.001%), neg=0, invalid=762 0269: dt=0.002734, rms=0.592 (0.000%), neg=0, invalid=762 0270: dt=0.001367, rms=0.592 (0.000%), neg=0, invalid=762 0271: dt=0.000684, rms=0.592 (0.000%), neg=0, invalid=762 0272: dt=0.000488, rms=0.592 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.594, neg=0, invalid=762 0273: dt=108.571429, rms=0.589 (0.721%), neg=0, invalid=762 0274: dt=44.800000, rms=0.584 (0.954%), neg=0, invalid=762 0275: dt=32.000000, rms=0.582 (0.332%), neg=0, invalid=762 0276: dt=2.400000, rms=0.582 (0.037%), neg=0, invalid=762 0277: dt=0.150000, rms=0.582 (0.002%), neg=0, invalid=762 0278: dt=0.037500, rms=0.582 (0.001%), neg=0, invalid=762 0279: dt=0.009375, rms=0.582 (0.000%), neg=0, invalid=762 0280: dt=0.001953, rms=0.582 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.595, neg=0, invalid=762 0281: dt=4.032000, rms=0.591 (0.788%), neg=0, invalid=762 0282: dt=1.008000, rms=0.590 (0.116%), neg=0, invalid=762 0283: dt=0.720000, rms=0.589 (0.079%), neg=0, invalid=762 0284: dt=0.063000, rms=0.589 (0.004%), neg=0, invalid=762 0285: dt=0.031500, rms=0.589 (0.004%), neg=0, invalid=762 0286: dt=0.015750, rms=0.589 (0.002%), neg=0, invalid=762 0287: dt=0.007875, rms=0.589 (0.001%), neg=0, invalid=762 0288: dt=0.000630, rms=0.589 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.591, neg=0, invalid=762 0289: dt=11.520000, rms=0.586 (0.833%), neg=0, invalid=762 0290: dt=4.032000, rms=0.585 (0.181%), neg=0, invalid=762 0291: dt=1.008000, rms=0.584 (0.040%), neg=0, invalid=762 0292: dt=1.008000, rms=0.584 (0.041%), neg=0, invalid=762 0293: dt=1.008000, rms=0.584 (0.041%), neg=0, invalid=762 0294: dt=0.504000, rms=0.584 (0.018%), neg=0, invalid=762 0295: dt=0.504000, rms=0.584 (0.019%), neg=0, invalid=762 0296: dt=0.252000, rms=0.584 (0.008%), neg=0, invalid=762 0297: dt=0.003938, rms=0.584 (0.001%), neg=0, invalid=762 0298: dt=0.001969, rms=0.584 (0.000%), neg=0, invalid=762 0299: dt=0.000984, rms=0.584 (0.000%), neg=0, invalid=762 0300: dt=0.000492, rms=0.584 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0301: dt=0.000000, rms=0.601 (0.192%), neg=0, invalid=762 0302: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=762 0303: dt=0.100000, rms=0.601 (-0.017%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0304: dt=0.112000, rms=0.601 (0.193%), neg=0, invalid=762 0305: dt=0.080000, rms=0.601 (-0.001%), neg=0, invalid=762 0306: dt=0.080000, rms=0.601 (0.000%), neg=0, invalid=762 0307: dt=0.080000, rms=0.601 (0.001%), neg=0, invalid=762 0308: dt=0.080000, rms=0.601 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.574, neg=0, invalid=762 0309: dt=0.448000, rms=0.557 (2.838%), neg=0, invalid=762 0310: dt=0.448000, rms=0.554 (0.632%), neg=0, invalid=762 0311: dt=0.448000, rms=0.552 (0.349%), neg=0, invalid=762 0312: dt=0.448000, rms=0.551 (0.202%), neg=0, invalid=762 0313: dt=0.448000, rms=0.550 (0.152%), neg=0, invalid=762 0314: dt=0.448000, rms=0.549 (0.105%), neg=0, invalid=762 0315: dt=0.448000, rms=0.549 (0.097%), neg=0, invalid=762 0316: dt=0.448000, rms=0.549 (0.054%), neg=0, invalid=762 0317: dt=0.448000, rms=0.548 (0.070%), neg=0, invalid=762 0318: dt=0.448000, rms=0.548 (0.039%), neg=0, invalid=762 0319: dt=0.448000, rms=0.548 (0.048%), neg=0, invalid=762 0320: dt=0.448000, rms=0.547 (0.069%), neg=0, invalid=762 0321: dt=0.224000, rms=0.547 (0.013%), neg=0, invalid=762 0322: dt=0.224000, rms=0.547 (0.027%), neg=0, invalid=762 0323: dt=0.224000, rms=0.547 (0.038%), neg=0, invalid=762 0324: dt=0.224000, rms=0.547 (0.040%), neg=0, invalid=762 0325: dt=0.224000, rms=0.547 (0.002%), neg=0, invalid=762 0326: dt=0.224000, rms=0.547 (0.006%), neg=0, invalid=762 0327: dt=0.224000, rms=0.547 (0.013%), neg=0, invalid=762 0328: dt=0.224000, rms=0.547 (0.024%), neg=0, invalid=762 0329: dt=0.224000, rms=0.546 (0.020%), neg=0, invalid=762 0330: dt=0.320000, rms=0.546 (0.002%), neg=0, invalid=762 0331: dt=0.320000, rms=0.546 (0.005%), neg=0, invalid=762 0332: dt=0.320000, rms=0.546 (0.005%), neg=0, invalid=762 0333: dt=0.160000, rms=0.546 (0.005%), neg=0, invalid=762 0334: dt=0.160000, rms=0.546 (0.009%), neg=0, invalid=762 0335: dt=0.160000, rms=0.546 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=762 0336: dt=0.320000, rms=0.541 (1.123%), neg=0, invalid=762 0337: dt=0.448000, rms=0.539 (0.441%), neg=0, invalid=762 0338: dt=0.448000, rms=0.539 (0.043%), neg=0, invalid=762 0339: dt=0.448000, rms=0.539 (-0.006%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.537, neg=0, invalid=762 0340: dt=4.624000, rms=0.536 (0.235%), neg=0, invalid=762 0341: dt=0.011560, rms=0.536 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.537, neg=0, invalid=762 0342: dt=129.472000, rms=0.536 (0.259%), neg=0, invalid=762 0343: dt=110.976000, rms=0.536 (0.008%), neg=0, invalid=762 0344: dt=110.976000, rms=0.536 (0.016%), neg=0, invalid=762 0345: dt=110.976000, rms=0.536 (0.012%), neg=0, invalid=762 0346: dt=110.976000, rms=0.536 (0.005%), neg=0, invalid=762 0347: dt=129.472000, rms=0.536 (0.013%), neg=0, invalid=762 0348: dt=8.092000, rms=0.536 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.537, neg=0, invalid=762 0349: dt=20.736000, rms=0.535 (0.269%), neg=0, invalid=762 0350: dt=9.072000, rms=0.535 (0.003%), neg=0, invalid=762 0351: dt=9.072000, rms=0.535 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.537, neg=0, invalid=762 0352: dt=103.680000, rms=0.535 (0.403%), neg=0, invalid=762 0353: dt=64.447552, rms=0.534 (0.126%), neg=0, invalid=762 0354: dt=64.447552, rms=0.533 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0355: dt=64.447552, rms=0.533 (0.095%), neg=0, invalid=762 0356: dt=64.447552, rms=0.532 (0.143%), neg=0, invalid=762 0357: dt=64.447552, rms=0.531 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0358: dt=64.447552, rms=0.531 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0359: dt=64.447552, rms=0.530 (0.089%), neg=0, invalid=762 0360: dt=36.288000, rms=0.530 (0.029%), neg=0, invalid=762 0361: dt=36.288000, rms=0.530 (0.014%), neg=0, invalid=762 0362: dt=36.288000, rms=0.530 (0.024%), neg=0, invalid=762 0363: dt=36.288000, rms=0.530 (0.030%), neg=0, invalid=762 0364: dt=36.288000, rms=0.530 (0.032%), neg=0, invalid=762 0365: dt=36.288000, rms=0.529 (0.035%), neg=0, invalid=762 0366: dt=36.288000, rms=0.529 (0.036%), neg=0, invalid=762 0367: dt=36.288000, rms=0.529 (0.038%), neg=0, invalid=762 0368: dt=36.288000, rms=0.529 (0.040%), neg=0, invalid=762 0369: dt=36.288000, rms=0.529 (0.041%), neg=0, invalid=762 0370: dt=36.288000, rms=0.528 (0.038%), neg=0, invalid=762 0371: dt=36.288000, rms=0.528 (0.037%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.530, neg=0, invalid=762 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0372: dt=25.600000, rms=0.527 (0.494%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 3 iterations, nbhd size=0, neg = 0 0373: dt=44.800000, rms=0.527 (0.160%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0374: dt=44.800000, rms=0.526 (0.186%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 10 iterations, nbhd size=1, neg = 0 0375: dt=44.800000, rms=0.524 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 0376: dt=44.800000, rms=0.524 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 10 iterations, nbhd size=1, neg = 0 0377: dt=44.800000, rms=0.523 (0.108%), neg=0, invalid=762 iter 0, gcam->neg = 26 after 4 iterations, nbhd size=0, neg = 0 0378: dt=44.800000, rms=0.522 (0.156%), neg=0, invalid=762 iter 0, gcam->neg = 31 after 18 iterations, nbhd size=1, neg = 0 0379: dt=44.800000, rms=0.521 (0.161%), neg=0, invalid=762 iter 0, gcam->neg = 28 after 13 iterations, nbhd size=1, neg = 0 0380: dt=44.800000, rms=0.520 (0.209%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 10 iterations, nbhd size=1, neg = 0 0381: dt=44.800000, rms=0.519 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 29 after 18 iterations, nbhd size=1, neg = 0 0382: dt=44.800000, rms=0.519 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 31 after 12 iterations, nbhd size=1, neg = 0 0383: dt=44.800000, rms=0.518 (0.155%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 13 iterations, nbhd size=1, neg = 0 0384: dt=44.800000, rms=0.517 (0.108%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 15 iterations, nbhd size=1, neg = 0 0385: dt=44.800000, rms=0.517 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0386: dt=44.800000, rms=0.516 (0.170%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0387: dt=25.600000, rms=0.515 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0388: dt=25.600000, rms=0.515 (0.062%), neg=0, invalid=762 0389: dt=25.600000, rms=0.515 (0.061%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0390: dt=25.600000, rms=0.514 (0.064%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0391: dt=25.600000, rms=0.514 (0.043%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0392: dt=66.838710, rms=0.511 (0.946%), neg=0, invalid=762 0393: dt=32.000000, rms=0.509 (0.339%), neg=0, invalid=762 0394: dt=38.400000, rms=0.508 (0.180%), neg=0, invalid=762 0395: dt=38.400000, rms=0.508 (0.070%), neg=0, invalid=762 0396: dt=38.400000, rms=0.507 (0.238%), neg=0, invalid=762 0397: dt=38.400000, rms=0.506 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0398: dt=38.400000, rms=0.505 (0.140%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0399: dt=38.400000, rms=0.505 (-0.056%), neg=0, invalid=762 0400: dt=25.600000, rms=0.505 (0.047%), neg=0, invalid=762 0401: dt=38.400000, rms=0.505 (0.059%), neg=0, invalid=762 0402: dt=19.200000, rms=0.505 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0403: dt=3.456000, rms=0.512 (0.313%), neg=0, invalid=762 0404: dt=2.000000, rms=0.512 (0.007%), neg=0, invalid=762 0405: dt=2.000000, rms=0.512 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.513, neg=0, invalid=762 0406: dt=7.937984, rms=0.511 (0.409%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0407: dt=9.704918, rms=0.511 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0408: dt=9.704918, rms=0.510 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0409: dt=9.704918, rms=0.510 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0410: dt=9.704918, rms=0.509 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 79 after 12 iterations, nbhd size=1, neg = 0 0411: dt=62.726368, rms=0.503 (1.288%), neg=0, invalid=762 0412: dt=6.909091, rms=0.502 (0.068%), neg=0, invalid=762 0413: dt=6.909091, rms=0.502 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0414: dt=6.909091, rms=0.502 (-0.132%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 0415: dt=0.000000, rms=0.508 (0.267%), neg=0, invalid=762 0416: dt=0.000000, rms=0.508 (0.000%), neg=0, invalid=762 0417: dt=0.100000, rms=0.508 (-0.068%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 0418: dt=0.000000, rms=0.508 (0.267%), neg=0, invalid=762 0419: dt=0.000000, rms=0.508 (0.000%), neg=0, invalid=762 0420: dt=0.100000, rms=0.508 (-0.048%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 iter 0, gcam->neg = 1258 after 15 iterations, nbhd size=1, neg = 0 0421: dt=1.915657, rms=0.469 (6.115%), neg=0, invalid=762 0422: dt=0.000013, rms=0.469 (0.010%), neg=0, invalid=762 0423: dt=0.000013, rms=0.469 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 0424: dt=0.096000, rms=0.469 (0.397%), neg=0, invalid=762 0425: dt=0.007000, rms=0.469 (0.004%), neg=0, invalid=762 0426: dt=0.007000, rms=0.469 (0.002%), neg=0, invalid=762 0427: dt=0.007000, rms=0.469 (-0.004%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 0428: dt=0.000000, rms=0.456 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 0429: dt=-0.002604, rms=0.456 (0.000%), neg=0, invalid=762 0430: dt=0.000000, rms=0.456 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 0431: dt=1.296000, rms=0.456 (0.000%), neg=0, invalid=762 0432: dt=0.000000, rms=0.456 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 0433: dt=36.288000, rms=0.456 (0.022%), neg=0, invalid=762 0434: dt=103.680000, rms=0.455 (0.029%), neg=0, invalid=762 0435: dt=331.776000, rms=0.455 (0.073%), neg=0, invalid=762 0436: dt=31.104000, rms=0.455 (0.009%), neg=0, invalid=762 0437: dt=31.104000, rms=0.455 (0.001%), neg=0, invalid=762 0438: dt=31.104000, rms=0.455 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 0439: dt=6.400000, rms=0.456 (0.028%), neg=0, invalid=762 0440: dt=1.600000, rms=0.456 (0.001%), neg=0, invalid=762 0441: dt=1.600000, rms=0.456 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0442: dt=89.400347, rms=0.453 (0.510%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0443: dt=25.600000, rms=0.452 (0.179%), neg=0, invalid=762 0444: dt=25.600000, rms=0.452 (0.069%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0445: dt=25.600000, rms=0.452 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0446: dt=25.600000, rms=0.451 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0447: dt=25.600000, rms=0.451 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0448: dt=25.600000, rms=0.450 (0.135%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=1, neg = 0 0449: dt=25.600000, rms=0.450 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0450: dt=25.600000, rms=0.449 (0.098%), neg=0, invalid=762 0451: dt=38.400000, rms=0.449 (0.022%), neg=0, invalid=762 0452: dt=38.400000, rms=0.449 (0.024%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0453: dt=38.400000, rms=0.449 (0.037%), neg=0, invalid=762 0454: dt=38.400000, rms=0.449 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0455: dt=38.400000, rms=0.448 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0456: dt=38.400000, rms=0.448 (0.044%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0457: dt=1.008000, rms=0.451 (0.003%), neg=0, invalid=762 0458: dt=0.252000, rms=0.451 (0.000%), neg=0, invalid=762 0459: dt=0.252000, rms=0.451 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0460: dt=12.895522, rms=0.451 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 33 after 15 iterations, nbhd size=1, neg = 0 0461: dt=41.882353, rms=0.449 (0.327%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0462: dt=14.254545, rms=0.449 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0463: dt=14.254545, rms=0.448 (0.139%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 12 iterations, nbhd size=1, neg = 0 0464: dt=14.254545, rms=0.447 (0.135%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 11 iterations, nbhd size=1, neg = 0 0465: dt=14.254545, rms=0.447 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 12 iterations, nbhd size=1, neg = 0 0466: dt=14.254545, rms=0.446 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 16 iterations, nbhd size=1, neg = 0 0467: dt=14.254545, rms=0.446 (0.124%), neg=0, invalid=762 iter 0, gcam->neg = 50 after 12 iterations, nbhd size=1, neg = 0 0468: dt=14.254545, rms=0.446 (0.085%), neg=0, invalid=762 0469: dt=7.783784, rms=0.445 (0.041%), neg=0, invalid=762 0470: dt=7.783784, rms=0.445 (0.016%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0471: dt=7.783784, rms=0.445 (0.016%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0472: dt=7.783784, rms=0.445 (0.006%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0473: dt=0.000050, rms=0.451 (0.000%), neg=0, invalid=762 0474: dt=0.000000, rms=0.451 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0475: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.441, neg=0, invalid=762 iter 0, gcam->neg = 951 after 15 iterations, nbhd size=1, neg = 0 0476: dt=1.280000, rms=0.430 (2.568%), neg=0, invalid=762 0477: dt=0.000013, rms=0.430 (0.000%), neg=0, invalid=762 0478: dt=0.000013, rms=0.430 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=762 0479: dt=0.112000, rms=0.429 (0.077%), neg=0, invalid=762 0480: dt=0.080000, rms=0.429 (0.017%), neg=0, invalid=762 0481: dt=0.080000, rms=0.429 (0.007%), neg=0, invalid=762 0482: dt=0.080000, rms=0.429 (-0.037%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 2 minutes and 2 seconds. mri_ca_register utimesec 11824.199448 mri_ca_register stimesec 11.048320 mri_ca_register ru_maxrss 1337220 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 6617332 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63288 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 8796 mri_ca_register ru_nivcsw 33523 FSRUNTIME@ mri_ca_register 3.0338 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 20:02:15 CEST 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname tars-551 machine x86_64 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 2 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.96 Atlas used for the 3D morph was /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.08946 ( 4) Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (302 voxels, overlap=0.360) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (302 voxels, peak = 3), gca=8.0 gca peak = 0.17677 (13) mri peak = 0.08036 ( 4) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (531 voxels, overlap=0.394) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (531 voxels, peak = 3), gca=5.2 gca peak = 0.28129 (95) mri peak = 0.09853 (81) Right_Pallidum (52): linear fit = 0.87 x + 0.0 (123 voxels, overlap=0.032) Right_Pallidum (52): linear fit = 0.87 x + 0.0 (123 voxels, peak = 82), gca=82.2 gca peak = 0.16930 (96) mri peak = 0.09250 (84) Left_Pallidum (13): linear fit = 0.86 x + 0.0 (466 voxels, overlap=0.152) Left_Pallidum (13): linear fit = 0.86 x + 0.0 (466 voxels, peak = 82), gca=82.1 gca peak = 0.24553 (55) mri peak = 0.08528 (55) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (365 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (365 voxels, peak = 54), gca=54.2 gca peak = 0.30264 (59) mri peak = 0.06186 (57) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (317 voxels, overlap=1.015) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (317 voxels, peak = 56), gca=55.8 gca peak = 0.07580 (103) mri peak = 0.05253 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28242 voxels, overlap=0.941) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28242 voxels, peak = 104), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.04725 (101) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (29763 voxels, overlap=0.905) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (29763 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04121 (51) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (18646 voxels, overlap=0.720) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (18646 voxels, peak = 51), gca=51.3 gca peak = 0.11620 (58) mri peak = 0.04076 (50) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (23156 voxels, overlap=0.858) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (23156 voxels, peak = 52), gca=51.9 gca peak = 0.30970 (66) mri peak = 0.06467 (58) Right_Caudate (50): linear fit = 0.87 x + 0.0 (926 voxels, overlap=0.907) Right_Caudate (50): linear fit = 0.87 x + 0.0 (926 voxels, peak = 57), gca=57.1 gca peak = 0.15280 (69) mri peak = 0.06940 (63) Left_Caudate (11): linear fit = 0.86 x + 0.0 (735 voxels, overlap=0.346) Left_Caudate (11): linear fit = 0.86 x + 0.0 (735 voxels, peak = 59), gca=59.0 gca peak = 0.13902 (56) mri peak = 0.04033 (52) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (13263 voxels, overlap=0.978) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (13263 voxels, peak = 53), gca=52.9 gca peak = 0.14777 (55) mri peak = 0.03929 (53) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (13068 voxels, overlap=0.962) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (13068 voxels, peak = 52), gca=52.0 gca peak = 0.16765 (84) mri peak = 0.05042 (80) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (2940 voxels, overlap=1.000) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (2940 voxels, peak = 78), gca=77.7 gca peak = 0.18739 (84) mri peak = 0.04610 (80) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (2471 voxels, overlap=0.992) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (2471 voxels, peak = 82), gca=81.9 gca peak = 0.29869 (57) mri peak = 0.08205 (63) Left_Amygdala (18): linear fit = 0.92 x + 0.0 (162 voxels, overlap=0.999) Left_Amygdala (18): linear fit = 0.92 x + 0.0 (162 voxels, peak = 52), gca=52.2 gca peak = 0.33601 (57) mri peak = 0.08128 (52) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (131 voxels, overlap=0.502) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (131 voxels, peak = 52), gca=52.2 gca peak = 0.11131 (90) mri peak = 0.13477 (75) Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (4202 voxels, overlap=0.477) Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (4202 voxels, peak = 79), gca=78.8 gca peak = 0.11793 (83) mri peak = 0.11931 (75) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3779 voxels, overlap=0.837) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3779 voxels, peak = 79), gca=79.3 gca peak = 0.08324 (81) mri peak = 0.07279 (65) Left_Putamen (12): linear fit = 0.89 x + 0.0 (1831 voxels, overlap=0.656) Left_Putamen (12): linear fit = 0.89 x + 0.0 (1831 voxels, peak = 72), gca=72.5 gca peak = 0.10360 (77) mri peak = 0.09603 (66) Right_Putamen (51): linear fit = 0.86 x + 0.0 (615 voxels, overlap=0.259) Right_Putamen (51): linear fit = 0.86 x + 0.0 (615 voxels, peak = 66), gca=65.8 gca peak = 0.08424 (78) mri peak = 0.11780 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (5382 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.05 x + 0.0 (5382 voxels, peak = 82), gca=82.3 gca peak = 0.12631 (89) mri peak = 0.14238 (80) Right_VentralDC (60): linear fit = 0.94 x + 0.0 (968 voxels, overlap=0.752) Right_VentralDC (60): linear fit = 0.94 x + 0.0 (968 voxels, peak = 84), gca=84.1 gca peak = 0.14500 (87) mri peak = 0.14900 (80) Left_VentralDC (28): linear fit = 0.94 x + 0.0 (995 voxels, overlap=0.835) Left_VentralDC (28): linear fit = 0.94 x + 0.0 (995 voxels, peak = 81), gca=81.3 gca peak = 0.14975 (24) mri peak = 0.07757 (54) gca peak = 0.19357 (14) mri peak = 0.08371 (12) Fourth_Ventricle (15): linear fit = 0.43 x + 0.0 (294 voxels, overlap=0.495) Fourth_Ventricle (15): linear fit = 0.43 x + 0.0 (294 voxels, peak = 6), gca=6.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.92 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.30837 ( 7) mri peak = 0.08946 ( 4) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (302 voxels, overlap=0.256) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (302 voxels, peak = 3), gca=3.0 gca peak = 0.30173 ( 5) mri peak = 0.08036 ( 4) Right_Lateral_Ventricle (43): linear fit = 1.89 x + 0.0 (531 voxels, overlap=0.606) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (531 voxels, peak = 9), gca=7.5 gca peak = 0.26111 (81) mri peak = 0.09853 (81) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (123 voxels, overlap=1.009) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (123 voxels, peak = 80), gca=79.8 gca peak = 0.19284 (81) mri peak = 0.09250 (84) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (466 voxels, overlap=0.981) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (466 voxels, peak = 81), gca=81.0 gca peak = 0.29530 (55) mri peak = 0.08528 (55) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (365 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (365 voxels, peak = 55), gca=55.0 gca peak = 0.29344 (53) mri peak = 0.06186 (57) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (317 voxels, overlap=1.016) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (317 voxels, peak = 56), gca=56.4 gca peak = 0.07876 (103) mri peak = 0.05253 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28242 voxels, overlap=0.948) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28242 voxels, peak = 103), gca=103.0 gca peak = 0.07821 (106) mri peak = 0.04725 (101) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29763 voxels, overlap=0.935) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29763 voxels, peak = 107), gca=106.5 gca peak = 0.11072 (51) mri peak = 0.04121 (51) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (18646 voxels, overlap=0.998) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (18646 voxels, peak = 50), gca=50.2 gca peak = 0.12857 (52) mri peak = 0.04076 (50) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (23156 voxels, overlap=0.998) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (23156 voxels, peak = 51), gca=51.2 gca peak = 0.29496 (57) mri peak = 0.06467 (58) Right_Caudate (50): linear fit = 1.00 x + 0.0 (926 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.00 x + 0.0 (926 voxels, peak = 57), gca=57.0 gca peak = 0.14974 (59) mri peak = 0.06940 (63) Left_Caudate (11): linear fit = 0.99 x + 0.0 (735 voxels, overlap=0.992) Left_Caudate (11): linear fit = 0.99 x + 0.0 (735 voxels, peak = 58), gca=58.1 gca peak = 0.14765 (52) mri peak = 0.04033 (52) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (13263 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (13263 voxels, peak = 50), gca=50.2 gca peak = 0.15520 (52) mri peak = 0.03929 (53) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (13068 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (13068 voxels, peak = 52), gca=51.7 gca peak = 0.17489 (78) mri peak = 0.05042 (80) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (2940 voxels, overlap=0.970) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (2940 voxels, peak = 82), gca=81.5 gca peak = 0.18659 (82) mri peak = 0.04610 (80) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (2471 voxels, overlap=0.972) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (2471 voxels, peak = 87), gca=86.5 gca peak = 0.30458 (53) mri peak = 0.08205 (63) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (162 voxels, overlap=1.027) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (162 voxels, peak = 53), gca=53.0 gca peak = 0.33346 (52) mri peak = 0.08128 (52) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (131 voxels, overlap=0.898) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (131 voxels, peak = 52), gca=52.0 gca peak = 0.11596 (77) mri peak = 0.13477 (75) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4202 voxels, overlap=0.652) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4202 voxels, peak = 79), gca=78.9 gca peak = 0.10619 (77) mri peak = 0.11931 (75) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3779 voxels, overlap=0.847) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3779 voxels, peak = 78), gca=78.2 gca peak = 0.08598 (71) mri peak = 0.07279 (65) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1831 voxels, overlap=1.000) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1831 voxels, peak = 70), gca=69.9 gca peak = 0.10238 (68) mri peak = 0.09603 (66) Right_Putamen (51): linear fit = 1.00 x + 0.0 (615 voxels, overlap=0.984) Right_Putamen (51): linear fit = 1.00 x + 0.0 (615 voxels, peak = 68), gca=68.0 gca peak = 0.08167 (85) mri peak = 0.11780 (80) Brain_Stem (16): linear fit = 1.00 x + 0.0 (5382 voxels, overlap=0.674) Brain_Stem (16): linear fit = 1.00 x + 0.0 (5382 voxels, peak = 85), gca=84.6 gca peak = 0.12420 (85) mri peak = 0.14238 (80) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (968 voxels, overlap=0.706) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (968 voxels, peak = 85), gca=84.6 gca peak = 0.16562 (80) mri peak = 0.14900 (80) Left_VentralDC: unreasonable value (79.6/80.0), not in range [80, 110] - rejecting gca peak = 0.33708 (10) mri peak = 0.07757 (54) gca peak = 0.45928 ( 6) mri peak = 0.08371 (12) Fourth_Ventricle (15): linear fit = 1.79 x + 0.0 (294 voxels, overlap=0.945) Fourth_Ventricle (15): linear fit = 1.79 x + 0.0 (294 voxels, peak = 11), gca=10.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18199 (30) gca peak Left_Thalamus = 1.00000 (87) gca peak Third_Ventricle = 0.33708 (10) gca peak Fourth_Ventricle = 0.45928 ( 6) gca peak CSF = 0.26605 (13) gca peak Left_Accumbens_area = 0.81464 (53) gca peak Left_VentralDC = 0.16562 (80) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.68929 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24867 (23) gca peak Right_Accumbens_area = 0.32354 (56) gca peak Right_vessel = 0.81765 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65560 (13) gca peak WM_hypointensities = 0.07285 (77) gca peak non_WM_hypointensities = 0.12093 (55) gca peak Optic_Chiasm = 0.71095 (75) not using caudate to estimate GM means setting label Left_VentralDC based on Right_VentralDC = 1.00 x + 0: 85 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.97 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 119664 voxels changed in iteration 0 of unlikely voxel relabeling 296 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 50688 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 877 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 106505 changed. image ll: -2.184, PF=0.500 pass 2: 34803 changed. image ll: -2.183, PF=0.500 pass 3: 11897 changed. pass 4: 4734 changed. 68243 voxels changed in iteration 0 of unlikely voxel relabeling 386 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8208 voxels changed in iteration 0 of unlikely voxel relabeling 194 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6750 voxels changed in iteration 0 of unlikely voxel relabeling 73 voxels changed in iteration 1 of unlikely voxel relabeling 27 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 6209 voxels changed in iteration 0 of unlikely voxel relabeling 24 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4009.242502 mri_ca_label stimesec 1.920708 mri_ca_label ru_maxrss 2105440 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 734347 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63280 mri_ca_label ru_oublock 520 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 285 mri_ca_label ru_nivcsw 16360 auto-labeling took 66 minutes and 5 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/transforms/cc_up.lta 0050815 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/norm.mgz 21853 voxels in left wm, 41277 in right wm, xrange [124, 133] searching rotation angles z=[-8 6], y=[-9 5] searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 global minimum found at slice 128.8, rotations (-1.78, -0.72) final transformation (x=128.8, yr=-1.775, zr=-0.718): 0.99944 0.01253 -0.03098 1.58180; -0.01252 0.99992 0.00039 19.57518; 0.03098 -0.00000 0.99952 6.06746; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 131] in xformed coordinates best xformed slice 127 cc center is found at 127 110 118 eigenvectors: -0.00020 -0.00216 1.00000; -0.15918 -0.98725 -0.00217; 0.98725 -0.15918 -0.00015; writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 21:09:02 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 21:09:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1767 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 55 (55), valley at 0 (-1) csf peak at 27, setting threshold to 45 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 51 (51), valley at 0 (-1) csf peak at 25, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 8 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 21:12:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1588882 voxels in mask (pct= 9.47) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 21:12:12 CEST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 106.4 +- 6.0 [79.0 --> 125.0] GM (69.0) : 67.4 +- 9.6 [30.0 --> 95.0] setting bottom of white matter range to 77.0 setting top of gray matter range to 86.6 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 10651 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2823 filled 14 bright non-wm voxels segmented. 6126 diagonally connected voxels added... white matter segmentation took 1.5 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 1.05 minutes reading wm segmentation from wm.seg.mgz... 4077 voxels added to wm to prevent paths from MTL structures to cortex 6488 additional wm voxels added 0 additional wm voxels added SEG EDIT: 61282 voxels turned on, 9932 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 89 new 89 115,126,128 old 89 new 89 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 93 found - 93 modified | TOTAL: 93 pass 2 (xy+): 0 found - 93 modified | TOTAL: 93 pass 1 (xy-): 81 found - 81 modified | TOTAL: 174 pass 2 (xy-): 0 found - 81 modified | TOTAL: 174 pass 1 (yz+): 89 found - 89 modified | TOTAL: 263 pass 2 (yz+): 0 found - 89 modified | TOTAL: 263 pass 1 (yz-): 75 found - 75 modified | TOTAL: 338 pass 2 (yz-): 0 found - 75 modified | TOTAL: 338 pass 1 (xz+): 84 found - 84 modified | TOTAL: 422 pass 2 (xz+): 0 found - 84 modified | TOTAL: 422 pass 1 (xz-): 79 found - 79 modified | TOTAL: 501 pass 2 (xz-): 0 found - 79 modified | TOTAL: 501 Iteration Number : 1 pass 1 (+++): 75 found - 75 modified | TOTAL: 75 pass 2 (+++): 0 found - 75 modified | TOTAL: 75 pass 1 (+++): 94 found - 94 modified | TOTAL: 169 pass 2 (+++): 0 found - 94 modified | TOTAL: 169 pass 1 (+++): 82 found - 82 modified | TOTAL: 251 pass 2 (+++): 0 found - 82 modified | TOTAL: 251 pass 1 (+++): 85 found - 85 modified | TOTAL: 336 pass 2 (+++): 0 found - 85 modified | TOTAL: 336 Iteration Number : 1 pass 1 (++): 201 found - 201 modified | TOTAL: 201 pass 2 (++): 0 found - 201 modified | TOTAL: 201 pass 1 (+-): 233 found - 233 modified | TOTAL: 434 pass 2 (+-): 1 found - 234 modified | TOTAL: 435 pass 3 (+-): 0 found - 234 modified | TOTAL: 435 pass 1 (--): 200 found - 200 modified | TOTAL: 635 pass 2 (--): 0 found - 200 modified | TOTAL: 635 pass 1 (-+): 235 found - 235 modified | TOTAL: 870 pass 2 (-+): 0 found - 235 modified | TOTAL: 870 Iteration Number : 2 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 32 found - 32 modified | TOTAL: 54 pass 2 (xy-): 0 found - 32 modified | TOTAL: 54 pass 1 (yz+): 21 found - 21 modified | TOTAL: 75 pass 2 (yz+): 0 found - 21 modified | TOTAL: 75 pass 1 (yz-): 16 found - 16 modified | TOTAL: 91 pass 2 (yz-): 0 found - 16 modified | TOTAL: 91 pass 1 (xz+): 24 found - 24 modified | TOTAL: 115 pass 2 (xz+): 0 found - 24 modified | TOTAL: 115 pass 1 (xz-): 22 found - 22 modified | TOTAL: 137 pass 2 (xz-): 0 found - 22 modified | TOTAL: 137 Iteration Number : 2 pass 1 (+++): 7 found - 7 modified | TOTAL: 7 pass 2 (+++): 0 found - 7 modified | TOTAL: 7 pass 1 (+++): 5 found - 5 modified | TOTAL: 12 pass 2 (+++): 0 found - 5 modified | TOTAL: 12 pass 1 (+++): 6 found - 6 modified | TOTAL: 18 pass 2 (+++): 0 found - 6 modified | TOTAL: 18 pass 1 (+++): 7 found - 7 modified | TOTAL: 25 pass 2 (+++): 0 found - 7 modified | TOTAL: 25 Iteration Number : 2 pass 1 (++): 16 found - 16 modified | TOTAL: 16 pass 2 (++): 0 found - 16 modified | TOTAL: 16 pass 1 (+-): 9 found - 9 modified | TOTAL: 25 pass 2 (+-): 0 found - 9 modified | TOTAL: 25 pass 1 (--): 9 found - 9 modified | TOTAL: 34 pass 2 (--): 0 found - 9 modified | TOTAL: 34 pass 1 (-+): 11 found - 11 modified | TOTAL: 45 pass 2 (-+): 0 found - 11 modified | TOTAL: 45 Iteration Number : 3 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 3 found - 3 modified | TOTAL: 8 pass 2 (xy-): 0 found - 3 modified | TOTAL: 8 pass 1 (yz+): 2 found - 2 modified | TOTAL: 10 pass 2 (yz+): 0 found - 2 modified | TOTAL: 10 pass 1 (yz-): 3 found - 3 modified | TOTAL: 13 pass 2 (yz-): 0 found - 3 modified | TOTAL: 13 pass 1 (xz+): 2 found - 2 modified | TOTAL: 15 pass 2 (xz+): 0 found - 2 modified | TOTAL: 15 pass 1 (xz-): 1 found - 1 modified | TOTAL: 16 pass 2 (xz-): 0 found - 1 modified | TOTAL: 16 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 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 (-+): 2 found - 2 modified | TOTAL: 4 pass 2 (-+): 0 found - 2 modified | TOTAL: 4 Iteration Number : 4 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+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 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 : 4 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 : 5 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 : 5 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 : 5 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 = 1935 (out of 419316: 0.461466) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 21:14:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01749 0.01056 -0.05910 1.28516; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15352; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01749 0.01056 -0.05910 1.28516; 0.00398 1.12784 0.29698 -52.10687; 0.05350 -0.25530 0.93116 20.15352; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 856 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (126, 107, 117), TAL = (2.0, -11.0, 21.0) talairach voxel to voxel transform 0.97960 0.00457 0.06071 -2.24416; 0.01060 0.82700 -0.26309 48.38084; -0.05338 0.22648 0.99831 -8.24954; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 107, 117) --> (2.0, -11.0, 21.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (2.00, -11.00, 21.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -11.00, 21.00) SRC: (111.15, 107.23, 127.02) search lh wm seed point around talairach space (-16.00, -11.00, 21.00), SRC: (146.41, 107.61, 125.10) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat Oct 7 21:15:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 4 found - 4 modified | TOTAL: 11 pass 2 (yz-): 0 found - 4 modified | TOTAL: 11 pass 1 (xz+): 3 found - 3 modified | TOTAL: 14 pass 2 (xz+): 0 found - 3 modified | TOTAL: 14 pass 1 (xz-): 1 found - 1 modified | TOTAL: 15 pass 2 (xz-): 0 found - 1 modified | TOTAL: 15 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 20 (out of 206691: 0.009676) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 46 vertices, 59 faces slice 50: 4023 vertices, 4246 faces slice 60: 11409 vertices, 11723 faces slice 70: 21756 vertices, 22190 faces slice 80: 32701 vertices, 33191 faces slice 90: 42537 vertices, 43012 faces slice 100: 53299 vertices, 53845 faces slice 110: 65498 vertices, 66198 faces slice 120: 76660 vertices, 77354 faces slice 130: 87090 vertices, 87782 faces slice 140: 97312 vertices, 98039 faces slice 150: 106654 vertices, 107411 faces slice 160: 113697 vertices, 114402 faces slice 170: 119358 vertices, 120087 faces slice 180: 124926 vertices, 125636 faces slice 190: 129499 vertices, 130207 faces slice 200: 132495 vertices, 133134 faces slice 210: 133882 vertices, 134468 faces slice 220: 133980 vertices, 134536 faces slice 230: 133980 vertices, 134536 faces slice 240: 133980 vertices, 134536 faces slice 250: 133980 vertices, 134536 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 133980 voxel in cpt #1: X=-556 [v=133980,e=403608,f=269072] located at (-29.023115, -14.950963, 12.139782) For the whole surface: X=-556 [v=133980,e=403608,f=269072] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 21:15:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/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-): 4 found - 4 modified | TOTAL: 7 pass 2 (yz-): 0 found - 4 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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 204800: 0.004395) 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 40: 14 vertices, 19 faces slice 50: 2354 vertices, 2530 faces slice 60: 9673 vertices, 10063 faces slice 70: 21026 vertices, 21535 faces slice 80: 32424 vertices, 33024 faces slice 90: 43206 vertices, 43816 faces slice 100: 54048 vertices, 54767 faces slice 110: 66922 vertices, 67793 faces slice 120: 79549 vertices, 80380 faces slice 130: 91125 vertices, 91989 faces slice 140: 102517 vertices, 103445 faces slice 150: 111023 vertices, 111808 faces slice 160: 116546 vertices, 117343 faces slice 170: 123213 vertices, 124025 faces slice 180: 129174 vertices, 129967 faces slice 190: 134369 vertices, 135143 faces slice 200: 138127 vertices, 138909 faces slice 210: 140553 vertices, 141225 faces slice 220: 140682 vertices, 141328 faces slice 230: 140682 vertices, 141328 faces slice 240: 140682 vertices, 141328 faces slice 250: 140682 vertices, 141328 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 140682 voxel in cpt #1: X=-646 [v=140682,e=423984,f=282656] located at (27.795120, -13.204027, 16.639727) For the whole surface: X=-646 [v=140682,e=423984,f=282656] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 21:15:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 21:15:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 25126 of (25126 25129) to complete... Waiting for PID 25129 of (25126 25129) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... 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... PIDs (25126 25129) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 21:15:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 21:15:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 25183 of (25183 25186) to complete... Waiting for PID 25186 of (25183 25186) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.1 mm, total surface area = 66127 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.205 (target=0.015) step 005: RMS=0.173 (target=0.015) step 010: RMS=0.151 (target=0.015) step 015: RMS=0.140 (target=0.015) step 020: RMS=0.137 (target=0.015) step 025: RMS=0.133 (target=0.015) step 030: RMS=0.130 (target=0.015) step 035: RMS=0.128 (target=0.015) step 040: RMS=0.126 (target=0.015) step 045: RMS=0.124 (target=0.015) step 050: RMS=0.122 (target=0.015) step 055: RMS=0.122 (target=0.015) step 060: RMS=0.121 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 41.640669 mris_inflate stimesec 0.107983 mris_inflate ru_maxrss 198768 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29189 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9456 mris_inflate ru_oublock 9472 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2211 mris_inflate ru_nivcsw 3303 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.4 mm, total surface area = 68377 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.213 (target=0.015) step 005: RMS=0.180 (target=0.015) step 010: RMS=0.157 (target=0.015) step 015: RMS=0.148 (target=0.015) step 020: RMS=0.145 (target=0.015) step 025: RMS=0.144 (target=0.015) step 030: RMS=0.143 (target=0.015) step 035: RMS=0.139 (target=0.015) step 040: RMS=0.138 (target=0.015) step 045: RMS=0.138 (target=0.015) step 050: RMS=0.135 (target=0.015) step 055: RMS=0.135 (target=0.015) step 060: RMS=0.135 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 40.138897 mris_inflate stimesec 0.085986 mris_inflate ru_maxrss 208820 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30679 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9928 mris_inflate ru_oublock 9944 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2288 mris_inflate ru_nivcsw 3221 PIDs (25183 25186) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 21:16:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 21:16:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 25285 of (25285 25288) to complete... Waiting for PID 25288 of (25285 25288) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.79 (0.00-->14.30) (max @ vno 67648 --> 67669) face area 0.02 +- 0.04 (-0.43-->0.79) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.307... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.724, avgs=0 005/300: dt: 0.9000, rms radial error=177.460, avgs=0 010/300: dt: 0.9000, rms radial error=176.897, avgs=0 015/300: dt: 0.9000, rms radial error=176.158, avgs=0 020/300: dt: 0.9000, rms radial error=175.316, avgs=0 025/300: dt: 0.9000, rms radial error=174.418, avgs=0 030/300: dt: 0.9000, rms radial error=173.494, avgs=0 035/300: dt: 0.9000, rms radial error=172.553, avgs=0 040/300: dt: 0.9000, rms radial error=171.605, avgs=0 045/300: dt: 0.9000, rms radial error=170.654, avgs=0 050/300: dt: 0.9000, rms radial error=169.704, avgs=0 055/300: dt: 0.9000, rms radial error=168.755, avgs=0 060/300: dt: 0.9000, rms radial error=167.810, avgs=0 065/300: dt: 0.9000, rms radial error=166.868, avgs=0 070/300: dt: 0.9000, rms radial error=165.930, avgs=0 075/300: dt: 0.9000, rms radial error=164.997, avgs=0 080/300: dt: 0.9000, rms radial error=164.069, avgs=0 085/300: dt: 0.9000, rms radial error=163.145, avgs=0 090/300: dt: 0.9000, rms radial error=162.225, avgs=0 095/300: dt: 0.9000, rms radial error=161.311, avgs=0 100/300: dt: 0.9000, rms radial error=160.400, avgs=0 105/300: dt: 0.9000, rms radial error=159.493, avgs=0 110/300: dt: 0.9000, rms radial error=158.591, avgs=0 115/300: dt: 0.9000, rms radial error=157.693, avgs=0 120/300: dt: 0.9000, rms radial error=156.799, avgs=0 125/300: dt: 0.9000, rms radial error=155.910, avgs=0 130/300: dt: 0.9000, rms radial error=155.026, avgs=0 135/300: dt: 0.9000, rms radial error=154.146, avgs=0 140/300: dt: 0.9000, rms radial error=153.271, avgs=0 145/300: dt: 0.9000, rms radial error=152.401, avgs=0 150/300: dt: 0.9000, rms radial error=151.535, avgs=0 155/300: dt: 0.9000, rms radial error=150.674, avgs=0 160/300: dt: 0.9000, rms radial error=149.818, avgs=0 165/300: dt: 0.9000, rms radial error=148.966, avgs=0 170/300: dt: 0.9000, rms radial error=148.120, avgs=0 175/300: dt: 0.9000, rms radial error=147.277, avgs=0 180/300: dt: 0.9000, rms radial error=146.440, avgs=0 185/300: dt: 0.9000, rms radial error=145.607, avgs=0 190/300: dt: 0.9000, rms radial error=144.779, avgs=0 195/300: dt: 0.9000, rms radial error=143.959, avgs=0 200/300: dt: 0.9000, rms radial error=143.149, avgs=0 205/300: dt: 0.9000, rms radial error=142.344, avgs=0 210/300: dt: 0.9000, rms radial error=141.543, avgs=0 215/300: dt: 0.9000, rms radial error=140.747, avgs=0 220/300: dt: 0.9000, rms radial error=139.955, avgs=0 225/300: dt: 0.9000, rms radial error=139.168, avgs=0 230/300: dt: 0.9000, rms radial error=138.385, avgs=0 235/300: dt: 0.9000, rms radial error=137.606, avgs=0 240/300: dt: 0.9000, rms radial error=136.832, avgs=0 245/300: dt: 0.9000, rms radial error=136.062, avgs=0 250/300: dt: 0.9000, rms radial error=135.296, avgs=0 255/300: dt: 0.9000, rms radial error=134.535, avgs=0 260/300: dt: 0.9000, rms radial error=133.778, avgs=0 265/300: dt: 0.9000, rms radial error=133.024, avgs=0 270/300: dt: 0.9000, rms radial error=132.276, avgs=0 275/300: dt: 0.9000, rms radial error=131.531, avgs=0 280/300: dt: 0.9000, rms radial error=130.790, avgs=0 285/300: dt: 0.9000, rms radial error=130.054, avgs=0 290/300: dt: 0.9000, rms radial error=129.322, avgs=0 295/300: dt: 0.9000, rms radial error=128.594, avgs=0 300/300: dt: 0.9000, rms radial error=127.869, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16254.00 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3210.63 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00032 epoch 3 (K=160.0), pass 1, starting sse = 568.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00236 epoch 4 (K=640.0), pass 1, starting sse = 115.07 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/10 = 0.00655 final distance error %33.61 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 230.111017 mris_sphere stimesec 0.203968 mris_sphere ru_maxrss 198968 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 29237 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 9456 mris_sphere ru_oublock 9496 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7640 mris_sphere ru_nivcsw 17960 FSRUNTIME@ mris_sphere 0.0639 hours 1 threads 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 0.91 +- 0.77 (0.00-->10.89) (max @ vno 88377 --> 89542) face area 0.02 +- 0.05 (-0.26-->0.98) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.312... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.164, avgs=0 005/300: dt: 0.9000, rms radial error=176.903, avgs=0 010/300: dt: 0.9000, rms radial error=176.342, avgs=0 015/300: dt: 0.9000, rms radial error=175.606, avgs=0 020/300: dt: 0.9000, rms radial error=174.769, avgs=0 025/300: dt: 0.9000, rms radial error=173.874, avgs=0 030/300: dt: 0.9000, rms radial error=172.946, avgs=0 035/300: dt: 0.9000, rms radial error=172.001, avgs=0 040/300: dt: 0.9000, rms radial error=171.048, avgs=0 045/300: dt: 0.9000, rms radial error=170.092, avgs=0 050/300: dt: 0.9000, rms radial error=169.137, avgs=0 055/300: dt: 0.9000, rms radial error=168.184, avgs=0 060/300: dt: 0.9000, rms radial error=167.234, avgs=0 065/300: dt: 0.9000, rms radial error=166.288, avgs=0 070/300: dt: 0.9000, rms radial error=165.347, avgs=0 075/300: dt: 0.9000, rms radial error=164.410, avgs=0 080/300: dt: 0.9000, rms radial error=163.478, avgs=0 085/300: dt: 0.9000, rms radial error=162.549, avgs=0 090/300: dt: 0.9000, rms radial error=161.628, avgs=0 095/300: dt: 0.9000, rms radial error=160.712, avgs=0 100/300: dt: 0.9000, rms radial error=159.800, avgs=0 105/300: dt: 0.9000, rms radial error=158.893, avgs=0 110/300: dt: 0.9000, rms radial error=157.991, avgs=0 115/300: dt: 0.9000, rms radial error=157.094, avgs=0 120/300: dt: 0.9000, rms radial error=156.202, avgs=0 125/300: dt: 0.9000, rms radial error=155.314, avgs=0 130/300: dt: 0.9000, rms radial error=154.432, avgs=0 135/300: dt: 0.9000, rms radial error=153.553, avgs=0 140/300: dt: 0.9000, rms radial error=152.679, avgs=0 145/300: dt: 0.9000, rms radial error=151.809, avgs=0 150/300: dt: 0.9000, rms radial error=150.945, avgs=0 155/300: dt: 0.9000, rms radial error=150.085, avgs=0 160/300: dt: 0.9000, rms radial error=149.230, avgs=0 165/300: dt: 0.9000, rms radial error=148.379, avgs=0 170/300: dt: 0.9000, rms radial error=147.534, avgs=0 175/300: dt: 0.9000, rms radial error=146.692, avgs=0 180/300: dt: 0.9000, rms radial error=145.862, avgs=0 185/300: dt: 0.9000, rms radial error=145.036, avgs=0 190/300: dt: 0.9000, rms radial error=144.216, avgs=0 195/300: dt: 0.9000, rms radial error=143.400, avgs=0 200/300: dt: 0.9000, rms radial error=142.588, avgs=0 205/300: dt: 0.9000, rms radial error=141.781, avgs=0 210/300: dt: 0.9000, rms radial error=140.979, avgs=0 215/300: dt: 0.9000, rms radial error=140.180, avgs=0 220/300: dt: 0.9000, rms radial error=139.387, avgs=0 225/300: dt: 0.9000, rms radial error=138.597, avgs=0 230/300: dt: 0.9000, rms radial error=137.812, avgs=0 235/300: dt: 0.9000, rms radial error=137.032, avgs=0 240/300: dt: 0.9000, rms radial error=136.255, avgs=0 245/300: dt: 0.9000, rms radial error=135.483, avgs=0 250/300: dt: 0.9000, rms radial error=134.716, avgs=0 255/300: dt: 0.9000, rms radial error=133.952, avgs=0 260/300: dt: 0.9000, rms radial error=133.193, avgs=0 265/300: dt: 0.9000, rms radial error=132.438, avgs=0 270/300: dt: 0.9000, rms radial error=131.687, avgs=0 275/300: dt: 0.9000, rms radial error=130.939, avgs=0 280/300: dt: 0.9000, rms radial error=130.197, avgs=0 285/300: dt: 0.9000, rms radial error=129.458, avgs=0 290/300: dt: 0.9000, rms radial error=128.723, avgs=0 295/300: dt: 0.9000, rms radial error=127.992, avgs=0 300/300: dt: 0.9000, rms radial error=127.266, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17033.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 3347.00 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00023 epoch 3 (K=160.0), pass 1, starting sse = 603.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00221 epoch 4 (K=640.0), pass 1, starting sse = 123.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00547 final distance error %33.06 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 228.029334 mris_sphere stimesec 0.121981 mris_sphere ru_maxrss 209024 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30728 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9968 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7726 mris_sphere ru_nivcsw 17202 FSRUNTIME@ mris_sphere 0.0634 hours 1 threads PIDs (25285 25288) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 21:20:16 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 21:20:16 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 21:20:16 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050815 lh #@# Fix Topology rh Sat Oct 7 21:20:16 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050815 rh Waiting for PID 25499 of (25499 25502) to complete... Waiting for PID 25502 of (25499 25502) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050815 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-556 (nv=133980, nf=269072, ne=403608, g=279) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 66798 ambiguous faces found in tessellation segmenting defects... 167 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 4 -merging segment 62 into 45 -merging segment 63 into 45 -merging segment 72 into 66 -merging segment 87 into 75 -merging segment 88 into 77 -merging segment 94 into 77 -merging segment 97 into 77 -merging segment 113 into 77 -merging segment 104 into 101 -merging segment 99 into 114 -merging segment 135 into 117 -merging segment 130 into 118 -merging segment 119 into 129 -merging segment 143 into 140 -merging segment 155 into 153 -merging segment 150 into 153 -merging segment 162 into 159 -merging segment 166 into 165 148 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4220 (-4.7110) -vertex loglikelihood: -6.8818 (-3.4409) -normal dot loglikelihood: -3.5614 (-3.5614) -quad curv loglikelihood: -6.3474 (-3.1737) Total Loglikelihood : -26.2126 CORRECTING DEFECT 0 (vertices=636, convex hull=453, v0=32) L defect detected... After retessellation of defect 0 (v0=32), euler #=-142 (96227,279247,182878) : difference with theory (-145) = -3 CORRECTING DEFECT 1 (vertices=67, convex hull=106, v0=1363) After retessellation of defect 1 (v0=1363), euler #=-141 (96253,279375,182981) : difference with theory (-144) = -3 CORRECTING DEFECT 2 (vertices=51, convex hull=62, v0=2263) After retessellation of defect 2 (v0=2263), euler #=-140 (96270,279451,183041) : difference with theory (-143) = -3 CORRECTING DEFECT 3 (vertices=416, convex hull=192, v0=2332) After retessellation of defect 3 (v0=2332), euler #=-139 (96385,279887,183363) : difference with theory (-142) = -3 CORRECTING DEFECT 4 (vertices=38, convex hull=55, v0=2501) After retessellation of defect 4 (v0=2501), euler #=-137 (96392,279930,183401) : difference with theory (-141) = -4 CORRECTING DEFECT 5 (vertices=11, convex hull=21, v0=2799) After retessellation of defect 5 (v0=2799), euler #=-136 (96393,279939,183410) : difference with theory (-140) = -4 CORRECTING DEFECT 6 (vertices=26, convex hull=51, v0=3096) After retessellation of defect 6 (v0=3096), euler #=-135 (96410,280007,183462) : difference with theory (-139) = -4 CORRECTING DEFECT 7 (vertices=1551, convex hull=519, v0=3388) L defect detected... After retessellation of defect 7 (v0=3388), euler #=-134 (96759,281327,184434) : difference with theory (-138) = -4 CORRECTING DEFECT 8 (vertices=271, convex hull=241, v0=4774) After retessellation of defect 8 (v0=4774), euler #=-133 (96867,281769,184769) : difference with theory (-137) = -4 CORRECTING DEFECT 9 (vertices=28, convex hull=28, v0=4817) After retessellation of defect 9 (v0=4817), euler #=-132 (96870,281785,184783) : difference with theory (-136) = -4 CORRECTING DEFECT 10 (vertices=23, convex hull=65, v0=5280) After retessellation of defect 10 (v0=5280), euler #=-131 (96879,281841,184831) : difference with theory (-135) = -4 CORRECTING DEFECT 11 (vertices=60, convex hull=119, v0=6097) After retessellation of defect 11 (v0=6097), euler #=-130 (96913,281992,184949) : difference with theory (-134) = -4 CORRECTING DEFECT 12 (vertices=44, convex hull=73, v0=6930) After retessellation of defect 12 (v0=6930), euler #=-129 (96934,282085,185022) : difference with theory (-133) = -4 CORRECTING DEFECT 13 (vertices=5, convex hull=23, v0=7967) After retessellation of defect 13 (v0=7967), euler #=-128 (96934,282092,185030) : difference with theory (-132) = -4 CORRECTING DEFECT 14 (vertices=22, convex hull=84, v0=9295) After retessellation of defect 14 (v0=9295), euler #=-127 (96945,282153,185081) : difference with theory (-131) = -4 CORRECTING DEFECT 15 (vertices=35, convex hull=36, v0=9559) After retessellation of defect 15 (v0=9559), euler #=-126 (96951,282186,185109) : difference with theory (-130) = -4 CORRECTING DEFECT 16 (vertices=314, convex hull=64, v0=10606) After retessellation of defect 16 (v0=10606), euler #=-125 (96996,282348,185227) : difference with theory (-129) = -4 CORRECTING DEFECT 17 (vertices=603, convex hull=150, v0=10629) After retessellation of defect 17 (v0=10629), euler #=-124 (97072,282649,185453) : difference with theory (-128) = -4 CORRECTING DEFECT 18 (vertices=19, convex hull=42, v0=11231) After retessellation of defect 18 (v0=11231), euler #=-123 (97081,282690,185486) : difference with theory (-127) = -4 CORRECTING DEFECT 19 (vertices=97, convex hull=69, v0=11947) After retessellation of defect 19 (v0=11947), euler #=-122 (97094,282759,185543) : difference with theory (-126) = -4 CORRECTING DEFECT 20 (vertices=471, convex hull=128, v0=12684) After retessellation of defect 20 (v0=12684), euler #=-121 (97172,283055,185762) : difference with theory (-125) = -4 CORRECTING DEFECT 21 (vertices=36, convex hull=88, v0=13448) After retessellation of defect 21 (v0=13448), euler #=-120 (97191,283154,185843) : difference with theory (-124) = -4 CORRECTING DEFECT 22 (vertices=177, convex hull=79, v0=14462) After retessellation of defect 22 (v0=14462), euler #=-119 (97224,283288,185945) : difference with theory (-123) = -4 CORRECTING DEFECT 23 (vertices=28, convex hull=85, v0=15107) After retessellation of defect 23 (v0=15107), euler #=-118 (97233,283344,185993) : difference with theory (-122) = -4 CORRECTING DEFECT 24 (vertices=29, convex hull=50, v0=15768) After retessellation of defect 24 (v0=15768), euler #=-117 (97242,283387,186028) : difference with theory (-121) = -4 CORRECTING DEFECT 25 (vertices=1805, convex hull=353, v0=16252) L defect detected... normal vector of length zero at vertex 101325 with 3 faces After retessellation of defect 25 (v0=16252), euler #=-116 (97363,283938,186459) : difference with theory (-120) = -4 CORRECTING DEFECT 26 (vertices=138, convex hull=163, v0=18828) After retessellation of defect 26 (v0=18828), euler #=-115 (97434,284237,186688) : difference with theory (-119) = -4 CORRECTING DEFECT 27 (vertices=456, convex hull=177, v0=19416) After retessellation of defect 27 (v0=19416), euler #=-114 (97515,284564,186935) : difference with theory (-118) = -4 CORRECTING DEFECT 28 (vertices=8, convex hull=24, v0=19466) After retessellation of defect 28 (v0=19466), euler #=-113 (97515,284570,186942) : difference with theory (-117) = -4 CORRECTING DEFECT 29 (vertices=328, convex hull=160, v0=20296) After retessellation of defect 29 (v0=20296), euler #=-112 (97585,284854,187157) : difference with theory (-116) = -4 CORRECTING DEFECT 30 (vertices=57, convex hull=90, v0=21563) After retessellation of defect 30 (v0=21563), euler #=-111 (97608,284962,187243) : difference with theory (-115) = -4 CORRECTING DEFECT 31 (vertices=508, convex hull=131, v0=22114) After retessellation of defect 31 (v0=22114), euler #=-110 (97677,285233,187446) : difference with theory (-114) = -4 CORRECTING DEFECT 32 (vertices=28, convex hull=59, v0=22566) After retessellation of defect 32 (v0=22566), euler #=-109 (97685,285283,187489) : difference with theory (-113) = -4 CORRECTING DEFECT 33 (vertices=28, convex hull=42, v0=22639) After retessellation of defect 33 (v0=22639), euler #=-108 (97694,285325,187523) : difference with theory (-112) = -4 CORRECTING DEFECT 34 (vertices=47, convex hull=87, v0=23171) After retessellation of defect 34 (v0=23171), euler #=-107 (97718,285433,187608) : difference with theory (-111) = -4 CORRECTING DEFECT 35 (vertices=16, convex hull=27, v0=27757) After retessellation of defect 35 (v0=27757), euler #=-106 (97719,285445,187620) : difference with theory (-110) = -4 CORRECTING DEFECT 36 (vertices=19, convex hull=33, v0=27905) After retessellation of defect 36 (v0=27905), euler #=-105 (97723,285472,187644) : difference with theory (-109) = -4 CORRECTING DEFECT 37 (vertices=31, convex hull=23, v0=30410) After retessellation of defect 37 (v0=30410), euler #=-104 (97724,285485,187657) : difference with theory (-108) = -4 CORRECTING DEFECT 38 (vertices=35, convex hull=86, v0=31086) After retessellation of defect 38 (v0=31086), euler #=-103 (97743,285574,187728) : difference with theory (-107) = -4 CORRECTING DEFECT 39 (vertices=210, convex hull=94, v0=31337) After retessellation of defect 39 (v0=31337), euler #=-102 (97786,285743,187855) : difference with theory (-106) = -4 CORRECTING DEFECT 40 (vertices=36, convex hull=43, v0=31720) After retessellation of defect 40 (v0=31720), euler #=-101 (97790,285771,187880) : difference with theory (-105) = -4 CORRECTING DEFECT 41 (vertices=18, convex hull=55, v0=31979) After retessellation of defect 41 (v0=31979), euler #=-100 (97799,285818,187919) : difference with theory (-104) = -4 CORRECTING DEFECT 42 (vertices=447, convex hull=174, v0=33018) After retessellation of defect 42 (v0=33018), euler #=-99 (97872,286121,188150) : difference with theory (-103) = -4 CORRECTING DEFECT 43 (vertices=313, convex hull=201, v0=33371) After retessellation of defect 43 (v0=33371), euler #=-98 (98000,286609,188511) : difference with theory (-102) = -4 CORRECTING DEFECT 44 (vertices=1244, convex hull=720, v0=33812) XL defect detected... After retessellation of defect 44 (v0=33812), euler #=-98 (98359,288080,189623) : difference with theory (-101) = -3 CORRECTING DEFECT 45 (vertices=23, convex hull=23, v0=33833) After retessellation of defect 45 (v0=33833), euler #=-97 (98361,288096,189638) : difference with theory (-100) = -3 CORRECTING DEFECT 46 (vertices=46, convex hull=23, v0=34258) After retessellation of defect 46 (v0=34258), euler #=-96 (98367,288120,189657) : difference with theory (-99) = -3 CORRECTING DEFECT 47 (vertices=196, convex hull=126, v0=34654) After retessellation of defect 47 (v0=34654), euler #=-95 (98414,288320,189811) : difference with theory (-98) = -3 CORRECTING DEFECT 48 (vertices=41, convex hull=72, v0=35489) After retessellation of defect 48 (v0=35489), euler #=-94 (98433,288405,189878) : difference with theory (-97) = -3 CORRECTING DEFECT 49 (vertices=28, convex hull=26, v0=38615) After retessellation of defect 49 (v0=38615), euler #=-93 (98434,288417,189890) : difference with theory (-96) = -3 CORRECTING DEFECT 50 (vertices=27, convex hull=17, v0=38950) After retessellation of defect 50 (v0=38950), euler #=-92 (98435,288424,189897) : difference with theory (-95) = -3 CORRECTING DEFECT 51 (vertices=8, convex hull=23, v0=39243) After retessellation of defect 51 (v0=39243), euler #=-91 (98435,288433,189907) : difference with theory (-94) = -3 CORRECTING DEFECT 52 (vertices=28, convex hull=32, v0=42446) After retessellation of defect 52 (v0=42446), euler #=-90 (98437,288450,189923) : difference with theory (-93) = -3 CORRECTING DEFECT 53 (vertices=146, convex hull=138, v0=42454) After retessellation of defect 53 (v0=42454), euler #=-89 (98471,288623,190063) : difference with theory (-92) = -3 CORRECTING DEFECT 54 (vertices=11, convex hull=33, v0=42915) After retessellation of defect 54 (v0=42915), euler #=-88 (98472,288638,190078) : difference with theory (-91) = -3 CORRECTING DEFECT 55 (vertices=37, convex hull=81, v0=43420) After retessellation of defect 55 (v0=43420), euler #=-87 (98494,288740,190159) : difference with theory (-90) = -3 CORRECTING DEFECT 56 (vertices=72, convex hull=112, v0=44623) After retessellation of defect 56 (v0=44623), euler #=-86 (98544,288939,190309) : difference with theory (-89) = -3 CORRECTING DEFECT 57 (vertices=53, convex hull=72, v0=44708) After retessellation of defect 57 (v0=44708), euler #=-85 (98572,289051,190394) : difference with theory (-88) = -3 CORRECTING DEFECT 58 (vertices=78, convex hull=70, v0=45435) After retessellation of defect 58 (v0=45435), euler #=-84 (98615,289210,190511) : difference with theory (-87) = -3 CORRECTING DEFECT 59 (vertices=21, convex hull=32, v0=45552) After retessellation of defect 59 (v0=45552), euler #=-83 (98618,289232,190531) : difference with theory (-86) = -3 CORRECTING DEFECT 60 (vertices=5, convex hull=21, v0=46397) After retessellation of defect 60 (v0=46397), euler #=-82 (98619,289241,190540) : difference with theory (-85) = -3 CORRECTING DEFECT 61 (vertices=50, convex hull=29, v0=47621) After retessellation of defect 61 (v0=47621), euler #=-81 (98628,289277,190568) : difference with theory (-84) = -3 CORRECTING DEFECT 62 (vertices=110, convex hull=68, v0=47793) After retessellation of defect 62 (v0=47793), euler #=-80 (98638,289338,190620) : difference with theory (-83) = -3 CORRECTING DEFECT 63 (vertices=428, convex hull=376, v0=48803) After retessellation of defect 63 (v0=48803), euler #=-78 (98784,289960,191098) : difference with theory (-82) = -4 CORRECTING DEFECT 64 (vertices=16, convex hull=26, v0=49962) After retessellation of defect 64 (v0=49962), euler #=-77 (98785,289972,191110) : difference with theory (-81) = -4 CORRECTING DEFECT 65 (vertices=895, convex hull=265, v0=50091) After retessellation of defect 65 (v0=50091), euler #=-77 (99012,290799,191710) : difference with theory (-80) = -3 CORRECTING DEFECT 66 (vertices=299, convex hull=160, v0=50709) After retessellation of defect 66 (v0=50709), euler #=-76 (99102,291144,191966) : difference with theory (-79) = -3 CORRECTING DEFECT 67 (vertices=40, convex hull=22, v0=51557) After retessellation of defect 67 (v0=51557), euler #=-75 (99108,291172,191989) : difference with theory (-78) = -3 CORRECTING DEFECT 68 (vertices=221, convex hull=196, v0=51587) After retessellation of defect 68 (v0=51587), euler #=-74 (99207,291570,192289) : difference with theory (-77) = -3 CORRECTING DEFECT 69 (vertices=6, convex hull=24, v0=52367) After retessellation of defect 69 (v0=52367), euler #=-73 (99209,291582,192300) : difference with theory (-76) = -3 CORRECTING DEFECT 70 (vertices=6, convex hull=19, v0=52626) After retessellation of defect 70 (v0=52626), euler #=-72 (99211,291595,192312) : difference with theory (-75) = -3 CORRECTING DEFECT 71 (vertices=347, convex hull=118, v0=52993) After retessellation of defect 71 (v0=52993), euler #=-70 (99250,291769,192449) : difference with theory (-74) = -4 CORRECTING DEFECT 72 (vertices=13, convex hull=26, v0=53076) After retessellation of defect 72 (v0=53076), euler #=-69 (99251,291781,192461) : difference with theory (-73) = -4 CORRECTING DEFECT 73 (vertices=7796, convex hull=2497, v0=53236) XL defect detected... After retessellation of defect 73 (v0=53236), euler #=-72 (101034,298584,197478) : difference with theory (-72) = 0 CORRECTING DEFECT 74 (vertices=639, convex hull=311, v0=53316) After retessellation of defect 74 (v0=53316), euler #=-71 (101253,299398,198074) : difference with theory (-71) = 0 CORRECTING DEFECT 75 (vertices=145, convex hull=159, v0=53362) After retessellation of defect 75 (v0=53362), euler #=-70 (101346,299749,198333) : difference with theory (-70) = 0 CORRECTING DEFECT 76 (vertices=35, convex hull=60, v0=53849) After retessellation of defect 76 (v0=53849), euler #=-69 (101367,299833,198397) : difference with theory (-69) = 0 CORRECTING DEFECT 77 (vertices=45, convex hull=81, v0=55058) After retessellation of defect 77 (v0=55058), euler #=-68 (101380,299910,198462) : difference with theory (-68) = 0 CORRECTING DEFECT 78 (vertices=24, convex hull=44, v0=55282) After retessellation of defect 78 (v0=55282), euler #=-67 (101385,299942,198490) : difference with theory (-67) = 0 CORRECTING DEFECT 79 (vertices=55, convex hull=86, v0=55287) After retessellation of defect 79 (v0=55287), euler #=-66 (101408,300046,198572) : difference with theory (-66) = 0 CORRECTING DEFECT 80 (vertices=25, convex hull=29, v0=56306) After retessellation of defect 80 (v0=56306), euler #=-65 (101411,300064,198588) : difference with theory (-65) = 0 CORRECTING DEFECT 81 (vertices=100, convex hull=60, v0=58263) After retessellation of defect 81 (v0=58263), euler #=-64 (101420,300112,198628) : difference with theory (-64) = 0 CORRECTING DEFECT 82 (vertices=87, convex hull=34, v0=59176) After retessellation of defect 82 (v0=59176), euler #=-63 (101424,300134,198647) : difference with theory (-63) = 0 CORRECTING DEFECT 83 (vertices=43, convex hull=23, v0=59670) After retessellation of defect 83 (v0=59670), euler #=-62 (101428,300151,198661) : difference with theory (-62) = 0 CORRECTING DEFECT 84 (vertices=848, convex hull=367, v0=59951) After retessellation of defect 84 (v0=59951), euler #=-61 (101684,301100,199355) : difference with theory (-61) = 0 CORRECTING DEFECT 85 (vertices=43, convex hull=66, v0=59986) After retessellation of defect 85 (v0=59986), euler #=-60 (101708,301198,199430) : difference with theory (-60) = 0 CORRECTING DEFECT 86 (vertices=1329, convex hull=318, v0=60475) L defect detected... After retessellation of defect 86 (v0=60475), euler #=-60 (101948,302085,200077) : difference with theory (-59) = 1 CORRECTING DEFECT 87 (vertices=35, convex hull=25, v0=60479) After retessellation of defect 87 (v0=60479), euler #=-59 (101952,302107,200096) : difference with theory (-58) = 1 CORRECTING DEFECT 88 (vertices=33, convex hull=37, v0=61546) After retessellation of defect 88 (v0=61546), euler #=-58 (101953,302123,200112) : difference with theory (-57) = 1 CORRECTING DEFECT 89 (vertices=102, convex hull=60, v0=61970) After retessellation of defect 89 (v0=61970), euler #=-57 (101973,302213,200183) : difference with theory (-56) = 1 CORRECTING DEFECT 90 (vertices=26, convex hull=34, v0=64030) After retessellation of defect 90 (v0=64030), euler #=-56 (101975,302227,200196) : difference with theory (-55) = 1 CORRECTING DEFECT 91 (vertices=19, convex hull=39, v0=64946) After retessellation of defect 91 (v0=64946), euler #=-55 (101985,302273,200233) : difference with theory (-54) = 1 CORRECTING DEFECT 92 (vertices=11, convex hull=27, v0=66009) After retessellation of defect 92 (v0=66009), euler #=-53 (101986,302287,200248) : difference with theory (-53) = 0 CORRECTING DEFECT 93 (vertices=32, convex hull=62, v0=66092) After retessellation of defect 93 (v0=66092), euler #=-52 (102003,302358,200303) : difference with theory (-52) = 0 CORRECTING DEFECT 94 (vertices=117, convex hull=116, v0=66234) After retessellation of defect 94 (v0=66234), euler #=-51 (102011,302443,200381) : difference with theory (-51) = 0 CORRECTING DEFECT 95 (vertices=6, convex hull=22, v0=75310) After retessellation of defect 95 (v0=75310), euler #=-50 (102013,302458,200395) : difference with theory (-50) = 0 CORRECTING DEFECT 96 (vertices=6, convex hull=30, v0=75597) After retessellation of defect 96 (v0=75597), euler #=-49 (102015,302473,200409) : difference with theory (-49) = 0 CORRECTING DEFECT 97 (vertices=60, convex hull=83, v0=77203) After retessellation of defect 97 (v0=77203), euler #=-48 (102047,302604,200509) : difference with theory (-48) = 0 CORRECTING DEFECT 98 (vertices=27, convex hull=42, v0=77629) After retessellation of defect 98 (v0=77629), euler #=-47 (102051,302631,200533) : difference with theory (-47) = 0 CORRECTING DEFECT 99 (vertices=6, convex hull=25, v0=79441) After retessellation of defect 99 (v0=79441), euler #=-46 (102053,302644,200545) : difference with theory (-46) = 0 CORRECTING DEFECT 100 (vertices=39, convex hull=30, v0=79932) After retessellation of defect 100 (v0=79932), euler #=-45 (102055,302657,200557) : difference with theory (-45) = 0 CORRECTING DEFECT 101 (vertices=62, convex hull=56, v0=79981) After retessellation of defect 101 (v0=79981), euler #=-44 (102065,302708,200599) : difference with theory (-44) = 0 CORRECTING DEFECT 102 (vertices=558, convex hull=299, v0=80096) After retessellation of defect 102 (v0=80096), euler #=-43 (102253,303429,201133) : difference with theory (-43) = 0 CORRECTING DEFECT 103 (vertices=1817, convex hull=557, v0=83379) XL defect detected... After retessellation of defect 103 (v0=83379), euler #=-42 (102527,304539,201970) : difference with theory (-42) = 0 CORRECTING DEFECT 104 (vertices=78, convex hull=81, v0=85920) After retessellation of defect 104 (v0=85920), euler #=-41 (102536,304596,202019) : difference with theory (-41) = 0 CORRECTING DEFECT 105 (vertices=299, convex hull=207, v0=86347) After retessellation of defect 105 (v0=86347), euler #=-40 (102641,305006,202325) : difference with theory (-40) = 0 CORRECTING DEFECT 106 (vertices=835, convex hull=361, v0=86474) After retessellation of defect 106 (v0=86474), euler #=-38 (102869,305880,202973) : difference with theory (-39) = -1 CORRECTING DEFECT 107 (vertices=220, convex hull=117, v0=88119) After retessellation of defect 107 (v0=88119), euler #=-36 (102929,306110,203145) : difference with theory (-38) = -2 CORRECTING DEFECT 108 (vertices=52, convex hull=32, v0=90152) After retessellation of defect 108 (v0=90152), euler #=-35 (102935,306140,203170) : difference with theory (-37) = -2 CORRECTING DEFECT 109 (vertices=16, convex hull=20, v0=91006) After retessellation of defect 109 (v0=91006), euler #=-34 (102935,306146,203177) : difference with theory (-36) = -2 CORRECTING DEFECT 110 (vertices=24, convex hull=46, v0=91170) After retessellation of defect 110 (v0=91170), euler #=-33 (102949,306199,203217) : difference with theory (-35) = -2 CORRECTING DEFECT 111 (vertices=66, convex hull=109, v0=92256) After retessellation of defect 111 (v0=92256), euler #=-32 (102986,306355,203337) : difference with theory (-34) = -2 CORRECTING DEFECT 112 (vertices=1039, convex hull=515, v0=92429) L defect detected... After retessellation of defect 112 (v0=92429), euler #=-31 (103209,307295,204055) : difference with theory (-33) = -2 CORRECTING DEFECT 113 (vertices=42, convex hull=71, v0=92960) After retessellation of defect 113 (v0=92960), euler #=-30 (103218,307352,204104) : difference with theory (-32) = -2 CORRECTING DEFECT 114 (vertices=125, convex hull=109, v0=94862) After retessellation of defect 114 (v0=94862), euler #=-29 (103263,307545,204253) : difference with theory (-31) = -2 CORRECTING DEFECT 115 (vertices=10, convex hull=24, v0=95432) After retessellation of defect 115 (v0=95432), euler #=-28 (103264,307557,204265) : difference with theory (-30) = -2 CORRECTING DEFECT 116 (vertices=70, convex hull=34, v0=96758) After retessellation of defect 116 (v0=96758), euler #=-27 (103273,307596,204296) : difference with theory (-29) = -2 CORRECTING DEFECT 117 (vertices=768, convex hull=235, v0=96995) After retessellation of defect 117 (v0=96995), euler #=-25 (103281,307732,204426) : difference with theory (-28) = -3 CORRECTING DEFECT 118 (vertices=71, convex hull=91, v0=99746) After retessellation of defect 118 (v0=99746), euler #=-24 (103325,307898,204549) : difference with theory (-27) = -3 CORRECTING DEFECT 119 (vertices=568, convex hull=364, v0=100217) After retessellation of defect 119 (v0=100217), euler #=-23 (103529,308683,205131) : difference with theory (-26) = -3 CORRECTING DEFECT 120 (vertices=72, convex hull=106, v0=100238) After retessellation of defect 120 (v0=100238), euler #=-22 (103557,308811,205232) : difference with theory (-25) = -3 CORRECTING DEFECT 121 (vertices=5, convex hull=23, v0=101174) After retessellation of defect 121 (v0=101174), euler #=-21 (103558,308820,205241) : difference with theory (-24) = -3 CORRECTING DEFECT 122 (vertices=42, convex hull=34, v0=105276) After retessellation of defect 122 (v0=105276), euler #=-21 (103565,308855,205269) : difference with theory (-23) = -2 CORRECTING DEFECT 123 (vertices=941, convex hull=411, v0=106075) L defect detected... After retessellation of defect 123 (v0=106075), euler #=-21 (103892,310052,206139) : difference with theory (-22) = -1 CORRECTING DEFECT 124 (vertices=13, convex hull=25, v0=109922) After retessellation of defect 124 (v0=109922), euler #=-20 (103895,310067,206152) : difference with theory (-21) = -1 CORRECTING DEFECT 125 (vertices=61, convex hull=74, v0=110723) After retessellation of defect 125 (v0=110723), euler #=-19 (103926,310189,206244) : difference with theory (-20) = -1 CORRECTING DEFECT 126 (vertices=824, convex hull=768, v0=111024) XL defect detected... After retessellation of defect 126 (v0=111024), euler #=-19 (104374,311970,207577) : difference with theory (-19) = 0 CORRECTING DEFECT 127 (vertices=10, convex hull=13, v0=114710) After retessellation of defect 127 (v0=114710), euler #=-18 (104374,311973,207581) : difference with theory (-18) = 0 CORRECTING DEFECT 128 (vertices=230, convex hull=116, v0=115257) After retessellation of defect 128 (v0=115257), euler #=-17 (104440,312228,207771) : difference with theory (-17) = 0 CORRECTING DEFECT 129 (vertices=1317, convex hull=374, v0=115812) L defect detected... After retessellation of defect 129 (v0=115812), euler #=-20 (104582,312871,208269) : difference with theory (-16) = 4 CORRECTING DEFECT 130 (vertices=65, convex hull=99, v0=116683) After retessellation of defect 130 (v0=116683), euler #=-19 (104620,313019,208380) : difference with theory (-15) = 4 CORRECTING DEFECT 131 (vertices=94, convex hull=47, v0=116865) After retessellation of defect 131 (v0=116865), euler #=-18 (104629,313068,208421) : difference with theory (-14) = 4 CORRECTING DEFECT 132 (vertices=23, convex hull=24, v0=118548) After retessellation of defect 132 (v0=118548), euler #=-17 (104631,313082,208434) : difference with theory (-13) = 4 CORRECTING DEFECT 133 (vertices=39, convex hull=36, v0=120770) After retessellation of defect 133 (v0=120770), euler #=-16 (104634,313104,208454) : difference with theory (-12) = 4 CORRECTING DEFECT 134 (vertices=100, convex hull=118, v0=121263) After retessellation of defect 134 (v0=121263), euler #=-15 (104674,313274,208585) : difference with theory (-11) = 4 CORRECTING DEFECT 135 (vertices=248, convex hull=158, v0=123077) After retessellation of defect 135 (v0=123077), euler #=-14 (104751,313578,208813) : difference with theory (-10) = 4 CORRECTING DEFECT 136 (vertices=32, convex hull=26, v0=123578) After retessellation of defect 136 (v0=123578), euler #=-13 (104755,313599,208831) : difference with theory (-9) = 4 CORRECTING DEFECT 137 (vertices=506, convex hull=565, v0=124096) L defect detected... After retessellation of defect 137 (v0=124096), euler #=-10 (104963,314532,209559) : difference with theory (-8) = 2 CORRECTING DEFECT 138 (vertices=15, convex hull=52, v0=124683) After retessellation of defect 138 (v0=124683), euler #=-9 (104965,314556,209582) : difference with theory (-7) = 2 CORRECTING DEFECT 139 (vertices=32, convex hull=29, v0=126913) After retessellation of defect 139 (v0=126913), euler #=-8 (104970,314583,209605) : difference with theory (-6) = 2 CORRECTING DEFECT 140 (vertices=111, convex hull=104, v0=127143) After retessellation of defect 140 (v0=127143), euler #=-7 (105005,314732,209720) : difference with theory (-5) = 2 CORRECTING DEFECT 141 (vertices=70, convex hull=42, v0=127733) After retessellation of defect 141 (v0=127733), euler #=-6 (105010,314764,209748) : difference with theory (-4) = 2 CORRECTING DEFECT 142 (vertices=203, convex hull=131, v0=128241) After retessellation of defect 142 (v0=128241), euler #=-4 (105038,314910,209868) : difference with theory (-3) = 1 CORRECTING DEFECT 143 (vertices=9, convex hull=20, v0=128316) After retessellation of defect 143 (v0=128316), euler #=-3 (105039,314918,209876) : difference with theory (-2) = 1 CORRECTING DEFECT 144 (vertices=120, convex hull=199, v0=129222) After retessellation of defect 144 (v0=129222), euler #=-2 (105115,315234,210117) : difference with theory (-1) = 1 CORRECTING DEFECT 145 (vertices=55, convex hull=83, v0=131029) After retessellation of defect 145 (v0=131029), euler #=-1 (105141,315346,210204) : difference with theory (0) = 1 CORRECTING DEFECT 146 (vertices=97, convex hull=100, v0=132448) After retessellation of defect 146 (v0=132448), euler #=0 (105171,315480,210309) : difference with theory (1) = 1 CORRECTING DEFECT 147 (vertices=57, convex hull=50, v0=133574) After retessellation of defect 147 (v0=133574), euler #=2 (105178,315528,210352) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.92 +- 0.40 (0.05-->30.94) (max @ vno 55585 --> 60411) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.92 +- 0.40 (0.05-->30.94) (max @ vno 55585 --> 60411) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 444 mutations (34.4%), 847 crossovers (65.6%), 2642 vertices were eliminated building final representation... 28802 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=105178, nf=210352, ne=315528, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 663.5 minutes 0 defective edges removing intersecting faces 000: 2690 intersecting 001: 146 intersecting 002: 44 intersecting 003: 31 intersecting expanding nbhd size to 2 004: 37 intersecting expanding nbhd size to 3 005: 57 intersecting 006: 33 intersecting 007: 28 intersecting 008: 5 intersecting expanding nbhd size to 4 009: 5 intersecting mris_fix_topology utimesec 39807.188387 mris_fix_topology stimesec 7.190906 mris_fix_topology ru_maxrss 1081080 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 119867 mris_fix_topology ru_majflt 1 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 21440 mris_fix_topology ru_oublock 11312 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 665 mris_fix_topology ru_nivcsw 148731 FSRUNTIME@ mris_fix_topology lh 11.0582 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050815 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=-646 (nv=140682, nf=282656, ne=423984, g=324) 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 10 iterations marking ambiguous vertices... 85999 ambiguous faces found in tessellation segmenting defects... 195 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 15 into 0 -merging segment 29 into 5 -merging segment 19 into 17 -merging segment 45 into 36 -merging segment 65 into 62 -merging segment 85 into 62 -merging segment 80 into 73 -merging segment 123 into 74 -merging segment 77 into 78 -merging segment 99 into 92 -merging segment 107 into 98 -merging segment 102 into 98 -merging segment 106 into 98 -merging segment 128 into 104 -merging segment 125 into 114 -merging segment 127 into 116 -merging segment 133 into 121 -merging segment 139 into 138 -merging segment 147 into 145 -merging segment 162 into 156 -merging segment 167 into 159 -merging segment 159 into 168 -merging segment 176 into 168 -merging segment 180 into 175 171 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2377 (-4.6188) -vertex loglikelihood: -6.8313 (-3.4157) -normal dot loglikelihood: -3.5243 (-3.5243) -quad curv loglikelihood: -6.1633 (-3.0816) Total Loglikelihood : -25.7565 CORRECTING DEFECT 0 (vertices=9543, convex hull=1959, v0=0) XL defect detected... After retessellation of defect 0 (v0=0), euler #=-172 (93668,270763,176923) : difference with theory (-168) = 4 CORRECTING DEFECT 1 (vertices=32, convex hull=42, v0=546) After retessellation of defect 1 (v0=546), euler #=-171 (93672,270789,176946) : difference with theory (-167) = 4 CORRECTING DEFECT 2 (vertices=49, convex hull=36, v0=611) After retessellation of defect 2 (v0=611), euler #=-170 (93673,270805,176962) : difference with theory (-166) = 4 CORRECTING DEFECT 3 (vertices=6, convex hull=27, v0=625) After retessellation of defect 3 (v0=625), euler #=-169 (93674,270814,176971) : difference with theory (-165) = 4 CORRECTING DEFECT 4 (vertices=10, convex hull=33, v0=776) After retessellation of defect 4 (v0=776), euler #=-168 (93675,270827,176984) : difference with theory (-164) = 4 CORRECTING DEFECT 5 (vertices=5969, convex hull=1240, v0=2869) XL defect detected... After retessellation of defect 5 (v0=2869), euler #=-171 (94657,274505,179677) : difference with theory (-163) = 8 CORRECTING DEFECT 6 (vertices=326, convex hull=106, v0=2954) After retessellation of defect 6 (v0=2954), euler #=-170 (94692,274670,179808) : difference with theory (-162) = 8 CORRECTING DEFECT 7 (vertices=85, convex hull=95, v0=3008) After retessellation of defect 7 (v0=3008), euler #=-169 (94715,274786,179902) : difference with theory (-161) = 8 CORRECTING DEFECT 8 (vertices=278, convex hull=171, v0=6053) After retessellation of defect 8 (v0=6053), euler #=-168 (94774,275040,180098) : difference with theory (-160) = 8 CORRECTING DEFECT 9 (vertices=32, convex hull=82, v0=6654) After retessellation of defect 9 (v0=6654), euler #=-167 (94783,275099,180149) : difference with theory (-159) = 8 CORRECTING DEFECT 10 (vertices=725, convex hull=201, v0=7048) After retessellation of defect 10 (v0=7048), euler #=-166 (94884,275506,180456) : difference with theory (-158) = 8 CORRECTING DEFECT 11 (vertices=457, convex hull=368, v0=7470) After retessellation of defect 11 (v0=7470), euler #=-165 (95068,276269,181036) : difference with theory (-157) = 8 CORRECTING DEFECT 12 (vertices=75, convex hull=35, v0=7980) After retessellation of defect 12 (v0=7980), euler #=-164 (95072,276295,181059) : difference with theory (-156) = 8 CORRECTING DEFECT 13 (vertices=5, convex hull=17, v0=15738) After retessellation of defect 13 (v0=15738), euler #=-163 (95072,276299,181064) : difference with theory (-155) = 8 CORRECTING DEFECT 14 (vertices=92, convex hull=50, v0=16501) After retessellation of defect 14 (v0=16501), euler #=-162 (95081,276343,181100) : difference with theory (-154) = 8 CORRECTING DEFECT 15 (vertices=109, convex hull=50, v0=19093) After retessellation of defect 15 (v0=19093), euler #=-161 (95092,276394,181141) : difference with theory (-153) = 8 CORRECTING DEFECT 16 (vertices=284, convex hull=172, v0=19599) After retessellation of defect 16 (v0=19599), euler #=-159 (95169,276712,181384) : difference with theory (-152) = 7 CORRECTING DEFECT 17 (vertices=128, convex hull=72, v0=21735) After retessellation of defect 17 (v0=21735), euler #=-158 (95184,276785,181443) : difference with theory (-151) = 7 CORRECTING DEFECT 18 (vertices=478, convex hull=130, v0=22579) After retessellation of defect 18 (v0=22579), euler #=-157 (95277,277123,181689) : difference with theory (-150) = 7 CORRECTING DEFECT 19 (vertices=6, convex hull=26, v0=22760) After retessellation of defect 19 (v0=22760), euler #=-156 (95278,277133,181699) : difference with theory (-149) = 7 CORRECTING DEFECT 20 (vertices=184, convex hull=47, v0=23966) After retessellation of defect 20 (v0=23966), euler #=-155 (95287,277177,181735) : difference with theory (-148) = 7 CORRECTING DEFECT 21 (vertices=368, convex hull=178, v0=24853) After retessellation of defect 21 (v0=24853), euler #=-154 (95392,277586,182040) : difference with theory (-147) = 7 CORRECTING DEFECT 22 (vertices=34, convex hull=67, v0=29433) After retessellation of defect 22 (v0=29433), euler #=-153 (95412,277673,182108) : difference with theory (-146) = 7 CORRECTING DEFECT 23 (vertices=3662, convex hull=835, v0=30291) XL defect detected... After retessellation of defect 23 (v0=30291), euler #=-154 (95894,279564,183516) : difference with theory (-145) = 9 CORRECTING DEFECT 24 (vertices=167, convex hull=72, v0=31625) After retessellation of defect 24 (v0=31625), euler #=-153 (95908,279638,183577) : difference with theory (-144) = 9 CORRECTING DEFECT 25 (vertices=490, convex hull=182, v0=33963) After retessellation of defect 25 (v0=33963), euler #=-152 (96019,280054,183883) : difference with theory (-143) = 9 CORRECTING DEFECT 26 (vertices=227, convex hull=133, v0=34350) After retessellation of defect 26 (v0=34350), euler #=-151 (96069,280269,184049) : difference with theory (-142) = 9 CORRECTING DEFECT 27 (vertices=108, convex hull=62, v0=34711) After retessellation of defect 27 (v0=34711), euler #=-150 (96097,280377,184130) : difference with theory (-141) = 9 CORRECTING DEFECT 28 (vertices=18, convex hull=66, v0=35342) After retessellation of defect 28 (v0=35342), euler #=-149 (96105,280422,184168) : difference with theory (-140) = 9 CORRECTING DEFECT 29 (vertices=74, convex hull=104, v0=35649) After retessellation of defect 29 (v0=35649), euler #=-148 (96130,280542,184264) : difference with theory (-139) = 9 CORRECTING DEFECT 30 (vertices=36, convex hull=83, v0=37379) After retessellation of defect 30 (v0=37379), euler #=-147 (96145,280621,184329) : difference with theory (-138) = 9 CORRECTING DEFECT 31 (vertices=40, convex hull=70, v0=39464) After retessellation of defect 31 (v0=39464), euler #=-146 (96165,280707,184396) : difference with theory (-137) = 9 CORRECTING DEFECT 32 (vertices=180, convex hull=64, v0=39788) After retessellation of defect 32 (v0=39788), euler #=-145 (96190,280810,184475) : difference with theory (-136) = 9 CORRECTING DEFECT 33 (vertices=541, convex hull=472, v0=39820) L defect detected... After retessellation of defect 33 (v0=39820), euler #=-143 (96487,281963,185333) : difference with theory (-135) = 8 CORRECTING DEFECT 34 (vertices=33, convex hull=70, v0=41272) After retessellation of defect 34 (v0=41272), euler #=-142 (96503,282035,185390) : difference with theory (-134) = 8 CORRECTING DEFECT 35 (vertices=52, convex hull=38, v0=41639) After retessellation of defect 35 (v0=41639), euler #=-141 (96512,282074,185421) : difference with theory (-133) = 8 CORRECTING DEFECT 36 (vertices=288, convex hull=244, v0=42892) After retessellation of defect 36 (v0=42892), euler #=-140 (96628,282532,185764) : difference with theory (-132) = 8 CORRECTING DEFECT 37 (vertices=490, convex hull=215, v0=43344) After retessellation of defect 37 (v0=43344), euler #=-139 (96724,282913,186050) : difference with theory (-131) = 8 CORRECTING DEFECT 38 (vertices=51, convex hull=38, v0=44842) After retessellation of defect 38 (v0=44842), euler #=-138 (96733,282953,186082) : difference with theory (-130) = 8 CORRECTING DEFECT 39 (vertices=352, convex hull=201, v0=46114) After retessellation of defect 39 (v0=46114), euler #=-137 (96871,283460,186452) : difference with theory (-129) = 8 CORRECTING DEFECT 40 (vertices=205, convex hull=140, v0=46206) After retessellation of defect 40 (v0=46206), euler #=-136 (96911,283640,186593) : difference with theory (-128) = 8 CORRECTING DEFECT 41 (vertices=26, convex hull=30, v0=46732) After retessellation of defect 41 (v0=46732), euler #=-135 (96916,283667,186616) : difference with theory (-127) = 8 CORRECTING DEFECT 42 (vertices=69, convex hull=86, v0=47439) After retessellation of defect 42 (v0=47439), euler #=-134 (96951,283812,186727) : difference with theory (-126) = 8 CORRECTING DEFECT 43 (vertices=56, convex hull=97, v0=47636) After retessellation of defect 43 (v0=47636), euler #=-133 (96985,283954,186836) : difference with theory (-125) = 8 CORRECTING DEFECT 44 (vertices=66, convex hull=51, v0=48875) After retessellation of defect 44 (v0=48875), euler #=-132 (97009,284048,186907) : difference with theory (-124) = 8 CORRECTING DEFECT 45 (vertices=78, convex hull=102, v0=49150) After retessellation of defect 45 (v0=49150), euler #=-131 (97043,284191,187017) : difference with theory (-123) = 8 CORRECTING DEFECT 46 (vertices=40, convex hull=59, v0=49582) After retessellation of defect 46 (v0=49582), euler #=-130 (97052,284244,187062) : difference with theory (-122) = 8 CORRECTING DEFECT 47 (vertices=64, convex hull=125, v0=51883) After retessellation of defect 47 (v0=51883), euler #=-129 (97093,284422,187200) : difference with theory (-121) = 8 CORRECTING DEFECT 48 (vertices=53, convex hull=29, v0=52078) After retessellation of defect 48 (v0=52078), euler #=-128 (97094,284434,187212) : difference with theory (-120) = 8 CORRECTING DEFECT 49 (vertices=44, convex hull=75, v0=54500) After retessellation of defect 49 (v0=54500), euler #=-127 (97113,284521,187281) : difference with theory (-119) = 8 CORRECTING DEFECT 50 (vertices=332, convex hull=371, v0=54647) After retessellation of defect 50 (v0=54647), euler #=-126 (97317,285343,187900) : difference with theory (-118) = 8 CORRECTING DEFECT 51 (vertices=70, convex hull=101, v0=54902) After retessellation of defect 51 (v0=54902), euler #=-125 (97342,285464,187997) : difference with theory (-117) = 8 CORRECTING DEFECT 52 (vertices=631, convex hull=336, v0=55999) After retessellation of defect 52 (v0=55999), euler #=-124 (97414,285836,188298) : difference with theory (-116) = 8 CORRECTING DEFECT 53 (vertices=293, convex hull=261, v0=57683) After retessellation of defect 53 (v0=57683), euler #=-124 (97569,286447,188754) : difference with theory (-115) = 9 CORRECTING DEFECT 54 (vertices=37, convex hull=70, v0=57773) After retessellation of defect 54 (v0=57773), euler #=-123 (97585,286522,188814) : difference with theory (-114) = 9 CORRECTING DEFECT 55 (vertices=52, convex hull=72, v0=58306) After retessellation of defect 55 (v0=58306), euler #=-122 (97612,286632,188898) : difference with theory (-113) = 9 CORRECTING DEFECT 56 (vertices=34, convex hull=28, v0=58590) After retessellation of defect 56 (v0=58590), euler #=-121 (97620,286664,188923) : difference with theory (-112) = 9 CORRECTING DEFECT 57 (vertices=74, convex hull=41, v0=58725) After retessellation of defect 57 (v0=58725), euler #=-120 (97629,286711,188962) : difference with theory (-111) = 9 CORRECTING DEFECT 58 (vertices=604, convex hull=556, v0=59045) L defect detected... After retessellation of defect 58 (v0=59045), euler #=-117 (97891,287819,189811) : difference with theory (-110) = 7 CORRECTING DEFECT 59 (vertices=138, convex hull=126, v0=59883) After retessellation of defect 59 (v0=59883), euler #=-118 (97954,288076,190004) : difference with theory (-109) = 9 CORRECTING DEFECT 60 (vertices=76, convex hull=79, v0=60959) After retessellation of defect 60 (v0=60959), euler #=-117 (97977,288180,190086) : difference with theory (-108) = 9 CORRECTING DEFECT 61 (vertices=39, convex hull=38, v0=62027) After retessellation of defect 61 (v0=62027), euler #=-116 (97981,288204,190107) : difference with theory (-107) = 9 CORRECTING DEFECT 62 (vertices=136, convex hull=50, v0=62558) After retessellation of defect 62 (v0=62558), euler #=-115 (97994,288264,190155) : difference with theory (-106) = 9 CORRECTING DEFECT 63 (vertices=136, convex hull=159, v0=62639) After retessellation of defect 63 (v0=62639), euler #=-114 (98075,288583,190394) : difference with theory (-105) = 9 CORRECTING DEFECT 64 (vertices=20, convex hull=22, v0=62904) After retessellation of defect 64 (v0=62904), euler #=-113 (98075,288591,190403) : difference with theory (-104) = 9 CORRECTING DEFECT 65 (vertices=22, convex hull=59, v0=63236) After retessellation of defect 65 (v0=63236), euler #=-112 (98085,288643,190446) : difference with theory (-103) = 9 CORRECTING DEFECT 66 (vertices=90, convex hull=111, v0=63246) After retessellation of defect 66 (v0=63246), euler #=-111 (98135,288840,190594) : difference with theory (-102) = 9 CORRECTING DEFECT 67 (vertices=30, convex hull=67, v0=63436) After retessellation of defect 67 (v0=63436), euler #=-110 (98154,288922,190658) : difference with theory (-101) = 9 CORRECTING DEFECT 68 (vertices=132, convex hull=167, v0=63826) After retessellation of defect 68 (v0=63826), euler #=-108 (98223,289208,190877) : difference with theory (-100) = 8 CORRECTING DEFECT 69 (vertices=2657, convex hull=573, v0=65026) XL defect detected... After retessellation of defect 69 (v0=65026), euler #=-107 (98558,290512,191847) : difference with theory (-99) = 8 CORRECTING DEFECT 70 (vertices=22, convex hull=33, v0=65272) After retessellation of defect 70 (v0=65272), euler #=-106 (98561,290532,191865) : difference with theory (-98) = 8 CORRECTING DEFECT 71 (vertices=19, convex hull=13, v0=65374) After retessellation of defect 71 (v0=65374), euler #=-105 (98561,290536,191870) : difference with theory (-97) = 8 CORRECTING DEFECT 72 (vertices=377, convex hull=195, v0=66664) After retessellation of defect 72 (v0=66664), euler #=-103 (98590,290714,192021) : difference with theory (-96) = 7 CORRECTING DEFECT 73 (vertices=11, convex hull=27, v0=67756) After retessellation of defect 73 (v0=67756), euler #=-102 (98591,290724,192031) : difference with theory (-95) = 7 CORRECTING DEFECT 74 (vertices=58, convex hull=36, v0=69592) After retessellation of defect 74 (v0=69592), euler #=-101 (98599,290758,192058) : difference with theory (-94) = 7 CORRECTING DEFECT 75 (vertices=28, convex hull=29, v0=70294) After retessellation of defect 75 (v0=70294), euler #=-100 (98602,290776,192074) : difference with theory (-93) = 7 CORRECTING DEFECT 76 (vertices=52, convex hull=60, v0=72610) After retessellation of defect 76 (v0=72610), euler #=-99 (98621,290859,192139) : difference with theory (-92) = 7 CORRECTING DEFECT 77 (vertices=100, convex hull=117, v0=73113) After retessellation of defect 77 (v0=73113), euler #=-98 (98681,291092,192313) : difference with theory (-91) = 7 CORRECTING DEFECT 78 (vertices=28, convex hull=52, v0=75021) After retessellation of defect 78 (v0=75021), euler #=-98 (98694,291159,192367) : difference with theory (-90) = 8 CORRECTING DEFECT 79 (vertices=355, convex hull=184, v0=75998) After retessellation of defect 79 (v0=75998), euler #=-97 (98812,291610,192701) : difference with theory (-89) = 8 CORRECTING DEFECT 80 (vertices=22, convex hull=28, v0=76009) After retessellation of defect 80 (v0=76009), euler #=-96 (98815,291626,192715) : difference with theory (-88) = 8 CORRECTING DEFECT 81 (vertices=13, convex hull=32, v0=77040) After retessellation of defect 81 (v0=77040), euler #=-95 (98817,291641,192729) : difference with theory (-87) = 8 CORRECTING DEFECT 82 (vertices=55, convex hull=93, v0=77662) After retessellation of defect 82 (v0=77662), euler #=-94 (98847,291773,192832) : difference with theory (-86) = 8 CORRECTING DEFECT 83 (vertices=14, convex hull=24, v0=78080) After retessellation of defect 83 (v0=78080), euler #=-93 (98849,291785,192843) : difference with theory (-85) = 8 CORRECTING DEFECT 84 (vertices=16, convex hull=30, v0=79290) After retessellation of defect 84 (v0=79290), euler #=-91 (98852,291807,192864) : difference with theory (-84) = 7 CORRECTING DEFECT 85 (vertices=208, convex hull=197, v0=79364) After retessellation of defect 85 (v0=79364), euler #=-90 (98943,292169,193136) : difference with theory (-83) = 7 CORRECTING DEFECT 86 (vertices=28, convex hull=39, v0=79599) After retessellation of defect 86 (v0=79599), euler #=-89 (98946,292197,193162) : difference with theory (-82) = 7 CORRECTING DEFECT 87 (vertices=98, convex hull=62, v0=81156) After retessellation of defect 87 (v0=81156), euler #=-88 (98965,292281,193228) : difference with theory (-81) = 7 CORRECTING DEFECT 88 (vertices=326, convex hull=297, v0=82097) After retessellation of defect 88 (v0=82097), euler #=-88 (99084,292801,193629) : difference with theory (-80) = 8 CORRECTING DEFECT 89 (vertices=34, convex hull=70, v0=82476) After retessellation of defect 89 (v0=82476), euler #=-87 (99102,292882,193693) : difference with theory (-79) = 8 CORRECTING DEFECT 90 (vertices=1128, convex hull=554, v0=82711) L defect detected... After retessellation of defect 90 (v0=82711), euler #=-83 (99323,293839,194433) : difference with theory (-78) = 5 CORRECTING DEFECT 91 (vertices=260, convex hull=185, v0=83740) After retessellation of defect 91 (v0=83740), euler #=-82 (99390,294135,194663) : difference with theory (-77) = 5 CORRECTING DEFECT 92 (vertices=45, convex hull=78, v0=84149) After retessellation of defect 92 (v0=84149), euler #=-81 (99417,294249,194751) : difference with theory (-76) = 5 CORRECTING DEFECT 93 (vertices=84, convex hull=75, v0=86248) After retessellation of defect 93 (v0=86248), euler #=-80 (99437,294345,194828) : difference with theory (-75) = 5 CORRECTING DEFECT 94 (vertices=252, convex hull=235, v0=86548) After retessellation of defect 94 (v0=86548), euler #=-78 (99535,294757,195144) : difference with theory (-74) = 4 CORRECTING DEFECT 95 (vertices=59, convex hull=103, v0=87827) After retessellation of defect 95 (v0=87827), euler #=-77 (99566,294894,195251) : difference with theory (-73) = 4 CORRECTING DEFECT 96 (vertices=9, convex hull=14, v0=89843) After retessellation of defect 96 (v0=89843), euler #=-76 (99567,294900,195257) : difference with theory (-72) = 4 CORRECTING DEFECT 97 (vertices=15, convex hull=20, v0=90000) After retessellation of defect 97 (v0=90000), euler #=-75 (99568,294907,195264) : difference with theory (-71) = 4 CORRECTING DEFECT 98 (vertices=64, convex hull=24, v0=90359) After retessellation of defect 98 (v0=90359), euler #=-74 (99572,294924,195278) : difference with theory (-70) = 4 CORRECTING DEFECT 99 (vertices=123, convex hull=41, v0=91450) After retessellation of defect 99 (v0=91450), euler #=-73 (99579,294962,195310) : difference with theory (-69) = 4 CORRECTING DEFECT 100 (vertices=77, convex hull=93, v0=92043) After retessellation of defect 100 (v0=92043), euler #=-72 (99613,295104,195419) : difference with theory (-68) = 4 CORRECTING DEFECT 101 (vertices=39, convex hull=48, v0=92066) After retessellation of defect 101 (v0=92066), euler #=-71 (99620,295144,195453) : difference with theory (-67) = 4 CORRECTING DEFECT 102 (vertices=79, convex hull=98, v0=92882) After retessellation of defect 102 (v0=92882), euler #=-69 (99642,295255,195544) : difference with theory (-66) = 3 CORRECTING DEFECT 103 (vertices=165, convex hull=159, v0=93423) After retessellation of defect 103 (v0=93423), euler #=-68 (99714,295546,195764) : difference with theory (-65) = 3 CORRECTING DEFECT 104 (vertices=106, convex hull=211, v0=93444) After retessellation of defect 104 (v0=93444), euler #=-66 (99784,295851,196001) : difference with theory (-64) = 2 CORRECTING DEFECT 105 (vertices=535, convex hull=280, v0=94168) After retessellation of defect 105 (v0=94168), euler #=-65 (99919,296389,196405) : difference with theory (-63) = 2 CORRECTING DEFECT 106 (vertices=92, convex hull=52, v0=95528) After retessellation of defect 106 (v0=95528), euler #=-64 (99936,296458,196458) : difference with theory (-62) = 2 CORRECTING DEFECT 107 (vertices=122, convex hull=79, v0=95587) After retessellation of defect 107 (v0=95587), euler #=-63 (99945,296514,196506) : difference with theory (-61) = 2 CORRECTING DEFECT 108 (vertices=201, convex hull=116, v0=96646) After retessellation of defect 108 (v0=96646), euler #=-62 (100014,296778,196702) : difference with theory (-60) = 2 CORRECTING DEFECT 109 (vertices=726, convex hull=204, v0=97076) After retessellation of defect 109 (v0=97076), euler #=-60 (100118,297195,197017) : difference with theory (-59) = 1 CORRECTING DEFECT 110 (vertices=88, convex hull=34, v0=97295) After retessellation of defect 110 (v0=97295), euler #=-59 (100132,297249,197058) : difference with theory (-58) = 1 CORRECTING DEFECT 111 (vertices=52, convex hull=34, v0=97918) After retessellation of defect 111 (v0=97918), euler #=-58 (100141,297287,197088) : difference with theory (-57) = 1 CORRECTING DEFECT 112 (vertices=446, convex hull=155, v0=100207) After retessellation of defect 112 (v0=100207), euler #=-57 (100177,297474,197240) : difference with theory (-56) = 1 CORRECTING DEFECT 113 (vertices=21, convex hull=27, v0=100658) After retessellation of defect 113 (v0=100658), euler #=-56 (100180,297494,197258) : difference with theory (-55) = 1 CORRECTING DEFECT 114 (vertices=33, convex hull=80, v0=100853) After retessellation of defect 114 (v0=100853), euler #=-55 (100193,297566,197318) : difference with theory (-54) = 1 CORRECTING DEFECT 115 (vertices=425, convex hull=196, v0=100894) After retessellation of defect 115 (v0=100894), euler #=-54 (100261,297861,197546) : difference with theory (-53) = 1 CORRECTING DEFECT 116 (vertices=588, convex hull=327, v0=100976) After retessellation of defect 116 (v0=100976), euler #=-53 (100405,298443,197985) : difference with theory (-52) = 1 CORRECTING DEFECT 117 (vertices=13, convex hull=23, v0=102327) After retessellation of defect 117 (v0=102327), euler #=-52 (100408,298458,197998) : difference with theory (-51) = 1 CORRECTING DEFECT 118 (vertices=128, convex hull=166, v0=103665) After retessellation of defect 118 (v0=103665), euler #=-51 (100486,298771,198234) : difference with theory (-50) = 1 CORRECTING DEFECT 119 (vertices=32, convex hull=44, v0=104986) After retessellation of defect 119 (v0=104986), euler #=-50 (100491,298807,198266) : difference with theory (-49) = 1 CORRECTING DEFECT 120 (vertices=51, convex hull=65, v0=105713) After retessellation of defect 120 (v0=105713), euler #=-49 (100519,298920,198352) : difference with theory (-48) = 1 CORRECTING DEFECT 121 (vertices=763, convex hull=519, v0=105783) L defect detected... After retessellation of defect 121 (v0=105783), euler #=-49 (100730,299831,199052) : difference with theory (-47) = 2 CORRECTING DEFECT 122 (vertices=43, convex hull=23, v0=106829) After retessellation of defect 122 (v0=106829), euler #=-48 (100733,299846,199065) : difference with theory (-46) = 2 CORRECTING DEFECT 123 (vertices=11, convex hull=20, v0=107396) After retessellation of defect 123 (v0=107396), euler #=-47 (100736,299859,199076) : difference with theory (-45) = 2 CORRECTING DEFECT 124 (vertices=25, convex hull=62, v0=107675) After retessellation of defect 124 (v0=107675), euler #=-46 (100750,299923,199127) : difference with theory (-44) = 2 CORRECTING DEFECT 125 (vertices=41, convex hull=25, v0=109172) After retessellation of defect 125 (v0=109172), euler #=-45 (100755,299944,199144) : difference with theory (-43) = 2 CORRECTING DEFECT 126 (vertices=182, convex hull=54, v0=113647) After retessellation of defect 126 (v0=113647), euler #=-44 (100763,299996,199189) : difference with theory (-42) = 2 CORRECTING DEFECT 127 (vertices=98, convex hull=141, v0=113949) After retessellation of defect 127 (v0=113949), euler #=-42 (100798,300164,199324) : difference with theory (-41) = 1 CORRECTING DEFECT 128 (vertices=184, convex hull=130, v0=114261) After retessellation of defect 128 (v0=114261), euler #=-42 (100883,300483,199558) : difference with theory (-40) = 2 CORRECTING DEFECT 129 (vertices=605, convex hull=532, v0=115363) L defect detected... After retessellation of defect 129 (v0=115363), euler #=-42 (101157,301591,200392) : difference with theory (-39) = 3 CORRECTING DEFECT 130 (vertices=1302, convex hull=310, v0=115834) After retessellation of defect 130 (v0=115834), euler #=-41 (101189,301841,200611) : difference with theory (-38) = 3 CORRECTING DEFECT 131 (vertices=38, convex hull=72, v0=116414) After retessellation of defect 131 (v0=116414), euler #=-40 (101208,301923,200675) : difference with theory (-37) = 3 CORRECTING DEFECT 132 (vertices=42, convex hull=30, v0=116845) After retessellation of defect 132 (v0=116845), euler #=-39 (101210,301938,200689) : difference with theory (-36) = 3 CORRECTING DEFECT 133 (vertices=115, convex hull=118, v0=117355) After retessellation of defect 133 (v0=117355), euler #=-38 (101253,302116,200825) : difference with theory (-35) = 3 CORRECTING DEFECT 134 (vertices=22, convex hull=20, v0=118801) After retessellation of defect 134 (v0=118801), euler #=-37 (101254,302127,200836) : difference with theory (-34) = 3 CORRECTING DEFECT 135 (vertices=10, convex hull=18, v0=118848) After retessellation of defect 135 (v0=118848), euler #=-36 (101255,302135,200844) : difference with theory (-33) = 3 CORRECTING DEFECT 136 (vertices=33, convex hull=55, v0=119032) After retessellation of defect 136 (v0=119032), euler #=-35 (101264,302188,200889) : difference with theory (-32) = 3 CORRECTING DEFECT 137 (vertices=286, convex hull=119, v0=119471) After retessellation of defect 137 (v0=119471), euler #=-33 (101304,302375,201038) : difference with theory (-31) = 2 CORRECTING DEFECT 138 (vertices=38, convex hull=32, v0=120443) After retessellation of defect 138 (v0=120443), euler #=-32 (101310,302401,201059) : difference with theory (-30) = 2 CORRECTING DEFECT 139 (vertices=26, convex hull=33, v0=120592) After retessellation of defect 139 (v0=120592), euler #=-31 (101314,302424,201079) : difference with theory (-29) = 2 CORRECTING DEFECT 140 (vertices=234, convex hull=242, v0=121625) After retessellation of defect 140 (v0=121625), euler #=-30 (101418,302854,201406) : difference with theory (-28) = 2 CORRECTING DEFECT 141 (vertices=566, convex hull=131, v0=121911) After retessellation of defect 141 (v0=121911), euler #=-29 (101493,303156,201634) : difference with theory (-27) = 2 CORRECTING DEFECT 142 (vertices=389, convex hull=127, v0=123810) After retessellation of defect 142 (v0=123810), euler #=-28 (101523,303307,201756) : difference with theory (-26) = 2 CORRECTING DEFECT 143 (vertices=85, convex hull=36, v0=124145) After retessellation of defect 143 (v0=124145), euler #=-27 (101541,303373,201805) : difference with theory (-25) = 2 CORRECTING DEFECT 144 (vertices=30, convex hull=61, v0=125317) After retessellation of defect 144 (v0=125317), euler #=-26 (101560,303453,201867) : difference with theory (-24) = 2 CORRECTING DEFECT 145 (vertices=128, convex hull=120, v0=126170) After retessellation of defect 145 (v0=126170), euler #=-25 (101598,303620,201997) : difference with theory (-23) = 2 CORRECTING DEFECT 146 (vertices=600, convex hull=524, v0=127015) L defect detected... After retessellation of defect 146 (v0=127015), euler #=-21 (101865,304699,202813) : difference with theory (-22) = -1 CORRECTING DEFECT 147 (vertices=93, convex hull=123, v0=127514) After retessellation of defect 147 (v0=127514), euler #=-21 (101895,304854,202938) : difference with theory (-21) = 0 CORRECTING DEFECT 148 (vertices=507, convex hull=205, v0=128837) After retessellation of defect 148 (v0=128837), euler #=-20 (101990,305254,203244) : difference with theory (-20) = 0 CORRECTING DEFECT 149 (vertices=104, convex hull=76, v0=129504) After retessellation of defect 149 (v0=129504), euler #=-19 (102014,305359,203326) : difference with theory (-19) = 0 CORRECTING DEFECT 150 (vertices=47, convex hull=66, v0=130055) After retessellation of defect 150 (v0=130055), euler #=-18 (102031,305438,203389) : difference with theory (-18) = 0 CORRECTING DEFECT 151 (vertices=52, convex hull=32, v0=130485) After retessellation of defect 151 (v0=130485), euler #=-17 (102037,305469,203415) : difference with theory (-17) = 0 CORRECTING DEFECT 152 (vertices=75, convex hull=52, v0=130861) After retessellation of defect 152 (v0=130861), euler #=-16 (102042,305506,203448) : difference with theory (-16) = 0 CORRECTING DEFECT 153 (vertices=145, convex hull=165, v0=132086) After retessellation of defect 153 (v0=132086), euler #=-14 (102098,305756,203644) : difference with theory (-15) = -1 CORRECTING DEFECT 154 (vertices=39, convex hull=85, v0=133958) After retessellation of defect 154 (v0=133958), euler #=-13 (102123,305862,203726) : difference with theory (-14) = -1 CORRECTING DEFECT 155 (vertices=25, convex hull=25, v0=134377) After retessellation of defect 155 (v0=134377), euler #=-12 (102125,305877,203740) : difference with theory (-13) = -1 CORRECTING DEFECT 156 (vertices=57, convex hull=51, v0=134887) After retessellation of defect 156 (v0=134887), euler #=-11 (102134,305925,203780) : difference with theory (-12) = -1 CORRECTING DEFECT 157 (vertices=6, convex hull=13, v0=135488) After retessellation of defect 157 (v0=135488), euler #=-10 (102135,305931,203786) : difference with theory (-11) = -1 CORRECTING DEFECT 158 (vertices=147, convex hull=138, v0=135701) After retessellation of defect 158 (v0=135701), euler #=-10 (102191,306167,203966) : difference with theory (-10) = 0 CORRECTING DEFECT 159 (vertices=32, convex hull=33, v0=135902) After retessellation of defect 159 (v0=135902), euler #=-9 (102193,306186,203984) : difference with theory (-9) = 0 CORRECTING DEFECT 160 (vertices=55, convex hull=45, v0=136257) After retessellation of defect 160 (v0=136257), euler #=-8 (102201,306228,204019) : difference with theory (-8) = 0 CORRECTING DEFECT 161 (vertices=96, convex hull=56, v0=136764) After retessellation of defect 161 (v0=136764), euler #=-7 (102215,306296,204074) : difference with theory (-7) = 0 CORRECTING DEFECT 162 (vertices=134, convex hull=220, v0=137117) After retessellation of defect 162 (v0=137117), euler #=-6 (102300,306655,204349) : difference with theory (-6) = 0 CORRECTING DEFECT 163 (vertices=165, convex hull=108, v0=137252) After retessellation of defect 163 (v0=137252), euler #=-5 (102338,306818,204475) : difference with theory (-5) = 0 CORRECTING DEFECT 164 (vertices=124, convex hull=134, v0=137334) After retessellation of defect 164 (v0=137334), euler #=-4 (102379,306997,204614) : difference with theory (-4) = 0 CORRECTING DEFECT 165 (vertices=6, convex hull=26, v0=137767) After retessellation of defect 165 (v0=137767), euler #=-3 (102380,307006,204623) : difference with theory (-3) = 0 CORRECTING DEFECT 166 (vertices=114, convex hull=109, v0=138535) After retessellation of defect 166 (v0=138535), euler #=-2 (102421,307181,204758) : difference with theory (-2) = 0 CORRECTING DEFECT 167 (vertices=71, convex hull=74, v0=138571) After retessellation of defect 167 (v0=138571), euler #=-1 (102435,307254,204818) : difference with theory (-1) = 0 CORRECTING DEFECT 168 (vertices=39, convex hull=23, v0=139716) After retessellation of defect 168 (v0=139716), euler #=0 (102438,307271,204833) : difference with theory (0) = 0 CORRECTING DEFECT 169 (vertices=47, convex hull=51, v0=139923) After retessellation of defect 169 (v0=139923), euler #=1 (102449,307325,204877) : difference with theory (1) = 0 CORRECTING DEFECT 170 (vertices=42, convex hull=46, v0=140391) After retessellation of defect 170 (v0=140391), euler #=2 (102455,307359,204906) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.93 +- 0.44 (0.03-->15.61) (max @ vno 6662 --> 8203) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.93 +- 0.44 (0.03-->15.61) (max @ vno 6662 --> 8203) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 499 mutations (35.9%), 892 crossovers (64.1%), 2874 vertices were eliminated building final representation... 38227 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=102455, nf=204906, ne=307359, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 459.2 minutes 0 defective edges removing intersecting faces 000: 3169 intersecting 001: 250 intersecting 002: 110 intersecting 003: 61 intersecting 004: 39 intersecting expanding nbhd size to 2 005: 39 intersecting 006: 33 intersecting mris_fix_topology utimesec 27566.343278 mris_fix_topology stimesec 1.140826 mris_fix_topology ru_maxrss 805644 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 147879 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 9928 mris_fix_topology ru_oublock 11512 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 664 mris_fix_topology ru_nivcsw 32141 FSRUNTIME@ mris_fix_topology rh 7.6531 hours 1 threads PIDs (25499 25502) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 105178 - 315528 + 210352 = 2 --> 0 holes F =2V-4: 210352 = 210356-4 (0) 2E=3F: 631056 = 631056 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 102455 - 307359 + 204906 = 2 --> 0 holes F =2V-4: 204906 = 204910-4 (0) 2E=3F: 614718 = 614718 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 989 intersecting 001: 110 intersecting 002: 55 intersecting 003: 44 intersecting 004: 33 intersecting 005: 29 intersecting 006: 11 intersecting 007: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 1194 intersecting 001: 192 intersecting 002: 104 intersecting 003: 63 intersecting 004: 40 intersecting 005: 39 intersecting 006: 3 intersecting expanding nbhd size to 2 007: 5 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 8 08:24:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050815 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 8 08:24:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050815 rh Waiting for PID 23678 of (23678 23681) to complete... Waiting for PID 23681 of (23678 23681) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050815 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... 19852 bright wm thresholded. 80 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.orig... computing class statistics... border white: 244265 voxels (1.46%) border gray 309669 voxels (1.85%) WM (91.0): 92.5 +- 9.0 [70.0 --> 110.0] GM (66.0) : 64.8 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.8 (was 70) setting MAX_BORDER_WHITE to 103.0 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 37.6 (was 40) setting MAX_GRAY to 85.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.30 (0.02-->8.50) (max @ vno 57900 --> 100501) face area 0.28 +- 0.19 (0.00-->10.09) mean absolute distance = 0.85 +- 1.14 3442 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=94+-9.6, GM=62+-10.4 mean inside = 87.6, mean outside = 69.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=74.9, 611 (611) missing vertices, mean dist 0.3 [0.9 (%30.9)->0.8 (%69.1))] %56 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.35 (0.05-->9.16) (max @ vno 57900 --> 100501) face area 0.28 +- 0.19 (0.00-->7.98) mean absolute distance = 0.47 +- 0.83 4108 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2881487.0, rms=11.002 001: dt: 0.5000, sse=1783206.1, rms=8.323 (24.351%) 002: dt: 0.5000, sse=1308046.2, rms=6.736 (19.069%) 003: dt: 0.5000, sse=1086346.5, rms=5.807 (13.787%) 004: dt: 0.5000, sse=971036.9, rms=5.291 (8.886%) 005: dt: 0.5000, sse=914673.8, rms=5.012 (5.274%) 006: dt: 0.5000, sse=893262.7, rms=4.840 (3.421%) 007: dt: 0.5000, sse=863954.9, rms=4.723 (2.419%) 008: dt: 0.5000, sse=846846.9, rms=4.645 (1.669%) 009: dt: 0.5000, sse=848819.1, rms=4.581 (1.371%) rms = 4.54, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=830734.8, rms=4.538 (0.939%) 011: dt: 0.2500, sse=690083.1, rms=3.603 (20.597%) 012: dt: 0.2500, sse=655974.2, rms=3.349 (7.067%) 013: dt: 0.2500, sse=647141.2, rms=3.286 (1.867%) rms = 3.25, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=648000.8, rms=3.250 (1.111%) 015: dt: 0.1250, sse=632699.0, rms=3.161 (2.710%) rms = 3.15, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=630632.1, rms=3.148 (0.418%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=77.5, 797 (268) missing vertices, mean dist -0.2 [0.5 (%62.6)->0.3 (%37.4))] %61 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.34 (0.08-->9.15) (max @ vno 57900 --> 100501) face area 0.35 +- 0.24 (0.00-->10.06) mean absolute distance = 0.39 +- 0.61 3665 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=954787.9, rms=4.547 017: dt: 0.5000, sse=862911.3, rms=3.907 (14.068%) rms = 4.01, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=759871.4, rms=3.248 (16.877%) 019: dt: 0.2500, sse=719439.5, rms=2.922 (10.014%) 020: dt: 0.2500, sse=721324.3, rms=2.812 (3.776%) rms = 2.77, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=715259.1, rms=2.768 (1.555%) 022: dt: 0.1250, sse=692856.5, rms=2.693 (2.716%) rms = 2.68, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=690784.2, rms=2.677 (0.610%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=79.0, 909 (234) missing vertices, mean dist -0.1 [0.5 (%55.7)->0.3 (%44.3))] %67 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.34 (0.09-->9.15) (max @ vno 57900 --> 100501) face area 0.35 +- 0.24 (0.00-->10.13) mean absolute distance = 0.36 +- 0.51 3104 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=781754.2, rms=3.454 rms = 3.45, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=719762.1, rms=2.971 (13.981%) 025: dt: 0.2500, sse=696222.4, rms=2.636 (11.275%) 026: dt: 0.2500, sse=689879.2, rms=2.556 (3.008%) rms = 2.52, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=680180.4, rms=2.517 (1.548%) 028: dt: 0.1250, sse=665185.8, rms=2.449 (2.691%) rms = 2.43, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=662825.7, rms=2.433 (0.663%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.0, 1013 (223) missing vertices, mean dist -0.1 [0.4 (%52.3)->0.3 (%47.7))] %73 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=694664.8, rms=2.757 rms = 2.82, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=655369.1, rms=2.343 (14.996%) 031: dt: 0.2500, sse=640572.3, rms=2.089 (10.862%) rms = 2.05, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=630682.2, rms=2.048 (1.954%) rms = 2.01, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=625531.8, rms=2.010 (1.847%) positioning took 0.4 minutes generating cortex label... 22 non-cortical segments detected only using segment with 7639 vertices erasing segment 0 (vno[0] = 27689) erasing segment 1 (vno[0] = 31590) erasing segment 2 (vno[0] = 34934) erasing segment 4 (vno[0] = 41104) erasing segment 5 (vno[0] = 42790) erasing segment 6 (vno[0] = 44360) erasing segment 7 (vno[0] = 45082) erasing segment 8 (vno[0] = 47493) erasing segment 9 (vno[0] = 52825) erasing segment 10 (vno[0] = 57070) erasing segment 11 (vno[0] = 58575) erasing segment 12 (vno[0] = 58851) erasing segment 13 (vno[0] = 59982) erasing segment 14 (vno[0] = 62580) erasing segment 15 (vno[0] = 72640) erasing segment 16 (vno[0] = 73289) erasing segment 17 (vno[0] = 76165) erasing segment 18 (vno[0] = 76476) erasing segment 19 (vno[0] = 79344) erasing segment 20 (vno[0] = 80198) erasing segment 21 (vno[0] = 81022) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.area vertex spacing 0.92 +- 0.34 (0.02-->9.12) (max @ vno 57900 --> 100501) face area 0.35 +- 0.24 (0.00-->10.42) refinement took 4.3 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050815 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... 19852 bright wm thresholded. 80 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.orig... computing class statistics... border white: 244265 voxels (1.46%) border gray 309669 voxels (1.85%) WM (91.0): 92.5 +- 9.0 [70.0 --> 110.0] GM (66.0) : 64.8 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.8 (was 70) setting MAX_BORDER_WHITE to 104.0 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 36.6 (was 40) setting MAX_GRAY to 86.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 48.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.31 (0.02-->6.95) (max @ vno 8042 --> 93095) face area 0.28 +- 0.19 (0.00-->8.05) mean absolute distance = 0.89 +- 1.15 3336 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=95+-8.7, GM=61+-12.2 mean inside = 87.7, mean outside = 70.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=74.3, 789 (789) missing vertices, mean dist 0.3 [1.0 (%28.5)->0.8 (%71.5))] %62 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, 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 0.93 +- 0.36 (0.04-->6.71) (max @ vno 31423 --> 95598) face area 0.28 +- 0.19 (0.00-->6.24) mean absolute distance = 0.48 +- 0.86 3893 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2979444.5, rms=11.230 001: dt: 0.5000, sse=1854160.8, rms=8.613 (23.306%) 002: dt: 0.5000, sse=1357096.5, rms=6.999 (18.737%) 003: dt: 0.5000, sse=1119437.5, rms=6.045 (13.638%) 004: dt: 0.5000, sse=1000549.5, rms=5.502 (8.979%) 005: dt: 0.5000, sse=935369.8, rms=5.199 (5.504%) 006: dt: 0.5000, sse=908940.1, rms=5.032 (3.221%) 007: dt: 0.5000, sse=902222.4, rms=4.934 (1.935%) 008: dt: 0.5000, sse=870042.8, rms=4.852 (1.669%) 009: dt: 0.5000, sse=861255.6, rms=4.792 (1.240%) 010: dt: 0.5000, sse=854534.9, rms=4.725 (1.381%) rms = 4.69, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=851052.6, rms=4.692 (0.717%) 012: dt: 0.2500, sse=708804.6, rms=3.820 (18.580%) 013: dt: 0.2500, sse=678181.7, rms=3.577 (6.357%) 014: dt: 0.2500, sse=671280.8, rms=3.513 (1.778%) rms = 3.48, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=670412.4, rms=3.480 (0.942%) 016: dt: 0.1250, sse=652835.6, rms=3.404 (2.189%) rms = 3.39, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=652825.4, rms=3.389 (0.447%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=77.0, 922 (324) missing vertices, mean dist -0.2 [0.6 (%62.5)->0.4 (%37.5))] %66 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.35 (0.07-->6.63) (max @ vno 31423 --> 95598) face area 0.36 +- 0.24 (0.00-->7.99) mean absolute distance = 0.40 +- 0.63 3286 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=985730.9, rms=4.770 018: dt: 0.5000, sse=895735.5, rms=4.057 (14.954%) rms = 4.17, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=781482.6, rms=3.450 (14.964%) 020: dt: 0.2500, sse=777223.0, rms=3.156 (8.522%) 021: dt: 0.2500, sse=737962.9, rms=3.062 (2.975%) rms = 3.02, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=741413.8, rms=3.020 (1.366%) 023: dt: 0.1250, sse=724835.6, rms=2.949 (2.358%) rms = 2.92, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=714427.7, rms=2.925 (0.822%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=78.5, 1024 (254) missing vertices, mean dist -0.1 [0.5 (%55.6)->0.3 (%44.4))] %72 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.93 +- 0.35 (0.04-->6.47) (max @ vno 8042 --> 93095) face area 0.36 +- 0.24 (0.00-->8.25) mean absolute distance = 0.36 +- 0.52 2999 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=796480.4, rms=3.592 rms = 3.58, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=817199.9, rms=3.584 (0.220%) 026: dt: 0.2500, sse=709798.1, rms=2.890 (19.358%) 027: dt: 0.2500, sse=700685.1, rms=2.732 (5.490%) rms = 2.71, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=693323.7, rms=2.710 (0.810%) 029: dt: 0.1250, sse=676909.4, rms=2.602 (3.956%) rms = 2.59, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=674910.6, rms=2.586 (0.624%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=79.4, 1163 (219) missing vertices, mean dist -0.1 [0.4 (%52.1)->0.3 (%47.9))] %76 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=701542.8, rms=2.854 rms = 2.86, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=659176.4, rms=2.466 (13.600%) 032: dt: 0.2500, sse=661410.1, rms=2.219 (10.005%) rms = 2.18, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=637605.7, rms=2.185 (1.551%) rms = 2.14, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=628701.1, rms=2.144 (1.887%) positioning took 0.4 minutes generating cortex label... 24 non-cortical segments detected only using segment with 7525 vertices erasing segment 0 (vno[0] = 14778) erasing segment 1 (vno[0] = 26161) erasing segment 3 (vno[0] = 34785) erasing segment 4 (vno[0] = 36319) erasing segment 5 (vno[0] = 39918) erasing segment 6 (vno[0] = 45197) erasing segment 7 (vno[0] = 49781) erasing segment 8 (vno[0] = 56845) erasing segment 9 (vno[0] = 58442) erasing segment 10 (vno[0] = 60299) erasing segment 11 (vno[0] = 60563) erasing segment 12 (vno[0] = 62217) erasing segment 13 (vno[0] = 62862) erasing segment 14 (vno[0] = 63729) erasing segment 15 (vno[0] = 66165) erasing segment 16 (vno[0] = 66935) erasing segment 17 (vno[0] = 67678) erasing segment 18 (vno[0] = 69002) erasing segment 19 (vno[0] = 70433) erasing segment 20 (vno[0] = 71354) erasing segment 21 (vno[0] = 72187) erasing segment 22 (vno[0] = 76224) erasing segment 23 (vno[0] = 79661) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.area vertex spacing 0.92 +- 0.35 (0.03-->6.48) (max @ vno 8042 --> 93095) face area 0.36 +- 0.24 (0.00-->8.25) refinement took 4.3 minutes PIDs (23678 23681) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 8 08:28:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 8 08:28:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 23990 of (23990 23993) to complete... Waiting for PID 23993 of (23990 23993) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... 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... PIDs (23990 23993) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 8 08:28:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 8 08:28:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 24035 of (24035 24038) to complete... Waiting for PID 24038 of (24035 24038) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.4 mm, total surface area = 64693 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.205 (target=0.015) step 005: RMS=0.151 (target=0.015) step 010: RMS=0.126 (target=0.015) step 015: RMS=0.109 (target=0.015) step 020: RMS=0.096 (target=0.015) step 025: RMS=0.085 (target=0.015) step 030: RMS=0.076 (target=0.015) step 035: RMS=0.068 (target=0.015) step 040: RMS=0.062 (target=0.015) step 045: RMS=0.057 (target=0.015) step 050: RMS=0.054 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.047 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 44.014308 mris_inflate stimesec 0.066989 mris_inflate ru_maxrss 157948 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 24208 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8240 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2067 mris_inflate ru_nivcsw 2518 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.4 mm, total surface area = 63431 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.207 (target=0.015) step 005: RMS=0.151 (target=0.015) step 010: RMS=0.127 (target=0.015) step 015: RMS=0.108 (target=0.015) step 020: RMS=0.094 (target=0.015) step 025: RMS=0.085 (target=0.015) step 030: RMS=0.074 (target=0.015) step 035: RMS=0.066 (target=0.015) step 040: RMS=0.059 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.049 (target=0.015) step 055: RMS=0.046 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 32.013133 mris_inflate stimesec 0.065989 mris_inflate ru_maxrss 154580 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23362 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8032 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1885 mris_inflate ru_nivcsw 2605 PIDs (24035 24038) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 8 08:29:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sun Oct 8 08:29:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf mris_curvature -w rh.white.preaparc 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 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 24172 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24175 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24178 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24181 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24184 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24187 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24190 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24193 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24196 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24200 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24204 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... Waiting for PID 24207 of (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 37.656*4pi (473.203) --> -37 handles ICI = 248.1, FI = 1705.1, variation=29464.312 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 135 vertices thresholded to be in k1 ~ [-0.71 2.34], k2 ~ [-1.97 0.18] total integrated curvature = -0.301*4pi (-3.780) --> 1 handles ICI = 1.1, FI = 7.8, variation=142.354 97 vertices thresholded to be in [-0.44 0.06] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = -0.000, std = 0.005 87 vertices thresholded to be in [-0.34 0.88] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.022, std = 0.028 done. mris_curvature -w rh.white.preaparc total integrated curvature = 52.896*4pi (664.715) --> -52 handles ICI = 267.4, FI = 2061.2, variation=34277.255 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 111 vertices thresholded to be in k1 ~ [-0.78 3.62], k2 ~ [-0.28 0.17] total integrated curvature = -0.210*4pi (-2.636) --> 1 handles ICI = 1.2, FI = 8.7, variation=154.224 98 vertices thresholded to be in [-0.12 0.07] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.004 92 vertices thresholded to be in [-0.35 1.50] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.023, std = 0.030 done. PIDs (24172 24175 24178 24181 24184 24187 24190 24193 24196 24200 24204 24207) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 8 08:30:20 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050815 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ 0050815/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 269 ] Gb_filter = 0 WARN: S lookup min: -0.673045 WARN: S explicit min: 0.000000 vertex = 251 #----------------------------------------- #@# Curvature Stats rh Sun Oct 8 08:30:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050815 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 [ 0050815/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 [ 236 ] Gb_filter = 0 WARN: S lookup min: -0.138407 WARN: S explicit min: 0.000000 vertex = 107 #-------------------------------------------- #@# Sphere lh Sun Oct 8 08:30:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 8 08:30:27 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 24501 of (24501 24504) to complete... Waiting for PID 24504 of (24501 24504) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.293... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %27.66 pass 1: epoch 2 of 3 starting distance error %27.05 unfolding complete - removing small folds... starting distance error %25.86 removing remaining folds... final distance error %25.94 MRISunfold() return, current seed 1234 -01: dt=0.0000, 600 negative triangles 386: dt=0.9900, 600 negative triangles 387: dt=0.9900, 331 negative triangles 388: dt=0.9900, 327 negative triangles 389: dt=0.9900, 264 negative triangles 390: dt=0.9900, 281 negative triangles 391: dt=0.9900, 252 negative triangles 392: dt=0.9900, 211 negative triangles 393: dt=0.9900, 209 negative triangles 394: dt=0.9900, 191 negative triangles 395: dt=0.9900, 164 negative triangles 396: dt=0.9900, 157 negative triangles 397: dt=0.9900, 141 negative triangles 398: dt=0.9900, 121 negative triangles 399: dt=0.9900, 91 negative triangles 400: dt=0.9900, 92 negative triangles 401: dt=0.9900, 85 negative triangles 402: dt=0.9900, 82 negative triangles 403: dt=0.9900, 80 negative triangles 404: dt=0.9900, 69 negative triangles 405: dt=0.9900, 67 negative triangles 406: dt=0.9900, 70 negative triangles 407: dt=0.9900, 56 negative triangles 408: dt=0.9900, 57 negative triangles 409: dt=0.9900, 57 negative triangles 410: dt=0.9900, 55 negative triangles 411: dt=0.9900, 41 negative triangles 412: dt=0.9900, 49 negative triangles 413: dt=0.9900, 40 negative triangles 414: dt=0.9900, 34 negative triangles 415: dt=0.9900, 41 negative triangles 416: dt=0.9900, 35 negative triangles 417: dt=0.9900, 31 negative triangles 418: dt=0.9900, 32 negative triangles 419: dt=0.9900, 24 negative triangles 420: dt=0.9900, 28 negative triangles 421: dt=0.9900, 29 negative triangles 422: dt=0.9900, 17 negative triangles 423: dt=0.9900, 17 negative triangles 424: dt=0.9900, 13 negative triangles 425: dt=0.9900, 12 negative triangles 426: dt=0.9900, 12 negative triangles 427: dt=0.9900, 12 negative triangles 428: dt=0.9900, 11 negative triangles 429: dt=0.9900, 10 negative triangles 430: dt=0.9900, 11 negative triangles 431: dt=0.9900, 17 negative triangles 432: dt=0.9900, 13 negative triangles 433: dt=0.9900, 11 negative triangles 434: dt=0.9900, 10 negative triangles 435: dt=0.9900, 13 negative triangles 436: dt=0.9900, 12 negative triangles 437: dt=0.9900, 12 negative triangles 438: dt=0.9900, 12 negative triangles 439: dt=0.9405, 15 negative triangles 440: dt=0.9405, 16 negative triangles 441: dt=0.9405, 13 negative triangles 442: dt=0.9405, 9 negative triangles 443: dt=0.9405, 11 negative triangles 444: dt=0.9405, 10 negative triangles 445: dt=0.9405, 13 negative triangles 446: dt=0.9405, 12 negative triangles 447: dt=0.9405, 9 negative triangles 448: dt=0.9405, 10 negative triangles 449: dt=0.9405, 10 negative triangles 450: dt=0.9405, 9 negative triangles 451: dt=0.9405, 12 negative triangles 452: dt=0.9405, 7 negative triangles 453: dt=0.9405, 9 negative triangles 454: dt=0.9405, 9 negative triangles 455: dt=0.9405, 9 negative triangles 456: dt=0.9405, 5 negative triangles 457: dt=0.9405, 8 negative triangles 458: dt=0.9405, 6 negative triangles 459: dt=0.9405, 6 negative triangles 460: dt=0.9405, 5 negative triangles 461: dt=0.9405, 6 negative triangles 462: dt=0.9405, 4 negative triangles 463: dt=0.9405, 2 negative triangles 464: dt=0.9405, 7 negative triangles 465: dt=0.9405, 2 negative triangles 466: dt=0.9405, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.22 hours mris_sphere utimesec 4604.793964 mris_sphere stimesec 1.137827 mris_sphere ru_maxrss 219040 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 39109 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 7464 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 156926 mris_sphere ru_nivcsw 340000 FSRUNTIME@ mris_sphere 1.2235 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/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 = 2 == scaling brain by 0.311... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, 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 %26.00 pass 1: epoch 2 of 3 starting distance error %25.67 unfolding complete - removing small folds... starting distance error %24.46 removing remaining folds... final distance error %24.55 MRISunfold() return, current seed 1234 -01: dt=0.0000, 438 negative triangles 368: dt=0.9900, 438 negative triangles 369: dt=0.9900, 184 negative triangles 370: dt=0.9900, 179 negative triangles 371: dt=0.9900, 154 negative triangles 372: dt=0.9900, 169 negative triangles 373: dt=0.9900, 149 negative triangles 374: dt=0.9900, 121 negative triangles 375: dt=0.9900, 117 negative triangles 376: dt=0.9900, 97 negative triangles 377: dt=0.9900, 96 negative triangles 378: dt=0.9900, 80 negative triangles 379: dt=0.9900, 93 negative triangles 380: dt=0.9900, 75 negative triangles 381: dt=0.9900, 73 negative triangles 382: dt=0.9900, 57 negative triangles 383: dt=0.9900, 56 negative triangles 384: dt=0.9900, 52 negative triangles 385: dt=0.9900, 41 negative triangles 386: dt=0.9900, 45 negative triangles 387: dt=0.9900, 42 negative triangles 388: dt=0.9900, 40 negative triangles 389: dt=0.9900, 28 negative triangles 390: dt=0.9900, 30 negative triangles 391: dt=0.9900, 22 negative triangles 392: dt=0.9900, 21 negative triangles 393: dt=0.9900, 22 negative triangles 394: dt=0.9900, 20 negative triangles 395: dt=0.9900, 13 negative triangles 396: dt=0.9900, 11 negative triangles 397: dt=0.9900, 13 negative triangles 398: dt=0.9900, 12 negative triangles 399: dt=0.9900, 15 negative triangles 400: dt=0.9900, 12 negative triangles 401: dt=0.9900, 11 negative triangles 402: dt=0.9900, 8 negative triangles 403: dt=0.9900, 5 negative triangles 404: dt=0.9900, 10 negative triangles 405: dt=0.9900, 15 negative triangles 406: dt=0.9900, 8 negative triangles 407: dt=0.9900, 4 negative triangles 408: dt=0.9900, 5 negative triangles 409: dt=0.9900, 5 negative triangles 410: dt=0.9900, 2 negative triangles 411: dt=0.9900, 2 negative triangles 412: dt=0.9900, 2 negative triangles 413: dt=0.9900, 2 negative triangles 414: dt=0.9900, 2 negative triangles 415: dt=0.9900, 2 negative triangles 416: dt=0.9900, 4 negative triangles 417: dt=0.9900, 3 negative triangles 418: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.14 hours mris_sphere utimesec 4102.938258 mris_sphere stimesec 1.560762 mris_sphere ru_maxrss 211300 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 38190 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 7264 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 148670 mris_sphere ru_nivcsw 342388 FSRUNTIME@ mris_sphere 1.1394 hours 1 threads PIDs (24501 24504) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 8 09:43:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Sun Oct 8 09:43:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 27305 of (27305 27308) to complete... Waiting for PID 27308 of (27305 27308) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 5.353 curvature mean = 0.015, std = 0.812 curvature mean = 0.011, std = 0.877 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 225973.9, tmin=0.9559 d=32.00 min @ (-8.00, -8.00, 8.00) sse = 215899.4, tmin=1.9295 d=16.00 min @ (0.00, 4.00, -4.00) sse = 199716.1, tmin=2.9103 d=4.00 min @ (1.00, 0.00, 1.00) sse = 198268.9, tmin=4.8902 d=1.00 min @ (0.00, 0.25, -0.25) sse = 198176.1, tmin=6.8807 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 198171.1, tmin=7.8741 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 7.87 min curvature mean = -0.005, std = 0.835 curvature mean = 0.006, std = 0.954 curvature mean = -0.008, std = 0.845 curvature mean = 0.002, std = 0.980 curvature mean = -0.010, std = 0.847 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.049, std = 0.371 curvature mean = 0.039, std = 0.247 curvature mean = 0.060, std = 0.296 curvature mean = 0.028, std = 0.311 curvature mean = 0.056, std = 0.401 curvature mean = 0.026, std = 0.339 curvature mean = 0.034, std = 0.523 curvature mean = 0.025, std = 0.350 curvature mean = 0.012, std = 0.651 MRISregister() return, current seed 0 -01: dt=0.0000, 495 negative triangles 128: dt=0.9900, 495 negative triangles 129: dt=0.9900, 457 negative triangles 130: dt=0.9900, 413 negative triangles 131: dt=0.9900, 360 negative triangles 132: dt=0.9900, 339 negative triangles 133: dt=0.9900, 338 negative triangles 134: dt=0.9900, 295 negative triangles 135: dt=0.9900, 264 negative triangles 136: dt=0.9900, 273 negative triangles 137: dt=0.9900, 221 negative triangles 138: dt=0.9900, 206 negative triangles 139: dt=0.9900, 194 negative triangles 140: dt=0.9900, 175 negative triangles 141: dt=0.9900, 177 negative triangles 142: dt=0.9900, 174 negative triangles 143: dt=0.9900, 156 negative triangles 144: dt=0.9900, 133 negative triangles 145: dt=0.9900, 128 negative triangles 146: dt=0.9900, 127 negative triangles 147: dt=0.9900, 111 negative triangles 148: dt=0.9900, 99 negative triangles 149: dt=0.9900, 88 negative triangles 150: dt=0.9900, 73 negative triangles 151: dt=0.9900, 78 negative triangles 152: dt=0.9900, 75 negative triangles 153: dt=0.9900, 72 negative triangles 154: dt=0.9900, 69 negative triangles 155: dt=0.9900, 72 negative triangles 156: dt=0.9900, 70 negative triangles 157: dt=0.9900, 66 negative triangles 158: dt=0.9900, 55 negative triangles 159: dt=0.9900, 63 negative triangles 160: dt=0.9900, 45 negative triangles 161: dt=0.9900, 53 negative triangles 162: dt=0.9900, 42 negative triangles 163: dt=0.9900, 48 negative triangles 164: dt=0.9900, 38 negative triangles 165: dt=0.9900, 44 negative triangles 166: dt=0.9900, 39 negative triangles 167: dt=0.9900, 39 negative triangles 168: dt=0.9900, 44 negative triangles 169: dt=0.9900, 39 negative triangles 170: dt=0.9900, 38 negative triangles 171: dt=0.9900, 41 negative triangles 172: dt=0.9900, 39 negative triangles 173: dt=0.9900, 36 negative triangles 174: dt=0.9900, 36 negative triangles 175: dt=0.9900, 33 negative triangles 176: dt=0.9900, 39 negative triangles 177: dt=0.9900, 37 negative triangles 178: dt=0.9900, 34 negative triangles 179: dt=0.9900, 37 negative triangles 180: dt=0.9900, 44 negative triangles 181: dt=0.9900, 38 negative triangles 182: dt=0.9900, 36 negative triangles 183: dt=0.9900, 36 negative triangles 184: dt=0.9900, 30 negative triangles 185: dt=0.9900, 28 negative triangles 186: dt=0.9900, 33 negative triangles 187: dt=0.9900, 29 negative triangles 188: dt=0.9900, 28 negative triangles 189: dt=0.9900, 27 negative triangles 190: dt=0.9900, 24 negative triangles 191: dt=0.9900, 28 negative triangles 192: dt=0.9900, 27 negative triangles 193: dt=0.9900, 25 negative triangles 194: dt=0.9900, 27 negative triangles 195: dt=0.9900, 23 negative triangles 196: dt=0.9900, 27 negative triangles 197: dt=0.9900, 29 negative triangles 198: dt=0.9900, 30 negative triangles 199: dt=0.9900, 28 negative triangles 200: dt=0.9900, 27 negative triangles 201: dt=0.9900, 26 negative triangles 202: dt=0.9900, 28 negative triangles 203: dt=0.9900, 28 negative triangles 204: dt=0.9900, 24 negative triangles 205: dt=0.9405, 24 negative triangles 206: dt=0.9405, 25 negative triangles 207: dt=0.9405, 26 negative triangles 208: dt=0.9405, 24 negative triangles 209: dt=0.9405, 28 negative triangles 210: dt=0.9405, 30 negative triangles 211: dt=0.9405, 31 negative triangles 212: dt=0.9405, 28 negative triangles 213: dt=0.9405, 26 negative triangles 214: dt=0.9405, 26 negative triangles 215: dt=0.8935, 31 negative triangles 216: dt=0.8935, 28 negative triangles 217: dt=0.8935, 25 negative triangles 218: dt=0.8935, 27 negative triangles 219: dt=0.8935, 31 negative triangles 220: dt=0.8935, 24 negative triangles 221: dt=0.8935, 20 negative triangles 222: dt=0.8935, 25 negative triangles 223: dt=0.8935, 22 negative triangles 224: dt=0.8935, 20 negative triangles 225: dt=0.8935, 22 negative triangles 226: dt=0.8935, 23 negative triangles 227: dt=0.8935, 22 negative triangles 228: dt=0.8935, 16 negative triangles 229: dt=0.8935, 22 negative triangles 230: dt=0.8935, 21 negative triangles 231: dt=0.8935, 22 negative triangles 232: dt=0.8935, 20 negative triangles 233: dt=0.8935, 19 negative triangles 234: dt=0.8935, 21 negative triangles 235: dt=0.8935, 22 negative triangles 236: dt=0.8935, 24 negative triangles 237: dt=0.8935, 29 negative triangles 238: dt=0.8488, 18 negative triangles 239: dt=0.8488, 18 negative triangles 240: dt=0.8488, 20 negative triangles 241: dt=0.8488, 16 negative triangles 242: dt=0.8488, 26 negative triangles 243: dt=0.8488, 21 negative triangles 244: dt=0.8488, 22 negative triangles 245: dt=0.8488, 14 negative triangles 246: dt=0.8488, 21 negative triangles 247: dt=0.8488, 17 negative triangles 248: dt=0.8488, 20 negative triangles 249: dt=0.8488, 19 negative triangles 250: dt=0.8488, 23 negative triangles 251: dt=0.8488, 19 negative triangles 252: dt=0.8488, 20 negative triangles 253: dt=0.8488, 19 negative triangles 254: dt=0.8488, 20 negative triangles 255: dt=0.8064, 22 negative triangles 256: dt=0.8064, 22 negative triangles 257: dt=0.8064, 15 negative triangles 258: dt=0.8064, 14 negative triangles 259: dt=0.8064, 12 negative triangles 260: dt=0.8064, 16 negative triangles 261: dt=0.8064, 14 negative triangles 262: dt=0.8064, 14 negative triangles 263: dt=0.8064, 16 negative triangles 264: dt=0.8064, 17 negative triangles 265: dt=0.8064, 17 negative triangles 266: dt=0.8064, 13 negative triangles 267: dt=0.8064, 14 negative triangles 268: dt=0.8064, 13 negative triangles 269: dt=0.7660, 12 negative triangles 270: dt=0.7660, 14 negative triangles 271: dt=0.7660, 17 negative triangles 272: dt=0.7660, 15 negative triangles 273: dt=0.7660, 14 negative triangles 274: dt=0.7660, 13 negative triangles 275: dt=0.7660, 12 negative triangles 276: dt=0.7660, 12 negative triangles 277: dt=0.7660, 11 negative triangles 278: dt=0.7660, 16 negative triangles 279: dt=0.7660, 14 negative triangles 280: dt=0.7660, 14 negative triangles 281: dt=0.7660, 14 negative triangles 282: dt=0.7660, 14 negative triangles 283: dt=0.7660, 11 negative triangles 284: dt=0.7660, 12 negative triangles 285: dt=0.7660, 11 negative triangles 286: dt=0.7660, 12 negative triangles 287: dt=0.7277, 11 negative triangles 288: dt=0.7277, 16 negative triangles 289: dt=0.7277, 13 negative triangles 290: dt=0.7277, 11 negative triangles 291: dt=0.7277, 13 negative triangles 292: dt=0.7277, 12 negative triangles 293: dt=0.7277, 16 negative triangles 294: dt=0.7277, 13 negative triangles 295: dt=0.7277, 12 negative triangles 296: dt=0.7277, 9 negative triangles 297: dt=0.7277, 8 negative triangles 298: dt=0.7277, 9 negative triangles 299: dt=0.7277, 10 negative triangles 300: dt=0.7277, 11 negative triangles 301: dt=0.7277, 11 negative triangles 302: dt=0.7277, 10 negative triangles 303: dt=0.7277, 11 negative triangles 304: dt=0.7277, 11 negative triangles 305: dt=0.7277, 12 negative triangles 306: dt=0.7277, 12 negative triangles 307: dt=0.6914, 17 negative triangles 308: dt=0.6914, 11 negative triangles 309: dt=0.6914, 6 negative triangles 310: dt=0.6914, 9 negative triangles 311: dt=0.6914, 6 negative triangles 312: dt=0.6914, 6 negative triangles 313: dt=0.6914, 6 negative triangles 314: dt=0.6914, 7 negative triangles 315: dt=0.6914, 5 negative triangles 316: dt=0.6914, 8 negative triangles 317: dt=0.6914, 6 negative triangles 318: dt=0.6914, 3 negative triangles 319: dt=0.6914, 3 negative triangles 320: dt=0.6914, 2 negative triangles 321: dt=0.6914, 5 negative triangles 322: dt=0.6914, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.97 hours mris_register utimesec 3483.557418 mris_register stimesec 1.839720 mris_register ru_maxrss 211236 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 31747 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 7520 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 265706 mris_register ru_nivcsw 187020 FSRUNTIME@ mris_register 0.9677 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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=tars-, 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=tars-, 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 = 5.549 curvature mean = 0.005, std = 0.795 curvature mean = 0.010, std = 0.888 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 275776.9, tmin=0.9268 d=32.00 min @ (0.00, 8.00, 8.00) sse = 235049.7, tmin=1.8654 d=16.00 min @ (4.00, 0.00, -4.00) sse = 233092.9, tmin=2.8154 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 229819.8, tmin=3.7816 d=4.00 min @ (1.00, 1.00, 0.00) sse = 229611.0, tmin=4.7519 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 229415.2, tmin=5.7256 d=1.00 min @ (-0.25, -0.25, 0.25) sse = 229364.6, tmin=6.6929 d=0.50 min @ (0.12, 0.00, 0.00) sse = 229350.8, tmin=7.6591 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 7.66 min curvature mean = -0.015, std = 0.815 curvature mean = 0.004, std = 0.957 curvature mean = -0.017, std = 0.825 curvature mean = 0.001, std = 0.982 curvature mean = -0.018, std = 0.828 curvature mean = -0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.046, std = 0.396 curvature mean = 0.036, std = 0.235 curvature mean = 0.049, std = 0.272 curvature mean = 0.022, std = 0.298 curvature mean = 0.048, std = 0.373 curvature mean = 0.020, std = 0.324 curvature mean = 0.029, std = 0.489 curvature mean = 0.020, std = 0.335 curvature mean = 0.010, std = 0.603 MRISregister() return, current seed 0 -01: dt=0.0000, 362 negative triangles 131: dt=0.9900, 362 negative triangles expanding nbhd size to 1 132: dt=0.9900, 427 negative triangles 133: dt=0.9900, 345 negative triangles 134: dt=0.9900, 342 negative triangles 135: dt=0.9900, 334 negative triangles 136: dt=0.9900, 320 negative triangles 137: dt=0.9900, 293 negative triangles 138: dt=0.9900, 277 negative triangles 139: dt=0.9900, 255 negative triangles 140: dt=0.9900, 238 negative triangles 141: dt=0.9900, 214 negative triangles 142: dt=0.9900, 208 negative triangles 143: dt=0.9900, 182 negative triangles 144: dt=0.9900, 167 negative triangles 145: dt=0.9900, 156 negative triangles 146: dt=0.9900, 145 negative triangles 147: dt=0.9900, 145 negative triangles 148: dt=0.9900, 132 negative triangles 149: dt=0.9900, 128 negative triangles 150: dt=0.9900, 121 negative triangles 151: dt=0.9900, 111 negative triangles 152: dt=0.9900, 108 negative triangles 153: dt=0.9900, 104 negative triangles 154: dt=0.9900, 93 negative triangles 155: dt=0.9900, 85 negative triangles 156: dt=0.9900, 81 negative triangles 157: dt=0.9900, 72 negative triangles 158: dt=0.9900, 68 negative triangles 159: dt=0.9900, 73 negative triangles 160: dt=0.9900, 68 negative triangles 161: dt=0.9900, 65 negative triangles 162: dt=0.9900, 65 negative triangles 163: dt=0.9900, 59 negative triangles 164: dt=0.9900, 59 negative triangles 165: dt=0.9900, 54 negative triangles 166: dt=0.9900, 51 negative triangles 167: dt=0.9900, 52 negative triangles 168: dt=0.9900, 53 negative triangles 169: dt=0.9900, 48 negative triangles 170: dt=0.9900, 49 negative triangles 171: dt=0.9900, 49 negative triangles 172: dt=0.9900, 43 negative triangles 173: dt=0.9900, 37 negative triangles 174: dt=0.9900, 37 negative triangles 175: dt=0.9900, 31 negative triangles 176: dt=0.9900, 34 negative triangles 177: dt=0.9900, 32 negative triangles 178: dt=0.9900, 32 negative triangles 179: dt=0.9900, 29 negative triangles 180: dt=0.9900, 27 negative triangles 181: dt=0.9900, 27 negative triangles 182: dt=0.9900, 25 negative triangles 183: dt=0.9900, 31 negative triangles 184: dt=0.9900, 23 negative triangles 185: dt=0.9900, 25 negative triangles 186: dt=0.9900, 21 negative triangles 187: dt=0.9900, 23 negative triangles 188: dt=0.9900, 18 negative triangles 189: dt=0.9900, 18 negative triangles 190: dt=0.9900, 17 negative triangles 191: dt=0.9900, 16 negative triangles 192: dt=0.9900, 17 negative triangles 193: dt=0.9900, 16 negative triangles 194: dt=0.9900, 17 negative triangles 195: dt=0.9900, 17 negative triangles 196: dt=0.9900, 15 negative triangles 197: dt=0.9900, 16 negative triangles 198: dt=0.9900, 15 negative triangles 199: dt=0.9900, 17 negative triangles 200: dt=0.9900, 16 negative triangles 201: dt=0.9900, 14 negative triangles 202: dt=0.9900, 14 negative triangles 203: dt=0.9900, 15 negative triangles 204: dt=0.9900, 15 negative triangles 205: dt=0.9900, 13 negative triangles 206: dt=0.9900, 11 negative triangles 207: dt=0.9900, 11 negative triangles 208: dt=0.9900, 13 negative triangles 209: dt=0.9900, 12 negative triangles 210: dt=0.9900, 11 negative triangles 211: dt=0.9900, 12 negative triangles 212: dt=0.9900, 10 negative triangles 213: dt=0.9900, 12 negative triangles 214: dt=0.9900, 12 negative triangles 215: dt=0.9900, 11 negative triangles 216: dt=0.9900, 12 negative triangles 217: dt=0.9900, 12 negative triangles 218: dt=0.9900, 11 negative triangles 219: dt=0.9900, 12 negative triangles 220: dt=0.9900, 10 negative triangles 221: dt=0.9900, 9 negative triangles 222: dt=0.9900, 7 negative triangles 223: dt=0.9900, 8 negative triangles 224: dt=0.9900, 5 negative triangles 225: dt=0.9900, 3 negative triangles 226: dt=0.9900, 4 negative triangles 227: dt=0.9900, 3 negative triangles 228: dt=0.9900, 3 negative triangles 229: dt=0.9900, 2 negative triangles 230: dt=0.9900, 2 negative triangles 231: dt=0.9900, 3 negative triangles 232: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.07 hours mris_register utimesec 4103.963102 mris_register stimesec 3.090530 mris_register ru_maxrss 209556 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 30395 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 7320 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 269711 mris_register ru_nivcsw 181004 FSRUNTIME@ mris_register 1.0732 hours 1 threads PIDs (27305 27308) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 10:48:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 10:48:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 29491 of (29491 29494) to complete... Waiting for PID 29494 of (29491 29494) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (29491 29494) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 10:48:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Sun Oct 8 10:48:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 29539 of (29539 29542) to complete... Waiting for PID 29542 of (29539 29542) to complete... mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (29539 29542) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 10:48:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Sun Oct 8 10:48:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 29589 of (29589 29592) to complete... Waiting for PID 29592 of (29589 29592) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1397 labels changed using aseg relabeling using gibbs priors... 000: 2611 changed, 105178 examined... 001: 614 changed, 10949 examined... 002: 142 changed, 3498 examined... 003: 49 changed, 810 examined... 004: 11 changed, 284 examined... 005: 2 changed, 75 examined... 006: 1 changed, 13 examined... 007: 1 changed, 6 examined... 008: 0 changed, 7 examined... 337 labels changed using aseg 000: 128 total segments, 88 labels (426 vertices) changed 001: 43 total segments, 3 labels (23 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 790 vertices marked for relabeling... 790 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 11 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1237 labels changed using aseg relabeling using gibbs priors... 000: 2400 changed, 102455 examined... 001: 585 changed, 10328 examined... 002: 135 changed, 3168 examined... 003: 46 changed, 812 examined... 004: 20 changed, 260 examined... 005: 5 changed, 111 examined... 006: 4 changed, 29 examined... 007: 0 changed, 29 examined... 236 labels changed using aseg 000: 105 total segments, 67 labels (429 vertices) changed 001: 43 total segments, 5 labels (21 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 13 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1003 vertices marked for relabeling... 1003 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 11 seconds. PIDs (29589 29592) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 10:48:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050815 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 10:48:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050815 rh Waiting for PID 29637 of (29637 29640) to complete... Waiting for PID 29640 of (29637 29640) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050815 lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... 19852 bright wm thresholded. 80 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.orig... computing class statistics... border white: 244265 voxels (1.46%) border gray 309669 voxels (1.85%) WM (91.0): 92.5 +- 9.0 [70.0 --> 110.0] GM (66.0) : 64.8 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.8 (was 70) setting MAX_BORDER_WHITE to 103.0 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 37.6 (was 40) setting MAX_GRAY to 85.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=94+-9.6, GM=62+-10.4 mean inside = 87.6, mean outside = 69.6 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.34 (0.02-->9.12) (max @ vno 57900 --> 100501) face area 0.35 +- 0.24 (0.00-->10.43) mean absolute distance = 0.64 +- 1.06 3137 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 120 points - only 0.00% unknown deleting segment 1 with 146 points - only 0.00% unknown deleting segment 2 with 24 points - only 0.00% unknown deleting segment 3 with 17 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown deleting segment 13 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown deleting segment 16 with 19 points - only 0.00% unknown deleting segment 17 with 13 points - only 0.00% unknown deleting segment 18 with 6 points - only 0.00% unknown mean border=75.0, 677 (677) missing vertices, mean dist 0.2 [1.1 (%20.6)->0.5 (%79.4))] %53 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.35 (0.10-->9.33) (max @ vno 57900 --> 100501) face area 0.35 +- 0.24 (0.00-->10.79) mean absolute distance = 0.45 +- 0.81 3660 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1409811.0, rms=6.645 001: dt: 0.5000, sse=995504.9, rms=4.761 (28.342%) 002: dt: 0.5000, sse=915047.6, rms=4.358 (8.470%) rms = 4.38, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=805625.1, rms=3.638 (16.533%) 004: dt: 0.2500, sse=766402.6, rms=3.303 (9.194%) 005: dt: 0.2500, sse=750508.5, rms=3.189 (3.464%) rms = 3.15, time step reduction 2 of 3 to 0.125... 006: dt: 0.2500, sse=747464.7, rms=3.148 (1.278%) 007: dt: 0.1250, sse=735538.9, rms=3.075 (2.331%) rms = 3.06, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=736256.2, rms=3.060 (0.468%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 105 points - only 0.00% unknown deleting segment 1 with 141 points - only 0.00% unknown deleting segment 2 with 46 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 18 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 18 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 26 points - only 0.00% unknown deleting segment 17 with 16 points - only 0.00% unknown deleting segment 18 with 6 points - only 0.00% unknown mean border=77.4, 743 (352) missing vertices, mean dist -0.2 [0.5 (%61.0)->0.3 (%39.0))] %61 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.34 (0.10-->9.33) (max @ vno 57900 --> 100501) face area 0.36 +- 0.24 (0.00-->11.19) mean absolute distance = 0.38 +- 0.60 3539 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=898863.9, rms=4.162 009: dt: 0.5000, sse=833734.6, rms=3.677 (11.654%) rms = 3.87, time step reduction 1 of 3 to 0.250... 010: dt: 0.2500, sse=744049.6, rms=3.035 (17.456%) 011: dt: 0.2500, sse=721136.3, rms=2.750 (9.395%) 012: dt: 0.2500, sse=730713.1, rms=2.680 (2.545%) rms = 2.64, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=703975.2, rms=2.641 (1.458%) 014: dt: 0.1250, sse=705966.8, rms=2.572 (2.615%) rms = 2.56, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=690163.2, rms=2.558 (0.523%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 117 points - only 0.00% unknown deleting segment 1 with 142 points - only 0.00% unknown deleting segment 2 with 80 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown deleting segment 11 with 19 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown deleting segment 14 with 6 points - only 16.67% unknown removing 4 vertex label from ripped group deleting segment 15 with 4 points - only 0.00% unknown deleting segment 16 with 27 points - only 0.00% unknown deleting segment 17 with 16 points - only 0.00% unknown deleting segment 18 with 6 points - only 0.00% unknown mean border=79.0, 914 (304) missing vertices, mean dist -0.1 [0.5 (%55.8)->0.3 (%44.2))] %68 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.34 (0.06-->9.37) (max @ vno 57900 --> 100501) face area 0.36 +- 0.24 (0.00-->11.13) mean absolute distance = 0.36 +- 0.51 3030 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=777084.2, rms=3.341 rms = 3.37, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=712962.2, rms=2.842 (14.937%) 017: dt: 0.2500, sse=691558.6, rms=2.516 (11.486%) 018: dt: 0.2500, sse=679185.6, rms=2.443 (2.874%) rms = 2.40, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=685165.2, rms=2.402 (1.708%) 020: dt: 0.1250, sse=662301.5, rms=2.335 (2.785%) rms = 2.32, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=658947.5, rms=2.321 (0.580%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 126 points - only 0.00% unknown deleting segment 1 with 142 points - only 0.00% unknown deleting segment 2 with 75 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 21 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 18 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown deleting segment 15 with 27 points - only 0.00% unknown deleting segment 16 with 16 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown mean border=80.0, 1069 (281) missing vertices, mean dist -0.1 [0.4 (%52.1)->0.3 (%47.9))] %73 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=688621.6, rms=2.644 rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=657385.4, rms=2.220 (16.027%) 023: dt: 0.2500, sse=641599.4, rms=1.961 (11.690%) rms = 1.93, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=639811.8, rms=1.932 (1.486%) rms = 1.89, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=628665.4, rms=1.889 (2.222%) positioning took 0.4 minutes generating cortex label... 21 non-cortical segments detected only using segment with 7658 vertices erasing segment 0 (vno[0] = 26833) erasing segment 1 (vno[0] = 31582) erasing segment 3 (vno[0] = 40160) erasing segment 4 (vno[0] = 40202) erasing segment 5 (vno[0] = 41086) erasing segment 6 (vno[0] = 43567) erasing segment 7 (vno[0] = 44360) erasing segment 8 (vno[0] = 44364) erasing segment 9 (vno[0] = 46671) erasing segment 10 (vno[0] = 53471) erasing segment 11 (vno[0] = 56144) erasing segment 12 (vno[0] = 57070) erasing segment 13 (vno[0] = 58575) erasing segment 14 (vno[0] = 62580) erasing segment 15 (vno[0] = 72640) erasing segment 16 (vno[0] = 73289) erasing segment 17 (vno[0] = 76165) erasing segment 18 (vno[0] = 79344) erasing segment 19 (vno[0] = 80198) erasing segment 20 (vno[0] = 81022) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.area vertex spacing 0.92 +- 0.35 (0.02-->9.43) (max @ vno 57900 --> 100501) face area 0.35 +- 0.24 (0.00-->10.98) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 87 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 8 with 37 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 33 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=48.0, 488 (488) missing vertices, mean dist 2.2 [1.7 (%0.1)->3.0 (%99.9))] %16 local maxima, %54 large gradients and %24 min vals, 480 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=21358006.0, rms=32.473 001: dt: 0.0500, sse=19037720.0, rms=30.609 (5.743%) 002: dt: 0.0500, sse=17342060.0, rms=29.170 (4.699%) 003: dt: 0.0500, sse=16018334.0, rms=27.996 (4.026%) 004: dt: 0.0500, sse=14930625.0, rms=26.993 (3.584%) 005: dt: 0.0500, sse=14004351.0, rms=26.108 (3.278%) 006: dt: 0.0500, sse=13194458.0, rms=25.309 (3.061%) 007: dt: 0.0500, sse=12472999.0, rms=24.575 (2.899%) 008: dt: 0.0500, sse=11820989.0, rms=23.892 (2.777%) 009: dt: 0.0500, sse=11226455.0, rms=23.253 (2.678%) 010: dt: 0.0500, sse=10679011.0, rms=22.647 (2.603%) positioning took 0.8 minutes mean border=47.9, 372 (228) missing vertices, mean dist 1.9 [0.9 (%0.2)->2.5 (%99.8))] %17 local maxima, %54 large gradients and %24 min vals, 429 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11438635.0, rms=23.464 011: dt: 0.0500, sse=10924911.0, rms=22.903 (2.390%) 012: dt: 0.0500, sse=10447501.0, rms=22.369 (2.331%) 013: dt: 0.0500, sse=10003930.0, rms=21.861 (2.270%) 014: dt: 0.0500, sse=9591207.0, rms=21.378 (2.211%) 015: dt: 0.0500, sse=9206844.0, rms=20.918 (2.153%) 016: dt: 0.0500, sse=8848977.0, rms=20.480 (2.093%) 017: dt: 0.0500, sse=8515137.0, rms=20.063 (2.037%) 018: dt: 0.0500, sse=8204153.0, rms=19.666 (1.977%) 019: dt: 0.0500, sse=7914475.5, rms=19.289 (1.916%) 020: dt: 0.0500, sse=7643852.5, rms=18.930 (1.861%) positioning took 0.8 minutes mean border=47.7, 405 (155) missing vertices, mean dist 1.6 [0.1 (%2.4)->2.2 (%97.6))] %17 local maxima, %54 large gradients and %24 min vals, 445 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=7752499.5, rms=19.074 021: dt: 0.0500, sse=7488101.0, rms=18.720 (1.858%) 022: dt: 0.0500, sse=7242915.5, rms=18.385 (1.788%) 023: dt: 0.0500, sse=7012005.5, rms=18.064 (1.746%) 024: dt: 0.0500, sse=6798514.5, rms=17.762 (1.672%) 025: dt: 0.0500, sse=6600465.0, rms=17.477 (1.604%) 026: dt: 0.0500, sse=6417150.5, rms=17.209 (1.533%) 027: dt: 0.0500, sse=6245653.5, rms=16.955 (1.480%) 028: dt: 0.0500, sse=6083227.5, rms=16.710 (1.444%) 029: dt: 0.0500, sse=5928435.0, rms=16.473 (1.417%) 030: dt: 0.0500, sse=5782635.5, rms=16.247 (1.373%) positioning took 0.8 minutes mean border=47.6, 490 (124) missing vertices, mean dist 1.4 [0.1 (%14.5)->2.2 (%85.5))] %17 local maxima, %54 large gradients and %23 min vals, 389 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5867619.5, rms=16.373 031: dt: 0.5000, sse=4806306.5, rms=14.644 (10.558%) 032: dt: 0.5000, sse=4160263.0, rms=13.474 (7.991%) 033: dt: 0.5000, sse=3685129.2, rms=12.549 (6.862%) 034: dt: 0.5000, sse=3364588.8, rms=11.874 (5.380%) 035: dt: 0.5000, sse=3103170.2, rms=11.300 (4.838%) 036: dt: 0.5000, sse=2910298.2, rms=10.849 (3.984%) 037: dt: 0.5000, sse=2745049.8, rms=10.453 (3.657%) 038: dt: 0.5000, sse=2620209.8, rms=10.138 (3.012%) 039: dt: 0.5000, sse=2507041.2, rms=9.848 (2.860%) 040: dt: 0.5000, sse=2422764.2, rms=9.622 (2.292%) 041: dt: 0.5000, sse=2343954.2, rms=9.411 (2.197%) 042: dt: 0.5000, sse=2288840.8, rms=9.255 (1.651%) 043: dt: 0.5000, sse=2237218.0, rms=9.111 (1.560%) 044: dt: 0.5000, sse=2197947.5, rms=8.996 (1.266%) 045: dt: 0.5000, sse=2160561.5, rms=8.888 (1.193%) 046: dt: 0.5000, sse=2137276.5, rms=8.816 (0.808%) 047: dt: 0.5000, sse=2107662.0, rms=8.731 (0.970%) 048: dt: 0.5000, sse=2088130.9, rms=8.670 (0.693%) 049: dt: 0.5000, sse=2062563.0, rms=8.595 (0.870%) 050: dt: 0.5000, sse=2043623.4, rms=8.536 (0.691%) 051: dt: 0.5000, sse=2017922.2, rms=8.460 (0.881%) rms = 8.43, time step reduction 1 of 3 to 0.250... 052: dt: 0.5000, sse=2007690.2, rms=8.425 (0.419%) 053: dt: 0.2500, sse=1946554.2, rms=8.216 (2.484%) 054: dt: 0.2500, sse=1929390.4, rms=8.160 (0.675%) rms = 8.15, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1928220.8, rms=8.155 (0.068%) 056: dt: 0.1250, sse=1913268.1, rms=8.105 (0.614%) rms = 8.09, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1909911.5, rms=8.094 (0.137%) positioning took 2.7 minutes mean border=46.2, 1948 (54) missing vertices, mean dist 0.5 [0.2 (%42.9)->1.3 (%57.1))] %31 local maxima, %40 large gradients and %21 min vals, 290 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=2093022.8, rms=8.045 058: dt: 0.5000, sse=1957293.4, rms=7.616 (5.338%) 059: dt: 0.5000, sse=1871210.9, rms=7.347 (3.521%) 060: dt: 0.5000, sse=1839755.8, rms=7.247 (1.365%) 061: dt: 0.5000, sse=1790172.9, rms=7.080 (2.303%) 062: dt: 0.5000, sse=1774245.9, rms=7.026 (0.769%) 063: dt: 0.5000, sse=1738868.1, rms=6.901 (1.771%) rms = 6.88, time step reduction 1 of 3 to 0.250... 064: dt: 0.5000, sse=1733914.2, rms=6.883 (0.267%) 065: dt: 0.2500, sse=1659795.4, rms=6.563 (4.649%) 066: dt: 0.2500, sse=1641185.6, rms=6.490 (1.112%) rms = 6.49, time step reduction 2 of 3 to 0.125... 067: dt: 0.2500, sse=1641471.8, rms=6.490 (0.001%) 068: dt: 0.1250, sse=1620309.1, rms=6.401 (1.372%) rms = 6.38, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1613983.2, rms=6.376 (0.384%) positioning took 1.3 minutes mean border=45.1, 2467 (33) missing vertices, mean dist 0.3 [0.2 (%46.4)->1.0 (%53.6))] %41 local maxima, %29 large gradients and %21 min vals, 326 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1763777.8, rms=6.783 rms = 6.75, time step reduction 1 of 3 to 0.250... 070: dt: 0.5000, sse=1749957.9, rms=6.754 (0.431%) 071: dt: 0.2500, sse=1673859.1, rms=6.458 (4.374%) 072: dt: 0.2500, sse=1652203.0, rms=6.377 (1.256%) rms = 6.35, time step reduction 2 of 3 to 0.125... 073: dt: 0.2500, sse=1645536.9, rms=6.354 (0.357%) 074: dt: 0.1250, sse=1617866.6, rms=6.238 (1.827%) rms = 6.20, time step reduction 3 of 3 to 0.062... 075: dt: 0.1250, sse=1607936.6, rms=6.199 (0.620%) positioning took 0.7 minutes mean border=44.3, 4014 (26) missing vertices, mean dist 0.3 [0.2 (%45.2)->0.8 (%54.8))] %48 local maxima, %22 large gradients and %21 min vals, 348 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1660951.2, rms=6.344 rms = 6.37, time step reduction 1 of 3 to 0.250... 076: dt: 0.2500, sse=1629650.9, rms=6.218 (1.984%) 077: dt: 0.2500, sse=1600364.6, rms=6.111 (1.718%) 078: dt: 0.2500, sse=1585998.5, rms=6.061 (0.819%) 079: dt: 0.2500, sse=1562716.9, rms=5.973 (1.453%) rms = 5.94, time step reduction 2 of 3 to 0.125... 080: dt: 0.2500, sse=1552947.9, rms=5.938 (0.584%) 081: dt: 0.1250, sse=1523969.1, rms=5.810 (2.163%) rms = 5.77, time step reduction 3 of 3 to 0.062... 082: dt: 0.1250, sse=1513993.8, rms=5.769 (0.697%) positioning took 0.9 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.area.pial vertex spacing 1.11 +- 0.57 (0.03-->13.31) (max @ vno 58870 --> 59579) face area 0.49 +- 0.49 (0.00-->12.55) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 105178 vertices processed 25000 of 105178 vertices processed 50000 of 105178 vertices processed 75000 of 105178 vertices processed 100000 of 105178 vertices processed 0 of 105178 vertices processed 25000 of 105178 vertices processed 50000 of 105178 vertices processed 75000 of 105178 vertices processed 100000 of 105178 vertices processed thickness calculation complete, 913:3597 truncations. 15682 vertices at 0 distance 55699 vertices at 1 distance 64207 vertices at 2 distance 37877 vertices at 3 distance 15474 vertices at 4 distance 5427 vertices at 5 distance 1946 vertices at 6 distance 753 vertices at 7 distance 384 vertices at 8 distance 221 vertices at 9 distance 150 vertices at 10 distance 97 vertices at 11 distance 74 vertices at 12 distance 71 vertices at 13 distance 67 vertices at 14 distance 57 vertices at 15 distance 28 vertices at 16 distance 19 vertices at 17 distance 13 vertices at 18 distance 9 vertices at 19 distance 17 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.thickness positioning took 13.8 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050815 rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... 19852 bright wm thresholded. 80 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.orig... computing class statistics... border white: 244265 voxels (1.46%) border gray 309669 voxels (1.85%) WM (91.0): 92.5 +- 9.0 [70.0 --> 110.0] GM (66.0) : 64.8 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.8 (was 70) setting MAX_BORDER_WHITE to 104.0 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 36.6 (was 40) setting MAX_GRAY to 86.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 48.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=95+-8.7, GM=61+-12.2 mean inside = 87.7, mean outside = 70.4 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.35 (0.03-->6.48) (max @ vno 8042 --> 93095) face area 0.36 +- 0.24 (0.00-->8.25) mean absolute distance = 0.66 +- 1.08 3181 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 117 points - only 0.00% unknown deleting segment 1 with 15 points - only 0.00% unknown deleting segment 2 with 13 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 5 with 19 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 32 points - only 0.00% unknown deleting segment 11 with 27 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 7 points - only 0.00% unknown mean border=74.4, 696 (683) missing vertices, mean dist 0.2 [1.1 (%20.7)->0.5 (%79.3))] %60 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, 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 0.93 +- 0.36 (0.07-->6.40) (max @ vno 8042 --> 93095) face area 0.36 +- 0.25 (0.00-->8.15) mean absolute distance = 0.47 +- 0.85 3643 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1435124.4, rms=6.845 001: dt: 0.5000, sse=1027571.1, rms=5.007 (26.853%) 002: dt: 0.5000, sse=947375.4, rms=4.568 (8.761%) rms = 4.58, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=839309.1, rms=3.913 (14.348%) 004: dt: 0.2500, sse=799334.9, rms=3.606 (7.828%) 005: dt: 0.2500, sse=782203.0, rms=3.481 (3.481%) rms = 3.44, time step reduction 2 of 3 to 0.125... 006: dt: 0.2500, sse=793909.2, rms=3.435 (1.307%) 007: dt: 0.1250, sse=779552.4, rms=3.360 (2.189%) rms = 3.34, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=761530.2, rms=3.342 (0.543%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 89 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown deleting segment 8 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown mean border=77.0, 830 (343) missing vertices, mean dist -0.2 [0.5 (%61.9)->0.4 (%38.1))] %66 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.36 (0.06-->6.33) (max @ vno 8042 --> 93095) face area 0.36 +- 0.25 (0.00-->8.20) mean absolute distance = 0.39 +- 0.62 3537 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=930591.2, rms=4.425 009: dt: 0.5000, sse=852285.6, rms=3.793 (14.282%) rms = 3.98, time step reduction 1 of 3 to 0.250... 010: dt: 0.2500, sse=755834.8, rms=3.192 (15.850%) 011: dt: 0.2500, sse=731899.6, rms=2.927 (8.304%) 012: dt: 0.2500, sse=715394.6, rms=2.847 (2.713%) rms = 2.83, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=716323.1, rms=2.828 (0.678%) 014: dt: 0.1250, sse=703269.4, rms=2.764 (2.250%) rms = 2.76, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=704509.8, rms=2.758 (0.231%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 90 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 22 points - only 0.00% unknown deleting segment 10 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown mean border=78.4, 990 (283) missing vertices, mean dist -0.1 [0.5 (%55.6)->0.3 (%44.4))] %72 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.93 +- 0.35 (0.07-->6.33) (max @ vno 8042 --> 93095) face area 0.36 +- 0.25 (0.00-->8.48) mean absolute distance = 0.36 +- 0.52 2987 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=781093.7, rms=3.426 rms = 3.46, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=721767.8, rms=2.968 (13.366%) 017: dt: 0.2500, sse=718658.6, rms=2.684 (9.588%) 018: dt: 0.2500, sse=691644.1, rms=2.628 (2.075%) rms = 2.60, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=689858.8, rms=2.605 (0.879%) 020: dt: 0.1250, sse=686712.9, rms=2.548 (2.164%) rms = 2.54, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=676708.6, rms=2.540 (0.327%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 86 points - only 0.00% unknown deleting segment 1 with 9 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 31 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 32 points - only 0.00% unknown deleting segment 10 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown mean border=79.3, 1144 (255) missing vertices, mean dist -0.1 [0.4 (%52.0)->0.3 (%48.0))] %77 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=701096.6, rms=2.794 rms = 2.79, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=728989.4, rms=2.791 (0.112%) 023: dt: 0.2500, sse=659659.9, rms=2.382 (14.666%) 024: dt: 0.2500, sse=653685.0, rms=2.228 (6.461%) rms = 2.28, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=634453.4, rms=2.150 (3.498%) 026: dt: 0.1250, sse=623466.3, rms=2.053 (4.497%) rms = 2.05, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=627555.4, rms=2.046 (0.328%) positioning took 0.6 minutes generating cortex label... 26 non-cortical segments detected only using segment with 7421 vertices erasing segment 0 (vno[0] = 14778) erasing segment 1 (vno[0] = 15489) erasing segment 2 (vno[0] = 25466) erasing segment 4 (vno[0] = 33969) erasing segment 5 (vno[0] = 34808) erasing segment 6 (vno[0] = 36319) erasing segment 7 (vno[0] = 39942) erasing segment 8 (vno[0] = 42877) erasing segment 9 (vno[0] = 45197) erasing segment 10 (vno[0] = 49781) erasing segment 11 (vno[0] = 58442) erasing segment 12 (vno[0] = 59698) erasing segment 13 (vno[0] = 60299) erasing segment 14 (vno[0] = 60320) erasing segment 15 (vno[0] = 62217) erasing segment 16 (vno[0] = 63729) erasing segment 17 (vno[0] = 66165) erasing segment 18 (vno[0] = 66935) erasing segment 19 (vno[0] = 67678) erasing segment 20 (vno[0] = 69002) erasing segment 21 (vno[0] = 70433) erasing segment 22 (vno[0] = 71354) erasing segment 23 (vno[0] = 72187) erasing segment 24 (vno[0] = 76224) erasing segment 25 (vno[0] = 79661) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.area vertex spacing 0.93 +- 0.35 (0.03-->6.33) (max @ vno 8042 --> 93095) face area 0.36 +- 0.25 (0.00-->8.38) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 56 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown deleting segment 10 with 17 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=47.7, 544 (544) missing vertices, mean dist 2.2 [2.0 (%0.2)->3.2 (%99.8))] %15 local maxima, %50 large gradients and %28 min vals, 543 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=20642994.0, rms=32.395 001: dt: 0.0500, sse=18425610.0, rms=30.555 (5.680%) 002: dt: 0.0500, sse=16805856.0, rms=29.138 (4.640%) 003: dt: 0.0500, sse=15542279.0, rms=27.982 (3.967%) 004: dt: 0.0500, sse=14507678.0, rms=26.998 (3.515%) 005: dt: 0.0500, sse=13628149.0, rms=26.133 (3.205%) 006: dt: 0.0500, sse=12860993.0, rms=25.354 (2.980%) 007: dt: 0.0500, sse=12178038.0, rms=24.640 (2.817%) 008: dt: 0.0500, sse=11562438.0, rms=23.978 (2.687%) 009: dt: 0.0500, sse=11000434.0, rms=23.357 (2.589%) 010: dt: 0.0500, sse=10484508.0, rms=22.772 (2.504%) positioning took 0.8 minutes mean border=47.5, 472 (288) missing vertices, mean dist 1.9 [1.3 (%0.2)->2.7 (%99.8))] %16 local maxima, %50 large gradients and %27 min vals, 549 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11224067.0, rms=23.588 011: dt: 0.0500, sse=10739652.0, rms=23.047 (2.297%) 012: dt: 0.0500, sse=10289740.0, rms=22.532 (2.234%) 013: dt: 0.0500, sse=9872329.0, rms=22.043 (2.168%) 014: dt: 0.0500, sse=9483367.0, rms=21.578 (2.111%) 015: dt: 0.0500, sse=9122432.0, rms=21.137 (2.044%) 016: dt: 0.0500, sse=8786406.0, rms=20.718 (1.983%) 017: dt: 0.0500, sse=8472888.0, rms=20.319 (1.925%) 018: dt: 0.0500, sse=8180250.0, rms=19.939 (1.868%) 019: dt: 0.0500, sse=7908023.5, rms=19.580 (1.804%) 020: dt: 0.0500, sse=7654060.5, rms=19.238 (1.746%) positioning took 0.8 minutes mean border=47.3, 509 (222) missing vertices, mean dist 1.7 [0.2 (%2.3)->2.4 (%97.7))] %16 local maxima, %50 large gradients and %27 min vals, 558 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=7751205.5, rms=19.369 021: dt: 0.0500, sse=7505159.5, rms=19.035 (1.727%) 022: dt: 0.0500, sse=7276913.5, rms=18.719 (1.659%) 023: dt: 0.0500, sse=7062102.5, rms=18.417 (1.614%) 024: dt: 0.0500, sse=6863334.0, rms=18.133 (1.543%) 025: dt: 0.0500, sse=6678552.5, rms=17.864 (1.480%) 026: dt: 0.0500, sse=6506994.0, rms=17.611 (1.415%) 027: dt: 0.0500, sse=6346352.5, rms=17.371 (1.364%) 028: dt: 0.0500, sse=6193666.0, rms=17.140 (1.332%) 029: dt: 0.0500, sse=6049486.0, rms=16.918 (1.293%) 030: dt: 0.0500, sse=5912709.0, rms=16.705 (1.259%) positioning took 0.8 minutes mean border=47.2, 595 (188) missing vertices, mean dist 1.5 [0.1 (%13.3)->2.4 (%86.7))] %17 local maxima, %50 large gradients and %26 min vals, 494 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5993684.0, rms=16.826 031: dt: 0.5000, sse=5029649.5, rms=15.260 (9.307%) 032: dt: 0.5000, sse=4407902.5, rms=14.150 (7.275%) 033: dt: 0.5000, sse=3951461.5, rms=13.278 (6.158%) 034: dt: 0.5000, sse=3624428.8, rms=12.609 (5.037%) 035: dt: 0.5000, sse=3354428.5, rms=12.032 (4.581%) 036: dt: 0.5000, sse=3145197.8, rms=11.561 (3.915%) 037: dt: 0.5000, sse=2968761.8, rms=11.150 (3.555%) 038: dt: 0.5000, sse=2828743.5, rms=10.811 (3.041%) 039: dt: 0.5000, sse=2704078.5, rms=10.501 (2.863%) 040: dt: 0.5000, sse=2603221.5, rms=10.241 (2.479%) 041: dt: 0.5000, sse=2511717.5, rms=10.002 (2.329%) 042: dt: 0.5000, sse=2438141.0, rms=9.803 (1.988%) 043: dt: 0.5000, sse=2376557.2, rms=9.636 (1.705%) 044: dt: 0.5000, sse=2328666.8, rms=9.502 (1.394%) 045: dt: 0.5000, sse=2288117.0, rms=9.388 (1.202%) 046: dt: 0.5000, sse=2259743.5, rms=9.305 (0.881%) 047: dt: 0.5000, sse=2230046.0, rms=9.220 (0.918%) 048: dt: 0.5000, sse=2208348.2, rms=9.155 (0.702%) 049: dt: 0.5000, sse=2188623.5, rms=9.097 (0.630%) 050: dt: 0.5000, sse=2168157.0, rms=9.035 (0.682%) 051: dt: 0.5000, sse=2147494.2, rms=8.975 (0.670%) 052: dt: 0.5000, sse=2131124.2, rms=8.924 (0.563%) 053: dt: 0.5000, sse=2110328.0, rms=8.862 (0.694%) rms = 8.82, time step reduction 1 of 3 to 0.250... 054: dt: 0.5000, sse=2097743.5, rms=8.822 (0.452%) 055: dt: 0.2500, sse=2051032.6, rms=8.661 (1.824%) rms = 8.62, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=2037178.6, rms=8.618 (0.499%) rms = 8.59, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=2028593.9, rms=8.588 (0.353%) positioning took 2.8 minutes mean border=45.9, 2170 (78) missing vertices, mean dist 0.5 [0.3 (%42.8)->1.4 (%57.2))] %29 local maxima, %39 large gradients and %24 min vals, 347 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=2181040.2, rms=8.385 058: dt: 0.5000, sse=2049738.9, rms=7.974 (4.912%) 059: dt: 0.5000, sse=1977017.8, rms=7.758 (2.707%) 060: dt: 0.5000, sse=1935452.5, rms=7.626 (1.703%) 061: dt: 0.5000, sse=1893975.6, rms=7.493 (1.734%) 062: dt: 0.5000, sse=1864669.2, rms=7.396 (1.306%) 063: dt: 0.5000, sse=1832039.6, rms=7.283 (1.523%) 064: dt: 0.5000, sse=1814537.6, rms=7.219 (0.879%) 065: dt: 0.5000, sse=1790519.5, rms=7.135 (1.159%) rms = 7.10, time step reduction 1 of 3 to 0.250... 066: dt: 0.5000, sse=1782580.8, rms=7.105 (0.425%) 067: dt: 0.2500, sse=1729368.8, rms=6.869 (3.323%) 068: dt: 0.2500, sse=1713154.1, rms=6.806 (0.918%) rms = 6.80, time step reduction 2 of 3 to 0.125... 069: dt: 0.2500, sse=1712528.0, rms=6.802 (0.052%) rms = 6.76, time step reduction 3 of 3 to 0.062... 070: dt: 0.1250, sse=1702783.2, rms=6.759 (0.628%) positioning took 1.5 minutes mean border=44.9, 2991 (60) missing vertices, mean dist 0.3 [0.2 (%45.0)->1.0 (%55.0))] %39 local maxima, %28 large gradients and %24 min vals, 408 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1840074.8, rms=7.097 071: dt: 0.5000, sse=1816687.1, rms=7.035 (0.875%) 072: dt: 0.5000, sse=1785595.2, rms=6.961 (1.058%) 073: dt: 0.5000, sse=1769733.0, rms=6.903 (0.830%) 074: dt: 0.5000, sse=1751266.4, rms=6.850 (0.776%) 075: dt: 0.5000, sse=1738347.5, rms=6.798 (0.758%) rms = 6.76, time step reduction 1 of 3 to 0.250... 076: dt: 0.5000, sse=1726588.1, rms=6.763 (0.505%) 077: dt: 0.2500, sse=1672544.1, rms=6.509 (3.758%) 078: dt: 0.2500, sse=1658735.2, rms=6.456 (0.822%) rms = 6.44, time step reduction 2 of 3 to 0.125... 079: dt: 0.2500, sse=1654944.0, rms=6.440 (0.242%) 080: dt: 0.1250, sse=1643638.0, rms=6.388 (0.813%) rms = 6.38, time step reduction 3 of 3 to 0.062... 081: dt: 0.1250, sse=1641039.6, rms=6.377 (0.159%) positioning took 1.4 minutes mean border=44.1, 4864 (49) missing vertices, mean dist 0.2 [0.2 (%44.8)->0.7 (%55.2))] %45 local maxima, %21 large gradients and %23 min vals, 391 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1691537.1, rms=6.478 rms = 6.47, time step reduction 1 of 3 to 0.250... 082: dt: 0.5000, sse=1682496.8, rms=6.474 (0.061%) 083: dt: 0.2500, sse=1632616.2, rms=6.264 (3.247%) 084: dt: 0.2500, sse=1611763.8, rms=6.183 (1.279%) rms = 6.15, time step reduction 2 of 3 to 0.125... 085: dt: 0.2500, sse=1603810.5, rms=6.154 (0.482%) 086: dt: 0.1250, sse=1587272.9, rms=6.078 (1.229%) rms = 6.06, time step reduction 3 of 3 to 0.062... 087: dt: 0.1250, sse=1581539.4, rms=6.056 (0.363%) positioning took 0.8 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.area.pial vertex spacing 1.13 +- 0.59 (0.04-->8.26) (max @ vno 8203 --> 93887) face area 0.51 +- 0.52 (0.00-->22.32) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 102455 vertices processed 25000 of 102455 vertices processed 50000 of 102455 vertices processed 75000 of 102455 vertices processed 100000 of 102455 vertices processed 0 of 102455 vertices processed 25000 of 102455 vertices processed 50000 of 102455 vertices processed 75000 of 102455 vertices processed 100000 of 102455 vertices processed thickness calculation complete, 1383:4788 truncations. 11978 vertices at 0 distance 44513 vertices at 1 distance 59315 vertices at 2 distance 42410 vertices at 3 distance 19958 vertices at 4 distance 7912 vertices at 5 distance 3134 vertices at 6 distance 1391 vertices at 7 distance 708 vertices at 8 distance 391 vertices at 9 distance 244 vertices at 10 distance 180 vertices at 11 distance 111 vertices at 12 distance 76 vertices at 13 distance 66 vertices at 14 distance 65 vertices at 15 distance 43 vertices at 16 distance 28 vertices at 17 distance 22 vertices at 18 distance 26 vertices at 19 distance 35 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.thickness positioning took 14.8 minutes PIDs (29637 29640) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 11:03:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 0050815 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.cortex.label Total face volume 214254 Total vertex volume 209700 (mask=0) #@# 0050815 lh 209700 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 11:03:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 0050815 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.cortex.label Total face volume 227482 Total vertex volume 223909 (mask=0) #@# 0050815 rh 223909 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 11:03:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 0050815 SUBJECTS_DIR is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 2 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/ribbon.mgz mris_volmask took 8.42 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 11:11:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050815 lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050815 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 11:11:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050815 rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050815 rh pial Waiting for PID 30635 of (30635 30638 30641 30644) to complete... Waiting for PID 30638 of (30635 30638 30641 30644) to complete... Waiting for PID 30641 of (30635 30638 30641 30644) to complete... Waiting for PID 30644 of (30635 30638 30641 30644) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050815 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 214254 Total vertex volume 209700 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 1090 752 1703 2.276 0.642 0.118 0.036 10 1.6 bankssts 654 434 1507 2.929 0.798 0.092 0.018 3 0.4 caudalanteriorcingulate 2348 1716 4018 2.088 0.585 0.160 0.063 47 6.3 caudalmiddlefrontal 2050 1446 4492 2.405 0.755 0.153 0.050 30 4.5 cuneus 553 409 1254 2.241 0.732 0.188 0.082 12 2.1 entorhinal 3436 2655 7892 2.473 0.745 0.170 0.063 69 9.8 fusiform 6060 4221 12070 2.331 0.725 0.144 0.048 84 12.4 inferiorparietal 3884 2739 8544 2.388 0.750 0.156 0.061 73 10.6 inferiortemporal 1326 869 2737 2.462 0.835 0.135 0.041 17 2.3 isthmuscingulate 7760 5249 13112 2.241 0.692 0.146 0.046 115 14.1 lateraloccipital 1950 1333 4638 3.027 0.902 0.124 0.044 22 3.5 lateralorbitofrontal 3597 2700 8015 2.316 0.750 0.163 0.055 79 9.2 lingual 2106 1565 6409 3.069 0.993 0.146 0.051 39 4.4 medialorbitofrontal 3705 2780 11179 2.752 0.890 0.161 0.058 72 8.9 middletemporal 893 702 1786 2.289 0.633 0.169 0.057 12 2.4 parahippocampal 1313 971 3058 2.487 0.853 0.158 0.063 21 3.5 paracentral 1725 1147 3735 2.582 0.724 0.145 0.062 29 4.6 parsopercularis 555 338 1037 2.409 0.635 0.162 0.088 14 2.1 parsorbitalis 1676 1277 4904 2.910 0.747 0.167 0.065 30 5.2 parstriangularis 1621 1209 2628 2.129 0.732 0.167 0.060 22 4.3 pericalcarine 3718 2814 7314 2.193 0.641 0.170 0.068 77 11.0 postcentral 1512 993 3018 2.541 1.018 0.150 0.063 34 4.0 posteriorcingulate 5719 4091 10777 2.247 0.704 0.158 0.062 88 16.2 precentral 4382 3089 9286 2.408 0.779 0.151 0.059 71 12.4 precuneus 831 527 2076 3.053 0.910 0.115 0.040 9 1.3 rostralanteriorcingulate 6028 4286 13253 2.473 0.845 0.148 0.056 99 14.2 rostralmiddlefrontal 8341 6016 20473 2.727 0.943 0.151 0.060 157 21.9 superiorfrontal 5614 4015 10611 2.232 0.637 0.139 0.046 78 11.3 superiorparietal 3807 3057 9573 2.598 0.780 0.144 0.045 54 7.6 superiortemporal 4399 3049 8955 2.326 0.677 0.148 0.055 72 10.4 supramarginal 487 307 1121 2.609 1.171 0.169 0.070 15 1.7 frontalpole 428 384 1040 2.143 0.852 0.232 0.118 13 2.1 temporalpole 521 376 1072 2.555 0.774 0.162 0.064 8 1.4 transversetemporal 2398 1670 6397 3.213 1.026 0.112 0.036 35 3.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050815 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 214254 Total vertex volume 209700 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 1090 712 1703 2.276 0.642 0.144 0.066 20 3.5 bankssts 654 637 1507 2.929 0.798 0.182 0.054 13 1.6 caudalanteriorcingulate 2348 2340 4018 2.088 0.585 0.190 0.055 29 6.4 caudalmiddlefrontal 2050 2269 4492 2.405 0.755 0.217 0.056 33 5.7 cuneus 553 727 1254 2.241 0.732 0.245 0.077 12 2.3 entorhinal 3436 3550 7892 2.473 0.745 0.212 0.093 83 17.6 fusiform 6060 5991 12070 2.331 0.725 0.191 0.065 119 20.6 inferiorparietal 3884 4379 8544 2.388 0.750 0.221 0.061 75 11.0 inferiortemporal 1326 1297 2737 2.462 0.835 0.195 0.055 27 3.2 isthmuscingulate 7760 6540 13112 2.241 0.692 0.159 0.046 123 16.5 lateraloccipital 1950 1629 4638 3.027 0.902 0.182 0.061 36 5.4 lateralorbitofrontal 3597 3938 8015 2.316 0.750 0.210 0.125 90 29.0 lingual 2106 2408 6409 3.069 0.993 0.229 0.065 43 6.4 medialorbitofrontal 3705 5173 11179 2.752 0.890 0.237 0.057 58 10.1 middletemporal 893 962 1786 2.289 0.633 0.197 0.048 12 2.2 parahippocampal 1313 1395 3058 2.487 0.853 0.202 0.062 24 3.8 paracentral 1725 1832 3735 2.582 0.724 0.200 0.053 25 4.3 parsopercularis 555 503 1037 2.409 0.635 0.200 0.074 12 2.1 parsorbitalis 1676 2013 4904 2.910 0.747 0.222 0.060 24 4.7 parstriangularis 1621 1234 2628 2.129 0.732 0.153 0.044 24 3.2 pericalcarine 3718 3838 7314 2.193 0.641 0.202 0.064 98 11.4 postcentral 1512 1227 3018 2.541 1.018 0.180 0.081 55 6.2 posteriorcingulate 5719 5537 10777 2.247 0.704 0.181 0.097 233 33.1 precentral 4382 4384 9286 2.408 0.779 0.201 0.062 76 13.8 precuneus 831 814 2076 3.053 0.910 0.216 0.069 32 2.4 rostralanteriorcingulate 6028 5978 13253 2.473 0.845 0.196 0.059 104 17.2 rostralmiddlefrontal 8341 8728 20473 2.727 0.943 0.199 0.057 143 22.1 superiorfrontal 5614 5733 10611 2.232 0.637 0.201 0.056 98 15.2 superiorparietal 3807 4080 9573 2.598 0.780 0.185 0.052 64 9.0 superiortemporal 4399 4710 8955 2.326 0.677 0.209 0.067 76 14.5 supramarginal 487 519 1121 2.609 1.171 0.188 0.044 7 1.1 frontalpole 428 604 1040 2.143 0.852 0.244 0.061 8 1.1 temporalpole 521 512 1072 2.555 0.774 0.180 0.051 8 1.3 transversetemporal 2398 2001 6397 3.213 1.026 0.187 0.057 57 6.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050815 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 227482 Total vertex volume 223909 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 887 670 1650 2.106 0.741 0.136 0.053 10 2.1 bankssts 704 460 1413 3.351 0.750 0.127 0.043 8 0.9 caudalanteriorcingulate 3028 2009 5129 2.196 0.705 0.168 0.081 84 10.6 caudalmiddlefrontal 1420 1246 3791 2.404 1.039 0.183 0.065 30 4.4 cuneus 417 290 1042 2.676 0.749 0.177 0.074 11 1.2 entorhinal 2548 2039 6511 2.758 0.745 0.178 0.060 49 7.2 fusiform 6153 4450 13981 2.492 0.747 0.152 0.051 105 14.4 inferiorparietal 3124 2273 8627 2.671 0.861 0.166 0.061 66 7.7 inferiortemporal 1272 839 2644 2.410 0.990 0.145 0.055 21 2.8 isthmuscingulate 5457 4285 13380 2.464 0.744 0.170 0.053 95 14.3 lateraloccipital 2684 1885 6477 2.729 1.078 0.144 0.055 51 6.1 lateralorbitofrontal 1405 1119 3515 2.676 0.904 0.172 0.060 23 4.5 lingual 2360 1673 7054 3.424 1.011 0.141 0.046 37 4.9 medialorbitofrontal 3753 2896 11624 2.898 0.903 0.157 0.059 64 10.1 middletemporal 825 567 1951 2.893 0.816 0.178 0.077 16 2.9 parahippocampal 1718 1204 3737 2.706 0.800 0.153 0.061 26 4.5 paracentral 1346 977 3435 2.735 0.846 0.135 0.056 17 3.0 parsopercularis 1067 848 3156 2.613 0.768 0.178 0.082 26 3.8 parsorbitalis 1864 1364 4703 2.761 0.756 0.150 0.058 37 4.6 parstriangularis 983 722 2071 2.402 0.789 0.140 0.042 13 1.7 pericalcarine 4068 2867 7294 2.172 0.736 0.150 0.061 66 11.8 postcentral 1590 1068 3144 2.679 1.012 0.162 0.060 30 4.3 posteriorcingulate 6884 4794 13684 2.457 0.778 0.156 0.064 117 19.4 precentral 3328 2444 8304 2.647 0.891 0.158 0.057 56 8.5 precuneus 611 395 1646 3.552 0.764 0.138 0.054 8 1.4 rostralanteriorcingulate 7734 5515 18580 2.625 0.783 0.158 0.061 151 20.8 rostralmiddlefrontal 9668 6729 25133 2.820 1.007 0.154 0.064 194 27.6 superiorfrontal 6275 4630 12939 2.299 0.716 0.157 0.054 97 15.2 superiorparietal 3420 2640 8314 2.720 0.858 0.162 0.051 63 7.7 superiortemporal 4247 2975 9915 2.552 0.769 0.147 0.051 65 9.2 supramarginal 462 312 1412 2.656 1.023 0.171 0.067 12 1.5 frontalpole 401 311 1865 3.544 0.798 0.190 0.093 9 1.4 temporalpole 281 194 553 3.469 0.985 0.131 0.045 3 0.5 transversetemporal 2391 1666 5108 2.833 1.065 0.125 0.055 39 4.4 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050815 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 227482 Total vertex volume 223909 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 887 874 1650 2.106 0.741 0.184 0.051 17 1.9 bankssts 704 493 1413 3.351 0.750 0.146 0.046 13 1.2 caudalanteriorcingulate 3028 2651 5129 2.196 0.705 0.198 0.068 83 9.6 caudalmiddlefrontal 1420 2029 3791 2.404 1.039 0.249 0.071 39 5.3 cuneus 417 496 1042 2.676 0.749 0.218 0.056 6 1.1 entorhinal 2548 2621 6511 2.758 0.745 0.217 0.073 65 7.8 fusiform 6153 6650 13981 2.492 0.747 0.193 0.052 101 14.7 inferiorparietal 3124 3844 8627 2.671 0.861 0.218 0.060 51 8.7 inferiortemporal 1272 1284 2644 2.410 0.990 0.197 0.061 63 3.3 isthmuscingulate 5457 6410 13380 2.464 0.744 0.213 0.053 95 13.4 lateraloccipital 2684 2643 6477 2.729 1.078 0.231 0.105 113 14.7 lateralorbitofrontal 1405 1459 3515 2.676 0.904 0.230 0.062 33 4.4 lingual 2360 2450 7054 3.424 1.011 0.236 0.126 92 18.0 medialorbitofrontal 3753 4909 11624 2.898 0.903 0.241 0.059 60 11.4 middletemporal 825 836 1951 2.893 0.816 0.212 0.072 17 2.6 parahippocampal 1718 1566 3737 2.706 0.800 0.193 0.063 32 5.3 paracentral 1346 1576 3435 2.735 0.846 0.227 0.060 24 3.8 parsopercularis 1067 1478 3156 2.613 0.768 0.242 0.062 41 3.6 parsorbitalis 1864 2040 4703 2.761 0.756 0.199 0.056 29 4.8 parstriangularis 983 997 2071 2.402 0.789 0.193 0.060 21 2.9 pericalcarine 4068 3906 7294 2.172 0.736 0.189 0.059 74 11.8 postcentral 1590 1284 3144 2.679 1.012 0.173 0.052 38 3.7 posteriorcingulate 6884 6315 13684 2.457 0.778 0.179 0.059 126 18.7 precentral 3328 3634 8304 2.647 0.891 0.223 0.076 66 10.5 precuneus 611 565 1646 3.552 0.764 0.182 0.055 9 1.5 rostralanteriorcingulate 7734 8256 18580 2.625 0.783 0.208 0.061 150 22.6 rostralmiddlefrontal 9668 10285 25133 2.820 1.007 0.203 0.060 211 28.1 superiorfrontal 6275 6640 12939 2.299 0.716 0.204 0.060 107 18.1 superiorparietal 3420 3421 8314 2.720 0.858 0.188 0.064 95 10.2 superiortemporal 4247 4532 9915 2.552 0.769 0.197 0.053 56 10.8 supramarginal 462 678 1412 2.656 1.023 0.257 0.065 8 1.4 frontalpole 401 704 1865 3.544 0.798 0.298 0.085 10 1.6 temporalpole 281 160 553 3.469 0.985 0.145 0.057 7 0.7 transversetemporal 2391 1828 5108 2.833 1.065 0.190 0.070 85 7.6 insula PIDs (30635 30638 30641 30644) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 11:12:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Sun Oct 8 11:12:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 30721 of (30721 30724) to complete... Waiting for PID 30724 of (30721 30724) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 75 labels changed using aseg relabeling using gibbs priors... 000: 6993 changed, 105178 examined... 001: 1578 changed, 27457 examined... 002: 446 changed, 8360 examined... 003: 193 changed, 2520 examined... 004: 82 changed, 1091 examined... 005: 40 changed, 488 examined... 006: 20 changed, 252 examined... 007: 12 changed, 114 examined... 008: 3 changed, 67 examined... 009: 0 changed, 18 examined... 29 labels changed using aseg 000: 270 total segments, 186 labels (1645 vertices) changed 001: 92 total segments, 8 labels (69 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 17 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 542 vertices marked for relabeling... 542 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 163 labels changed using aseg relabeling using gibbs priors... 000: 6941 changed, 102455 examined... 001: 1611 changed, 27384 examined... 002: 468 changed, 8430 examined... 003: 188 changed, 2652 examined... 004: 90 changed, 1083 examined... 005: 45 changed, 535 examined... 006: 24 changed, 245 examined... 007: 6 changed, 134 examined... 008: 7 changed, 39 examined... 009: 4 changed, 36 examined... 010: 3 changed, 19 examined... 011: 3 changed, 23 examined... 012: 1 changed, 20 examined... 013: 2 changed, 7 examined... 014: 0 changed, 10 examined... 98 labels changed using aseg 000: 264 total segments, 183 labels (1904 vertices) changed 001: 94 total segments, 13 labels (23 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 843 vertices marked for relabeling... 843 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 16 seconds. PIDs (30721 30724) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 11:13:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050815 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 11:13:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050815 rh white Waiting for PID 30781 of (30781 30784) to complete... Waiting for PID 30784 of (30781 30784) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050815 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 214254 Total vertex volume 209700 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 1030 658 2374 2.765 1.293 0.141 0.056 15 2.4 G&S_frontomargin 1375 935 3520 2.819 0.754 0.136 0.044 18 2.3 G&S_occipital_inf 1099 813 2779 2.361 0.803 0.175 0.067 19 3.0 G&S_paracentral 1532 1133 3373 2.458 0.722 0.177 0.072 30 4.8 G&S_subcentral 717 435 1321 2.223 0.979 0.152 0.067 17 2.0 G&S_transv_frontopol 1869 1285 4216 2.741 0.951 0.115 0.045 22 3.2 G&S_cingul-Ant 928 658 2088 2.724 0.953 0.104 0.029 6 1.0 G&S_cingul-Mid-Ant 1060 738 2468 3.011 0.765 0.142 0.053 15 2.1 G&S_cingul-Mid-Post 507 342 1276 2.692 0.791 0.155 0.050 10 1.2 G_cingul-Post-dorsal 355 261 1348 3.160 0.960 0.179 0.063 7 1.0 G_cingul-Post-ventral 1916 1390 4476 2.372 0.847 0.167 0.061 31 5.5 G_cuneus 1056 708 2528 2.471 0.729 0.176 0.083 25 4.1 G_front_inf-Opercular 381 302 1446 2.729 0.947 0.180 0.071 7 1.3 G_front_inf-Orbital 1094 817 3430 2.995 0.733 0.183 0.078 26 4.1 G_front_inf-Triangul 3301 2540 8278 2.399 0.702 0.178 0.073 82 10.0 G_front_middle 5892 4280 16596 2.859 0.955 0.168 0.069 129 18.5 G_front_sup 493 364 1517 3.220 0.929 0.141 0.063 8 1.6 G_Ins_lg&S_cent_ins 494 348 1786 3.695 0.853 0.168 0.051 19 1.2 G_insular_short 2218 1508 5240 2.467 0.680 0.163 0.055 46 4.7 G_occipital_middle 1343 964 2417 2.068 0.600 0.183 0.067 27 3.7 G_occipital_sup 1605 1236 4324 2.481 0.775 0.185 0.073 42 5.4 G_oc-temp_lat-fusifor 2512 1875 6052 2.308 0.768 0.174 0.062 61 6.8 G_oc-temp_med-Lingual 1031 742 2298 2.299 0.645 0.158 0.060 17 2.6 G_oc-temp_med-Parahip 1399 926 3424 2.876 0.895 0.146 0.061 28 3.4 G_orbital 2672 1839 6396 2.284 0.738 0.171 0.073 54 8.2 G_pariet_inf-Angular 2101 1491 4990 2.448 0.713 0.159 0.058 42 5.5 G_pariet_inf-Supramar 1942 1415 4704 2.359 0.668 0.161 0.063 42 5.1 G_parietal_sup 1273 1042 3320 2.239 0.646 0.188 0.075 36 4.2 G_postcentral 2560 1781 5320 2.272 0.757 0.173 0.074 51 9.0 G_precentral 2228 1601 5730 2.466 0.829 0.174 0.077 51 8.6 G_precuneus 962 770 3029 2.884 0.914 0.183 0.064 24 2.9 G_rectus 59 41 157 2.746 0.588 0.057 0.007 0 0.0 G_subcallosal 394 308 1032 2.479 0.828 0.189 0.076 8 1.4 G_temp_sup-G_T_transv 1260 1070 4265 2.710 0.884 0.189 0.069 31 3.9 G_temp_sup-Lateral 300 260 739 2.541 0.750 0.148 0.054 4 0.7 G_temp_sup-Plan_polar 773 558 1672 2.544 0.646 0.105 0.026 6 0.9 G_temp_sup-Plan_tempo 1919 1376 4867 2.437 0.744 0.162 0.062 43 5.4 G_temporal_inf 2363 1801 8402 2.833 0.890 0.183 0.071 59 7.3 G_temporal_middle 139 102 215 2.794 0.582 0.126 0.063 1 0.3 Lat_Fis-ant-Horizont 156 117 229 2.036 0.502 0.104 0.027 1 0.2 Lat_Fis-ant-Vertical 954 635 1211 2.274 0.552 0.126 0.046 10 1.8 Lat_Fis-post 2355 1653 3244 1.906 0.557 0.158 0.051 39 4.9 Pole_occipital 1271 999 3000 2.379 0.808 0.208 0.099 34 5.2 Pole_temporal 1869 1426 2825 2.073 0.636 0.153 0.052 30 4.2 S_calcarine 1831 1305 2380 2.027 0.580 0.137 0.052 22 4.2 S_central 662 456 1131 2.461 0.587 0.125 0.042 7 1.3 S_cingul-Marginalis 337 219 1175 3.514 1.203 0.073 0.021 1 0.3 S_circular_insula_ant 951 843 2709 3.401 0.967 0.109 0.027 8 0.9 S_circular_insula_inf 1245 850 1847 2.642 0.659 0.100 0.031 7 1.3 S_circular_insula_sup 687 549 1478 2.472 0.946 0.175 0.068 13 2.4 S_collat_transv_ant 607 401 656 1.815 0.430 0.120 0.033 4 0.8 S_collat_transv_post 1583 1146 3096 2.307 0.699 0.137 0.047 18 3.2 S_front_inf 1059 755 1726 2.312 0.616 0.121 0.035 11 1.5 S_front_middle 2122 1492 3253 2.304 0.732 0.123 0.044 28 3.9 S_front_sup 20 11 33 2.009 0.274 0.133 0.051 0 0.0 S_interm_prim-Jensen 2414 1637 3256 2.274 0.541 0.103 0.024 13 2.5 S_intrapariet&P_trans 1413 974 1788 2.086 0.460 0.123 0.026 11 1.6 S_oc_middle&Lunatus 1044 688 1409 2.309 0.536 0.099 0.022 5 1.0 S_oc_sup&transversal 614 419 978 2.548 0.730 0.124 0.040 6 1.0 S_occipital_ant 764 526 1087 2.147 0.741 0.130 0.048 8 1.6 S_oc-temp_lat 1727 1339 3302 2.508 0.666 0.162 0.051 23 4.7 S_oc-temp_med&Lingual 189 121 339 2.838 0.501 0.145 0.042 2 0.3 S_orbital_lateral 323 218 819 2.772 0.633 0.183 0.075 9 0.7 S_orbital_med-olfact 673 459 1385 3.086 0.867 0.122 0.047 6 1.5 S_orbital-H_Shaped 1542 1123 3126 2.611 0.699 0.121 0.031 12 2.0 S_parieto_occipital 1225 704 1153 2.002 0.882 0.121 0.046 22 2.3 S_pericallosal 1723 1173 2403 1.948 0.550 0.126 0.042 19 2.8 S_postcentral 930 618 1251 2.185 0.621 0.119 0.040 7 1.6 S_precentral-inf-part 815 571 1060 2.216 0.594 0.136 0.045 8 1.7 S_precentral-sup-part 548 398 1807 3.514 1.025 0.120 0.038 5 0.8 S_suborbital 874 587 1149 2.043 0.552 0.134 0.048 10 1.9 S_subparietal 1226 823 1983 2.325 0.751 0.123 0.034 11 1.9 S_temporal_inf 4372 3086 7651 2.403 0.717 0.119 0.031 34 5.8 S_temporal_sup 214 155 346 2.586 0.648 0.106 0.026 1 0.2 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050815 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 227482 Total vertex volume 223909 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 711 517 2078 2.713 0.927 0.147 0.052 12 1.7 G&S_frontomargin 722 553 2054 2.929 0.670 0.163 0.044 12 1.5 G&S_occipital_inf 1233 860 2759 2.466 0.760 0.169 0.073 22 3.8 G&S_paracentral 1521 1042 4030 2.676 0.773 0.154 0.067 29 4.7 G&S_subcentral 1132 829 3491 2.861 0.854 0.176 0.068 23 3.7 G&S_transv_frontopol 2592 1787 7463 3.366 0.979 0.121 0.042 27 4.4 G&S_cingul-Ant 1136 805 2279 2.669 0.879 0.131 0.044 13 1.8 G&S_cingul-Mid-Ant 1232 843 2699 2.722 0.912 0.135 0.047 14 2.4 G&S_cingul-Mid-Post 496 343 1165 2.517 0.948 0.183 0.069 12 1.6 G_cingul-Post-dorsal 373 273 1259 2.906 1.067 0.196 0.074 8 1.3 G_cingul-Post-ventral 1353 1210 3748 2.411 1.029 0.185 0.059 26 3.9 G_cuneus 1124 848 3434 2.693 0.808 0.163 0.066 20 3.1 G_front_inf-Opercular 271 184 567 2.310 0.804 0.146 0.055 7 0.5 G_front_inf-Orbital 914 701 2957 2.972 0.779 0.179 0.073 24 3.1 G_front_inf-Triangul 4493 3207 11934 2.490 0.799 0.188 0.084 135 17.2 G_front_middle 6535 4500 18996 2.993 1.026 0.170 0.073 160 21.3 G_front_sup 403 307 924 2.797 0.966 0.141 0.080 8 0.7 G_Ins_lg&S_cent_ins 673 451 1400 2.400 1.254 0.161 0.071 14 2.1 G_insular_short 1843 1397 5281 2.520 0.831 0.184 0.064 43 5.7 G_occipital_middle 1836 1444 3672 1.981 0.683 0.189 0.072 39 7.1 G_occipital_sup 959 779 3117 2.995 0.629 0.185 0.059 25 2.6 G_oc-temp_lat-fusifor 794 645 2339 2.881 0.926 0.187 0.069 17 3.1 G_oc-temp_med-Lingual 1041 712 2748 2.822 0.770 0.178 0.079 23 3.5 G_oc-temp_med-Parahip 2224 1667 6152 2.696 0.962 0.173 0.074 64 7.3 G_orbital 2621 1924 7802 2.610 0.838 0.185 0.069 74 8.7 G_pariet_inf-Angular 2162 1544 5721 2.587 0.840 0.163 0.059 43 5.5 G_pariet_inf-Supramar 1815 1340 4785 2.424 0.739 0.177 0.072 38 5.8 G_parietal_sup 1407 1061 2549 1.956 0.714 0.172 0.073 29 5.2 G_postcentral 2675 1790 5979 2.456 0.813 0.168 0.076 58 8.9 G_precentral 2010 1548 5456 2.528 0.846 0.189 0.074 46 6.7 G_precuneus 717 522 1991 2.789 0.811 0.186 0.060 19 2.1 G_rectus 365 206 814 3.223 1.386 0.104 0.049 6 0.6 G_subcallosal 180 149 504 3.364 1.159 0.161 0.043 3 0.3 G_temp_sup-G_T_transv 971 829 3174 2.694 0.770 0.181 0.057 20 2.4 G_temp_sup-Lateral 502 331 1024 2.903 0.859 0.204 0.085 14 2.0 G_temp_sup-Plan_polar 669 528 1868 2.710 0.707 0.125 0.033 6 0.8 G_temp_sup-Plan_tempo 1691 1278 5522 2.684 0.892 0.187 0.076 48 5.3 G_temporal_inf 2468 1885 8264 2.928 0.829 0.173 0.065 51 7.0 G_temporal_middle 256 196 400 2.202 0.538 0.102 0.025 1 0.3 Lat_Fis-ant-Horizont 105 90 216 1.992 0.619 0.104 0.024 0 0.1 Lat_Fis-ant-Vertical 1076 726 1649 2.644 0.788 0.115 0.038 8 1.6 Lat_Fis-post 2339 1880 6036 2.395 0.732 0.174 0.050 43 5.3 Pole_occipital 1127 892 4252 3.309 1.037 0.190 0.091 25 4.7 Pole_temporal 838 641 1653 2.455 0.845 0.149 0.052 10 1.7 S_calcarine 2041 1396 2589 2.234 0.693 0.144 0.060 27 5.1 S_central 731 519 1186 2.642 0.736 0.116 0.033 5 1.0 S_cingul-Marginalis 353 255 1101 3.183 1.304 0.113 0.034 4 0.3 S_circular_insula_ant 901 585 1822 3.321 0.953 0.113 0.033 8 1.4 S_circular_insula_inf 912 633 1745 2.889 0.834 0.095 0.038 13 0.8 S_circular_insula_sup 813 592 1361 2.377 0.689 0.163 0.059 13 2.1 S_collat_transv_ant 77 51 200 2.797 0.504 0.122 0.025 1 0.1 S_collat_transv_post 1701 1199 3103 2.446 0.836 0.145 0.054 23 4.0 S_front_inf 1672 1098 2548 2.548 0.642 0.129 0.044 20 3.0 S_front_middle 2317 1571 3666 2.343 0.688 0.131 0.055 31 5.6 S_front_sup 250 170 449 2.682 0.504 0.132 0.039 2 0.4 S_interm_prim-Jensen 2583 1830 4291 2.473 0.590 0.123 0.032 19 3.6 S_intrapariet&P_trans 652 455 944 2.177 0.583 0.119 0.026 5 0.8 S_oc_middle&Lunatus 926 645 1436 2.231 0.556 0.115 0.029 10 1.1 S_oc_sup&transversal 630 431 1026 2.263 0.646 0.132 0.051 7 1.4 S_occipital_ant 751 571 1228 2.450 0.485 0.123 0.030 4 1.0 S_oc-temp_lat 986 783 2583 2.998 0.822 0.165 0.056 12 2.8 S_oc-temp_med&Lingual 331 225 659 2.752 0.539 0.110 0.034 2 0.4 S_orbital_lateral 545 387 1279 2.811 1.110 0.135 0.052 6 1.2 S_orbital_med-olfact 946 682 2194 2.764 0.804 0.142 0.060 16 2.4 S_orbital-H_Shaped 1052 764 2699 2.927 0.871 0.135 0.052 12 2.4 S_parieto_occipital 1308 784 1391 2.423 1.074 0.132 0.052 22 2.6 S_pericallosal 1597 1151 2338 2.077 0.548 0.130 0.039 15 2.7 S_postcentral 1347 986 2376 2.441 0.768 0.151 0.060 28 3.8 S_precentral-inf-part 1299 881 1821 2.398 0.772 0.130 0.061 16 3.1 S_precentral-sup-part 221 161 575 3.911 1.060 0.097 0.019 1 0.2 S_suborbital 660 467 1590 2.724 0.874 0.121 0.035 8 0.9 S_subparietal 776 602 2007 2.775 0.886 0.143 0.031 8 1.0 S_temporal_inf 4371 3179 7212 2.326 0.734 0.126 0.039 40 7.4 S_temporal_sup 102 99 284 3.527 0.508 0.155 0.023 1 0.1 S_temporal_transverse PIDs (30781 30784) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 11:13:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Sun Oct 8 11:13:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 30832 of (30832 30835) to complete... Waiting for PID 30835 of (30832 30835) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1177 labels changed using aseg relabeling using gibbs priors... 000: 1644 changed, 105178 examined... 001: 372 changed, 7858 examined... 002: 87 changed, 2170 examined... 003: 44 changed, 555 examined... 004: 30 changed, 242 examined... 005: 15 changed, 163 examined... 006: 11 changed, 96 examined... 007: 18 changed, 74 examined... 008: 13 changed, 81 examined... 009: 9 changed, 58 examined... 010: 8 changed, 60 examined... 011: 8 changed, 55 examined... 012: 8 changed, 50 examined... 013: 5 changed, 38 examined... 014: 7 changed, 25 examined... 015: 5 changed, 34 examined... 016: 5 changed, 24 examined... 017: 2 changed, 29 examined... 018: 0 changed, 15 examined... 282 labels changed using aseg 000: 74 total segments, 40 labels (307 vertices) changed 001: 36 total segments, 2 labels (11 vertices) changed 002: 34 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 11 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 505 vertices marked for relabeling... 505 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050815 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1398 labels changed using aseg relabeling using gibbs priors... 000: 1726 changed, 102455 examined... 001: 449 changed, 8075 examined... 002: 133 changed, 2465 examined... 003: 46 changed, 749 examined... 004: 24 changed, 276 examined... 005: 15 changed, 130 examined... 006: 9 changed, 88 examined... 007: 4 changed, 61 examined... 008: 2 changed, 21 examined... 009: 2 changed, 15 examined... 010: 3 changed, 16 examined... 011: 2 changed, 19 examined... 012: 2 changed, 10 examined... 013: 2 changed, 10 examined... 014: 1 changed, 14 examined... 015: 2 changed, 6 examined... 016: 3 changed, 8 examined... 017: 3 changed, 16 examined... 018: 2 changed, 19 examined... 019: 4 changed, 13 examined... 020: 5 changed, 17 examined... 021: 4 changed, 26 examined... 022: 4 changed, 20 examined... 023: 5 changed, 26 examined... 024: 4 changed, 24 examined... 025: 4 changed, 24 examined... 026: 3 changed, 22 examined... 027: 4 changed, 17 examined... 028: 1 changed, 18 examined... 029: 2 changed, 7 examined... 030: 1 changed, 12 examined... 031: 3 changed, 7 examined... 032: 0 changed, 12 examined... 280 labels changed using aseg 000: 74 total segments, 41 labels (616 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 476 vertices marked for relabeling... 476 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 12 seconds. PIDs (30832 30835) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 11:13:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050815 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 11:13:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050815 rh white Waiting for PID 30895 of (30895 30898) to complete... Waiting for PID 30898 of (30895 30898) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050815 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 214254 Total vertex volume 209700 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 1162 789 2743 2.923 0.937 0.107 0.031 8 1.6 caudalanteriorcingulate 2473 1798 4231 2.075 0.605 0.159 0.064 59 6.7 caudalmiddlefrontal 2581 1905 5741 2.401 0.766 0.153 0.047 35 5.4 cuneus 391 293 937 2.223 0.740 0.179 0.080 8 1.4 entorhinal 3312 2505 7616 2.479 0.766 0.169 0.063 67 9.8 fusiform 6141 4253 12148 2.313 0.705 0.143 0.048 85 12.4 inferiorparietal 3925 2838 8595 2.383 0.742 0.158 0.062 74 10.8 inferiortemporal 1320 863 2742 2.477 0.839 0.137 0.043 18 2.5 isthmuscingulate 7672 5187 13103 2.249 0.694 0.147 0.047 115 14.4 lateraloccipital 2163 1467 5866 3.184 0.963 0.133 0.050 33 4.3 lateralorbitofrontal 3718 2787 8155 2.293 0.747 0.162 0.054 80 9.4 lingual 1832 1378 5829 3.088 0.953 0.160 0.055 38 4.4 medialorbitofrontal 4851 3572 12990 2.652 0.852 0.154 0.055 85 10.9 middletemporal 908 711 1849 2.283 0.632 0.166 0.056 12 2.4 parahippocampal 1590 1219 3745 2.476 0.815 0.164 0.067 28 4.9 paracentral 1663 1091 3458 2.584 0.703 0.147 0.065 29 4.6 parsopercularis 570 409 1413 2.640 0.709 0.145 0.059 8 1.4 parsorbitalis 2044 1531 5995 2.886 0.778 0.164 0.064 36 6.3 parstriangularis 1638 1226 2624 2.096 0.710 0.169 0.061 23 4.5 pericalcarine 4228 3139 7928 2.175 0.645 0.165 0.065 83 11.7 postcentral 1621 1058 3124 2.530 1.001 0.144 0.060 34 3.9 posteriorcingulate 5614 4010 10431 2.239 0.700 0.157 0.061 85 15.8 precentral 4274 3011 9291 2.420 0.781 0.153 0.062 73 12.5 precuneus 1190 784 2561 2.758 0.958 0.125 0.051 15 2.6 rostralanteriorcingulate 4182 2997 8739 2.364 0.742 0.157 0.061 74 10.9 rostralmiddlefrontal 9186 6498 21946 2.702 0.942 0.146 0.057 161 21.9 superiorfrontal 4474 3162 8315 2.236 0.607 0.134 0.044 61 8.4 superiorparietal 4960 3897 11678 2.523 0.815 0.147 0.052 74 11.3 superiortemporal 4163 2901 8565 2.332 0.672 0.148 0.054 68 9.9 supramarginal 589 449 1421 2.634 0.788 0.171 0.063 10 1.7 transversetemporal 2056 1464 5922 3.338 1.012 0.110 0.032 30 2.8 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050815 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 227482 Total vertex volume 223909 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 771 498 1564 3.390 0.784 0.126 0.041 9 1.0 caudalanteriorcingulate 3166 2102 5332 2.211 0.711 0.170 0.081 89 11.3 caudalmiddlefrontal 1688 1392 4747 2.508 1.045 0.164 0.055 26 4.1 cuneus 394 280 991 2.650 0.742 0.168 0.072 9 1.1 entorhinal 2371 1881 6182 2.778 0.726 0.172 0.058 44 6.5 fusiform 6062 4367 13751 2.489 0.757 0.153 0.051 105 14.2 inferiorparietal 3298 2429 8690 2.645 0.830 0.167 0.062 67 8.3 inferiortemporal 1231 798 2602 2.468 0.975 0.142 0.054 19 2.6 isthmuscingulate 5688 4491 13785 2.410 0.746 0.177 0.055 103 16.0 lateraloccipital 2968 2080 7337 2.690 1.040 0.148 0.058 62 7.3 lateralorbitofrontal 1345 1075 3394 2.668 0.918 0.171 0.058 21 4.2 lingual 1662 1182 4981 3.335 1.044 0.148 0.049 28 3.6 medialorbitofrontal 4626 3557 13776 2.826 0.914 0.158 0.059 79 12.4 middletemporal 826 583 1986 2.914 0.821 0.181 0.075 16 2.9 parahippocampal 1785 1247 3914 2.721 0.797 0.149 0.058 25 4.4 paracentral 1601 1165 4070 2.731 0.851 0.142 0.060 23 4.1 parsopercularis 690 560 1701 2.534 0.746 0.150 0.050 8 1.7 parsorbitalis 1810 1342 4711 2.760 0.738 0.149 0.059 35 4.2 parstriangularis 1046 770 2159 2.328 0.816 0.146 0.048 18 2.1 pericalcarine 4485 3180 7996 2.169 0.728 0.152 0.062 73 13.0 postcentral 1725 1182 3510 2.659 1.030 0.164 0.061 34 4.7 posteriorcingulate 6456 4476 12903 2.465 0.782 0.155 0.064 108 18.1 precentral 3473 2555 8498 2.628 0.876 0.159 0.058 60 9.0 precuneus 798 519 2066 3.504 0.982 0.123 0.046 9 1.5 rostralanteriorcingulate 6070 4363 15057 2.594 0.784 0.165 0.067 131 18.0 rostralmiddlefrontal 12284 8557 31421 2.825 0.974 0.152 0.062 235 33.7 superiorfrontal 5113 3780 10505 2.323 0.699 0.154 0.054 77 12.1 superiorparietal 4430 3401 11166 2.698 0.910 0.159 0.054 77 10.2 superiortemporal 4033 2820 9381 2.566 0.760 0.146 0.051 61 8.8 supramarginal 277 193 550 3.458 0.994 0.138 0.044 3 0.5 transversetemporal 2284 1587 5180 2.890 1.096 0.125 0.056 40 4.0 insula PIDs (30895 30898) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 11:14:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts pctsurfcon --s 0050815 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 11:14:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts pctsurfcon --s 0050815 --rh-only Waiting for PID 30955 of (30955 30967) to complete... Waiting for PID 30967 of (30955 30967) to complete... pctsurfcon --s 0050815 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts/pctsurfcon.log Sun Oct 8 11:14:25 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux tars-551 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30955/lh.wm.mgh --regheader 0050815 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 -0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 56547 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30955/lh.wm.mgh Dim: 105178 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30955/lh.gm.mgh --projfrac 0.3 --regheader 0050815 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 -0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 68242 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30955/lh.gm.mgh Dim: 105178 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30955/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30955/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.w-g.pct.mgh --annot 0050815 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.w-g.pct.mgh --annot 0050815 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-551 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.w-g.pct.mgh Vertex Area is 0.708728 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s 0050815 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts/pctsurfcon.log Sun Oct 8 11:14:25 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/scripts /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux tars-551 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30967/rh.wm.mgh --regheader 0050815 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 -0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 55901 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30967/rh.wm.mgh Dim: 102455 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30967/rh.gm.mgh --projfrac 0.3 --regheader 0050815 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 1.00000 -0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 65782 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30967/rh.gm.mgh Dim: 102455 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30967/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/tmp.pctsurfcon.30967/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.w-g.pct.mgh --annot 0050815 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.w-g.pct.mgh --annot 0050815 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-551 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.w-g.pct.mgh Vertex Area is 0.718579 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (30955 30967) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 11:14:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 890 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1307 voxels changed to hypointensity... 2375 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 11:14:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815 mri_aparc2aseg --s 0050815 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Sun Oct 8 11:14:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815 mri_aparc2aseg --s 0050815 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Sun Oct 8 11:14:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815 mri_aparc2aseg --s 0050815 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz Waiting for PID 31129 of (31129 31132 31135) to complete... Waiting for PID 31132 of (31129 31132 31135) to complete... Waiting for PID 31135 of (31129 31132 31135) to complete... mri_aparc2aseg --s 0050815 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050815 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.96 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 50 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 82 rescaling Left_Cerebellum_Cortex from 60 --> 50 rescaling Left_Thalamus from 94 --> 88 rescaling Left_Thalamus_Proper from 84 --> 79 rescaling Left_Caudate from 75 --> 58 rescaling Left_Putamen from 80 --> 70 rescaling Left_Pallidum from 98 --> 81 rescaling Third_Ventricle from 25 --> 10 rescaling Fourth_Ventricle from 22 --> 6 rescaling Brain_Stem from 81 --> 85 rescaling Left_Hippocampus from 57 --> 56 rescaling Left_Amygdala from 56 --> 53 rescaling CSF from 32 --> 13 rescaling Left_Accumbens_area from 62 --> 52 rescaling Left_VentralDC from 87 --> 85 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 51 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 52 rescaling Right_Thalamus_Proper from 85 --> 78 rescaling Right_Caudate from 62 --> 57 rescaling Right_Putamen from 80 --> 68 rescaling Right_Pallidum from 97 --> 80 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 52 rescaling Right_Accumbens_area from 65 --> 56 rescaling Right_VentralDC from 86 --> 85 rescaling Fifth_Ventricle from 40 --> 13 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 422829 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 183 changed. pass 2: 19 changed. pass 3: 6 changed. pass 4: 5 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050815 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050815 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.96 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 50 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 82 rescaling Left_Cerebellum_Cortex from 60 --> 50 rescaling Left_Thalamus from 94 --> 88 rescaling Left_Thalamus_Proper from 84 --> 79 rescaling Left_Caudate from 75 --> 58 rescaling Left_Putamen from 80 --> 70 rescaling Left_Pallidum from 98 --> 81 rescaling Third_Ventricle from 25 --> 10 rescaling Fourth_Ventricle from 22 --> 6 rescaling Brain_Stem from 81 --> 85 rescaling Left_Hippocampus from 57 --> 56 rescaling Left_Amygdala from 56 --> 53 rescaling CSF from 32 --> 13 rescaling Left_Accumbens_area from 62 --> 52 rescaling Left_VentralDC from 87 --> 85 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 51 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 52 rescaling Right_Thalamus_Proper from 85 --> 78 rescaling Right_Caudate from 62 --> 57 rescaling Right_Putamen from 80 --> 68 rescaling Right_Pallidum from 97 --> 80 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 52 rescaling Right_Accumbens_area from 65 --> 56 rescaling Right_VentralDC from 86 --> 85 rescaling Fifth_Ventricle from 40 --> 13 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 422908 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 183 changed. pass 2: 19 changed. pass 3: 6 changed. pass 4: 5 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050815 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050815 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.96 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 50 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 82 rescaling Left_Cerebellum_Cortex from 60 --> 50 rescaling Left_Thalamus from 94 --> 88 rescaling Left_Thalamus_Proper from 84 --> 79 rescaling Left_Caudate from 75 --> 58 rescaling Left_Putamen from 80 --> 70 rescaling Left_Pallidum from 98 --> 81 rescaling Third_Ventricle from 25 --> 10 rescaling Fourth_Ventricle from 22 --> 6 rescaling Brain_Stem from 81 --> 85 rescaling Left_Hippocampus from 57 --> 56 rescaling Left_Amygdala from 56 --> 53 rescaling CSF from 32 --> 13 rescaling Left_Accumbens_area from 62 --> 52 rescaling Left_VentralDC from 87 --> 85 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 51 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 52 rescaling Right_Thalamus_Proper from 85 --> 78 rescaling Right_Caudate from 62 --> 57 rescaling Right_Putamen from 80 --> 68 rescaling Right_Pallidum from 97 --> 80 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 52 rescaling Right_Accumbens_area from 65 --> 56 rescaling Right_VentralDC from 86 --> 85 rescaling Fifth_Ventricle from 40 --> 13 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 422908 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 183 changed. pass 2: 19 changed. pass 3: 6 changed. pass 4: 5 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (31129 31132 31135) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 11:21:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 11:21:28 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux tars-551 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname tars-551 machine x86_64 user ntraut input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Sun Oct 8 11:21:28 CEST 2017 Ended at Sun Oct 8 11:21:35 CEST 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 11:21:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/ASegStatsLUT.txt --subject 0050815 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/ASegStatsLUT.txt --subject 0050815 sysname Linux hostname tars-551 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) Computing euler number orig.nofix lheno = -556, rheno = -646 orig.nofix lhholes = 279, rhholes = 324 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Sun Oct 8 11:23:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815 mri_aparc2aseg --s 0050815 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050815 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8691 vertices from left hemi Ripped 8080 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 757111 Used brute-force search on 133 voxels Fixing Parahip LH WM Found 20 clusters 0 k 179.000000 1 k 4.000000 2 k 4.000000 3 k 9.000000 4 k 1.000000 5 k 34.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 1.000000 11 k 1.000000 12 k 2.000000 13 k 666.000000 14 k 1.000000 15 k 1.000000 16 k 2.000000 17 k 1.000000 18 k 1.000000 19 k 1.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1.000000 1 k 695.000000 2 k 33.000000 3 k 3.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050815 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050815 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-551 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 11:30:34 CEST 2017 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 31791 of (31791 31797 31803 31809 31814) to complete... Waiting for PID 31797 of (31791 31797 31803 31809 31814) to complete... Waiting for PID 31803 of (31791 31797 31803 31809 31814) to complete... Waiting for PID 31809 of (31791 31797 31803 31809 31814) to complete... Waiting for PID 31814 of (31791 31797 31803 31809 31814) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 175 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4304 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 311 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8220 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 222 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4299 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 353 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 413 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6197 mri_label2label: Done PIDs (31791 31797 31803 31809 31814) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 31878 of (31878 31884 31890 31896) to complete... Waiting for PID 31884 of (31878 31884 31890 31896) to complete... Waiting for PID 31890 of (31878 31884 31890 31896) to complete... Waiting for PID 31896 of (31878 31884 31890 31896) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 144 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4214 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 1104 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14693 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 401 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4582 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0050815 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 693 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4115 mri_label2label: Done PIDs (31878 31884 31890 31896) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label --trgsubject 0050815 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label --trgsubject 0050815 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0050815 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0050815 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0050815 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 31940 of (31940 31946 31952 31958 31964) to complete... Waiting for PID 31946 of (31940 31946 31952 31958 31964) to complete... Waiting for PID 31952 of (31940 31946 31952 31958 31964) to complete... Waiting for PID 31958 of (31940 31946 31952 31958 31964) to complete... Waiting for PID 31964 of (31940 31946 31952 31958 31964) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label --trgsubject 0050815 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 1305 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5946 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label --trgsubject 0050815 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 2711 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10825 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0050815 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 317 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2335 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0050815 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1475 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0050815 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1305 mri_label2label: Done PIDs (31940 31946 31952 31958 31964) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 32008 of (32008 32014 32020 32025 32030) to complete... Waiting for PID 32014 of (32008 32014 32020 32025 32030) to complete... Waiting for PID 32020 of (32008 32014 32020 32025 32030) to complete... Waiting for PID 32025 of (32008 32014 32020 32025 32030) to complete... Waiting for PID 32030 of (32008 32014 32020 32025 32030) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1056 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2204 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1567 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2083 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2478 mri_label2label: Done PIDs (32008 32014 32020 32025 32030) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 32081 of (32081 32087 32093 32098) to complete... Waiting for PID 32087 of (32081 32087 32093 32098) to complete... Waiting for PID 32093 of (32081 32087 32093 32098) to complete... Waiting for PID 32098 of (32081 32087 32093 32098) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1617 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 491 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7526 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 172 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2084 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1391 mri_label2label: Done PIDs (32081 32087 32093 32098) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 32151 of (32151 32157 32163 32169 32174) to complete... Waiting for PID 32157 of (32151 32157 32163 32169 32174) to complete... Waiting for PID 32163 of (32151 32157 32163 32169 32174) to complete... Waiting for PID 32169 of (32151 32157 32163 32169 32174) to complete... Waiting for PID 32174 of (32151 32157 32163 32169 32174) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 864 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4269 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 1220 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4554 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 594 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 560 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 0050815 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 105178 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 479 mri_label2label: Done PIDs (32151 32157 32163 32169 32174) completed and logs appended. mris_label2annot --s 0050815 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label cmdline mris_label2annot --s 0050815 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname tars-551 machine x86_64 user ntraut subject 0050815 hemi lh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 73146 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.BA_exvivo.annot mris_label2annot --s 0050815 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label cmdline mris_label2annot --s 0050815 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname tars-551 machine x86_64 user ntraut subject 0050815 hemi lh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 86730 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab 0050815 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 214254 Total vertex volume 209700 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 548 472 1579 2.356 0.711 0.224 0.084 15 2.2 BA1_exvivo 2423 1732 4045 2.047 0.575 0.136 0.045 29 4.8 BA2_exvivo 703 479 824 1.915 0.466 0.146 0.070 14 1.9 BA3a_exvivo 1370 1044 2717 2.138 0.574 0.160 0.058 30 2.8 BA3b_exvivo 1222 874 3054 2.521 0.863 0.171 0.068 20 3.6 BA4a_exvivo 853 648 1326 2.058 0.591 0.147 0.051 8 2.1 BA4p_exvivo 7011 5054 15611 2.449 0.843 0.164 0.065 133 21.1 BA6_exvivo 1656 1134 3169 2.368 0.667 0.153 0.062 28 4.4 BA44_exvivo 2467 1830 7055 2.789 0.753 0.168 0.069 48 8.0 BA45_exvivo 3006 2306 5746 2.203 0.782 0.174 0.063 57 8.1 V1_exvivo 7856 5483 14269 2.147 0.681 0.157 0.052 131 17.2 V2_exvivo 1780 1213 3881 2.714 0.675 0.139 0.045 23 3.1 MT_exvivo 638 438 1072 2.281 0.733 0.193 0.095 19 3.1 perirhinal_exvivo 499 420 975 2.229 0.676 0.194 0.074 9 1.7 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050815 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 214254 Total vertex volume 209700 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 337 287 1080 2.461 0.712 0.218 0.083 10 1.3 BA1_exvivo 970 761 1891 2.118 0.531 0.148 0.045 13 2.1 BA2_exvivo 541 360 580 1.889 0.471 0.142 0.060 9 1.1 BA3a_exvivo 812 608 1514 2.063 0.544 0.152 0.069 21 2.1 BA3b_exvivo 1130 796 2723 2.376 0.854 0.157 0.063 15 3.0 BA4a_exvivo 771 600 1279 2.112 0.668 0.157 0.053 8 2.0 BA4p_exvivo 3627 2760 8296 2.420 0.884 0.176 0.073 69 12.5 BA6_exvivo 1058 711 2044 2.365 0.698 0.155 0.068 21 3.0 BA44_exvivo 1018 758 3171 2.844 0.737 0.165 0.064 20 2.8 BA45_exvivo 3193 2417 6232 2.209 0.779 0.172 0.062 60 8.5 V1_exvivo 3901 2817 7073 2.047 0.665 0.166 0.054 69 9.3 V2_exvivo 483 316 1112 2.936 0.594 0.140 0.039 8 0.7 MT_exvivo 327 220 615 2.328 0.762 0.192 0.093 8 1.6 perirhinal_exvivo 280 238 602 2.408 0.674 0.204 0.077 5 1.0 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 11:33:07 CEST 2017 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 32303 of (32303 32309 32315 32320 32327) to complete... Waiting for PID 32309 of (32303 32309 32315 32320 32327) to complete... Waiting for PID 32315 of (32303 32309 32315 32320 32327) to complete... Waiting for PID 32320 of (32303 32309 32315 32320 32327) to complete... Waiting for PID 32327 of (32303 32309 32315 32320 32327) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 275 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6962 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 187 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4167 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 286 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4808 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 632 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6379 mri_label2label: Done PIDs (32303 32309 32315 32320 32327) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 32368 of (32368 32374 32380 32386) to complete... Waiting for PID 32374 of (32368 32374 32380 32386) to complete... Waiting for PID 32380 of (32368 32374 32380 32386) to complete... Waiting for PID 32386 of (32368 32374 32380 32386) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 297 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4770 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 1477 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13733 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 910 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7822 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0050815 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 920 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6275 mri_label2label: Done PIDs (32368 32374 32380 32386) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label --trgsubject 0050815 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0050815 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label --trgsubject 0050815 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0050815 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0050815 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 32434 of (32434 32440 32446 32452 32456) to complete... Waiting for PID 32440 of (32434 32440 32446 32452 32456) to complete... Waiting for PID 32446 of (32434 32440 32446 32452 32456) to complete... Waiting for PID 32452 of (32434 32440 32446 32452 32456) to complete... Waiting for PID 32456 of (32434 32440 32446 32452 32456) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label --trgsubject 0050815 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 422 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5149 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0050815 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 1230 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9246 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label --trgsubject 0050815 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 449 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2381 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0050815 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 237 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0050815 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 158 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 910 mri_label2label: Done PIDs (32434 32440 32446 32452 32456) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 32511 of (32511 32517 32523 32529 32534) to complete... Waiting for PID 32517 of (32511 32517 32523 32529 32534) to complete... Waiting for PID 32523 of (32511 32517 32523 32529 32534) to complete... Waiting for PID 32529 of (32511 32517 32523 32529 32534) to complete... Waiting for PID 32534 of (32511 32517 32523 32529 32534) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 940 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2762 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1799 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2248 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1470 mri_label2label: Done PIDs (32511 32517 32523 32529 32534) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 32576 of (32576 32582 32588 32594) to complete... Waiting for PID 32582 of (32576 32582 32588 32594) to complete... Waiting for PID 32588 of (32576 32582 32588 32594) to complete... Waiting for PID 32594 of (32576 32582 32588 32594) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 842 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7801 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1143 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1423 mri_label2label: Done PIDs (32576 32582 32588 32594) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 32636 of (32636 32642 32648 32654 32660) to complete... Waiting for PID 32642 of (32636 32642 32648 32654 32660) to complete... Waiting for PID 32648 of (32636 32642 32648 32654 32660) to complete... Waiting for PID 32654 of (32636 32642 32648 32654 32660) to complete... Waiting for PID 32660 of (32636 32642 32648 32654 32660) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3560 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 338 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 3775 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 453 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 851 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0050815 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050815 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 102455 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 350 mri_label2label: Done PIDs (32636 32642 32648 32654 32660) completed and logs appended. mris_label2annot --s 0050815 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label cmdline mris_label2annot --s 0050815 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname tars-551 machine x86_64 user ntraut subject 0050815 hemi rh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 71916 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.BA_exvivo.annot mris_label2annot --s 0050815 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label cmdline mris_label2annot --s 0050815 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname tars-551 machine x86_64 user ntraut subject 0050815 hemi rh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 86429 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab 0050815 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 227482 Total vertex volume 223909 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 728 541 1508 2.114 0.765 0.185 0.073 16 2.7 BA1_exvivo 2031 1439 2969 1.997 0.518 0.135 0.042 23 3.6 BA2_exvivo 832 552 1161 2.245 0.802 0.149 0.070 12 2.3 BA3a_exvivo 1241 877 2209 2.127 0.721 0.157 0.073 22 4.4 BA3b_exvivo 1283 878 2755 2.659 0.849 0.153 0.062 17 3.2 BA4a_exvivo 935 653 1677 2.483 0.669 0.154 0.058 14 2.3 BA4p_exvivo 7675 5197 16208 2.548 0.832 0.154 0.068 134 22.6 BA6_exvivo 2950 2142 7103 2.578 0.761 0.158 0.062 54 7.7 BA44_exvivo 3591 2753 9930 2.743 0.773 0.168 0.068 74 10.9 BA45_exvivo 1823 1329 3812 2.279 0.764 0.152 0.047 29 3.9 V1_exvivo 4580 3847 11863 2.487 0.879 0.184 0.062 86 14.1 V2_exvivo 1786 1281 3576 2.414 0.739 0.151 0.052 28 4.6 MT_exvivo 704 458 1343 2.614 0.788 0.185 0.086 22 2.5 perirhinal_exvivo 380 276 945 3.085 0.612 0.176 0.070 7 1.2 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050815 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050815/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 227482 Total vertex volume 223909 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1600775 mm^3 (det: 1.216976 ) lhCtxGM: 207923.393 207430.000 diff= 493.4 pctdiff= 0.237 rhCtxGM: 219225.721 218739.000 diff= 486.7 pctdiff= 0.222 lhCtxWM: 166547.161 166643.000 diff= -95.8 pctdiff=-0.058 rhCtxWM: 165772.612 167627.000 diff=-1854.4 pctdiff=-1.119 SubCortGMVol 60596.000 SupraTentVol 831910.888 (831001.000) diff=909.888 pctdiff=0.109 SupraTentVolNotVent 821976.888 (821067.000) diff=909.888 pctdiff=0.111 BrainSegVol 979951.000 (977322.000) diff=2629.000 pctdiff=0.268 BrainSegVolNotVent 966614.000 (965484.888) diff=1129.112 pctdiff=0.117 BrainSegVolNotVent 966614.000 CerebellumVol 145388.000 VentChorVol 9934.000 3rd4th5thCSF 3403.000 CSFVol 774.000, OptChiasmVol 159.000 MaskVol 1607483.000 366 287 552 1.699 0.463 0.186 0.114 10 2.5 BA1_exvivo 1148 863 1622 1.890 0.504 0.143 0.039 13 1.9 BA2_exvivo 723 483 880 2.280 0.775 0.154 0.067 10 2.0 BA3a_exvivo 882 628 1185 1.932 0.540 0.134 0.051 13 1.8 BA3b_exvivo 808 546 1687 2.673 0.854 0.162 0.067 13 2.0 BA4a_exvivo 783 568 1312 2.461 0.635 0.150 0.054 9 1.9 BA4p_exvivo 4977 3374 10331 2.518 0.838 0.152 0.067 83 14.1 BA6_exvivo 625 464 1665 2.520 0.770 0.160 0.072 11 1.9 BA44_exvivo 943 738 3097 2.954 0.827 0.177 0.074 23 2.9 BA45_exvivo 1715 1238 3571 2.272 0.773 0.148 0.043 27 3.3 V1_exvivo 1952 1811 5808 2.654 0.920 0.192 0.066 37 6.4 V2_exvivo 390 298 965 2.276 0.741 0.198 0.069 10 1.4 MT_exvivo 436 292 971 2.627 0.727 0.153 0.062 7 1.2 perirhinal_exvivo 278 199 715 2.945 0.786 0.198 0.088 8 1.1 entorhinal_exvivo Started at Sat Oct 7 16:31:06 CEST 2017 Ended at Sun Oct 8 11:35:36 CEST 2017 #@#%# recon-all-run-time-hours 19.075 recon-all -s 0050815 finished without error at Sun Oct 8 11:35:36 CEST 2017